Contacts of the helix formed by residues 118 - 152 (chain J) in PDB entry 3RWR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 118 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J VAL* 2.8 22.3 + - - +
117J GLU* 1.3 93.2 + - - +
119J PRO* 1.3 66.2 - - - +
120J ALA 3.6 1.1 - - - -
121J GLU* 3.9 33.3 + - + +
122J VAL* 3.2 27.7 + - - +
164J TBR 5.8 2.9 - - - +
532X GLN* 5.3 4.7 - - - +
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Residues in contact with PRO 119 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J HIS 3.7 10.1 - - - +
41J SER* 4.9 5.2 - - - -
42J ALA* 4.7 6.1 - - + +
116J VAL 4.0 5.6 - - - +
117J GLU 3.6 7.9 - - - +
118J ASN* 1.3 83.5 - - - +
120J ALA* 1.3 67.5 + - + +
121J GLU 3.2 0.7 + - - -
122J VAL* 3.3 5.0 + - + +
123J ILE* 2.7 58.5 + - + +
539K GLY 5.3 0.9 - - - +
540K HIS* 5.8 9.6 - - + -
532X GLN* 5.7 1.6 - - - +
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Residues in contact with ALA 120 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J PRO* 1.3 85.0 - - + +
121J GLU* 1.3 67.0 + - + +
123J ILE* 3.8 6.3 - - - +
124J ARG* 2.8 54.5 + - - +
538K ASP 3.8 10.5 - - - +
539K GLY* 4.4 5.3 + - - -
540K HIS* 5.3 3.1 - - + +
502X GLU* 5.7 4.5 - - - +
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Residues in contact with GLU 121 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J ASN* 3.9 33.6 + - + +
119J PRO 3.2 1.0 + - - -
120J ALA* 1.3 81.9 - - + +
122J VAL* 1.3 63.0 + - + +
124J ARG* 3.5 13.0 + - - +
125J GLU* 3.6 14.0 + - - +
164J TBR 5.1 13.1 - - + +
551X THR* 5.7 5.2 - - - +
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Residues in contact with VAL 122 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J THR* 6.0 4.0 - - + -
42J ALA* 3.5 26.9 - - + -
116J VAL* 4.0 10.3 - - + -
118J ASN* 3.2 30.3 - - - +
119J PRO 3.3 3.4 - - - +
121J GLU* 1.3 74.0 - - + +
123J ILE* 1.3 74.2 + - - +
124J ARG 3.0 2.5 - - - -
125J GLU* 2.8 25.9 + - - +
126J LEU* 3.4 5.7 + - - +
164J TBR 3.9 43.7 - - + -
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Residues in contact with ILE 123 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J THR* 4.7 10.1 - - - +
39J GLY* 4.3 4.3 - - - +
40J HIS 3.0 32.1 - - - +
41J SER* 4.6 0.9 - - - +
42J ALA* 4.3 13.9 - - + -
119J PRO* 2.7 45.1 + - + +
120J ALA 4.0 2.5 - - - +
122J VAL* 1.3 73.3 - - - +
124J ARG* 1.3 58.4 + - - +
126J LEU* 3.8 3.9 + - - +
127J ILE* 2.9 49.8 + - + +
539K GLY* 3.3 30.3 - - - +
623K ILE* 3.8 9.0 - - + -
627K ILE* 6.3 0.2 - - + -
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Residues in contact with ARG 124 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J ALA* 2.8 60.3 + - - +
121J GLU* 3.3 15.1 + - - +
122J VAL 3.0 0.8 - - - -
123J ILE* 1.3 73.7 - - - +
125J GLU* 1.3 66.3 + - - +
126J LEU 2.9 3.1 + - - -
127J ILE* 3.0 8.2 + - + +
128J CYS* 2.8 32.5 + - + +
515K SER 5.3 1.9 + - - -
516K ILE* 3.1 45.0 - - - +
517K THR* 4.3 18.2 - - - +
519K PHE* 5.5 7.4 - - + -
537K THR 6.0 0.2 - - - +
538K ASP* 3.1 30.8 + - - +
539K GLY* 4.8 0.9 - - - +
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Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J ARG* 2.9 34.3 + - - -
21J GLN* 3.6 10.4 + - - +
121J GLU 3.6 4.5 + - - +
122J VAL* 2.8 27.7 + - - +
124J ARG* 1.3 73.4 - - - +
126J LEU* 1.3 55.4 + - - +
128J CYS* 3.0 23.7 - - - -
129J TYR* 3.2 15.1 - - - +
164J TBR 2.2 62.9 - - + +
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Residues in contact with LEU 126 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ILE* 3.6 26.2 - - + -
19J PHE* 4.7 14.8 - - + +
21J GLN* 3.9 27.1 - - + +
35J THR 5.8 1.1 - - - +
37J THR* 4.8 11.9 - - + -
122J VAL 3.4 5.1 + - - +
123J ILE* 4.2 5.8 - - - +
124J ARG 2.9 1.0 + - - -
125J GLU* 1.3 76.8 + - - +
127J ILE* 1.3 63.5 + - + +
128J CYS 3.0 1.6 - - - -
129J TYR* 2.9 5.7 + - - -
130J CYS* 2.7 44.3 + - - -
627K ILE* 3.2 42.8 - - + -
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Residues in contact with ILE 127 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J ILE* 2.9 30.1 - - + +
124J ARG* 3.0 6.0 + - + +
126J LEU* 1.3 84.9 - - + +
128J CYS* 1.3 57.8 + - - +
130J CYS* 3.9 4.8 + - - +
131J LEU* 3.0 27.9 + - + +
519K PHE* 3.3 30.7 - - + -
537K THR* 5.1 2.9 - - + +
539K GLY* 4.9 4.3 - - - +
623K ILE* 3.4 34.8 - - + -
626K LEU* 3.4 25.6 - - + -
627K ILE* 4.2 18.6 - - + -
630K CYS* 4.7 0.2 - - - -
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Residues in contact with CYS 128 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J ARG* 2.8 21.9 + - + +
125J GLU* 3.0 32.3 - - - -
127J ILE* 1.3 71.8 - - - +
129J TYR* 1.3 63.6 + - - +
130J CYS 3.3 0.2 - - - -
131J LEU* 3.4 13.4 + - - +
132J ASP* 2.6 32.2 + - - +
507K ARG* 3.4 22.7 + - - +
517K THR* 5.6 5.4 - - + -
519K PHE* 4.3 13.7 - - + -
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Residues in contact with TYR 129 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J ARG* 3.3 68.8 + - + +
5J ILE* 3.8 20.6 - - + -
21J GLN* 4.6 1.3 - - - -
125J GLU 3.2 16.2 - - - +
126J LEU* 2.9 4.6 + - - +
128J CYS* 1.3 81.0 - - - +
130J CYS* 1.3 66.6 + - - +
132J ASP* 3.2 20.0 + - + +
133J THR* 3.2 39.2 + - - +
136J GLU* 5.4 2.0 - - - -
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Residues in contact with CYS 130 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ILE* 4.7 11.2 - - - -
126J LEU* 2.7 33.8 + - - +
127J ILE 3.9 4.3 - - - +
128J CYS 3.3 0.2 - - - -
129J TYR* 1.3 80.4 - - - +
131J LEU* 1.3 62.3 + - - +
133J THR* 3.4 6.2 + - - -
134J ILE* 3.1 24.6 + - - +
627K ILE* 3.4 29.4 - - + -
630K CYS* 3.2 28.0 - - + +
631K LEU* 3.4 15.5 - - + -
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Residues in contact with LEU 131 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J ILE* 3.0 16.4 - - + +
128J CYS* 3.5 10.5 - - - +
130J CYS* 1.3 76.7 - - - +
132J ASP* 1.3 55.1 + - - +
134J ILE* 3.4 2.6 + - - +
135J ALA* 2.7 42.4 + - + +
505K ILE* 3.4 34.8 - - + -
506K SER* 5.6 0.4 - - - -
507K ARG* 4.6 16.2 - - + +
519K PHE* 3.3 37.9 - - + -
626K LEU* 4.8 4.7 - - + -
630K CYS* 3.3 26.5 - - - -
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Residues in contact with ASP 132 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J CYS* 2.6 25.5 - - - +
129J TYR* 3.3 22.5 - - + +
131J LEU* 1.3 75.9 - - - +
133J THR* 1.3 57.4 + - - +
135J ALA* 4.6 1.6 - - - -
136J GLU* 2.6 64.1 + - - +
507K ARG* 3.4 23.9 + - - -
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Residues in contact with THR 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ILE* 6.1 0.2 - - - +
129J TYR* 3.2 39.4 + - - +
130J CYS* 3.9 7.0 - - - -
132J ASP* 1.3 76.7 - - - +
134J ILE* 1.3 58.3 + - - +
136J GLU* 3.9 5.6 - - - -
137J ASN* 3.1 33.8 + - + +
634K ILE* 3.9 15.2 - - + +
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Residues in contact with ILE 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J CYS 3.1 14.0 + - - +
131J LEU* 4.0 3.4 - - - +
133J THR* 1.3 77.3 - - - +
135J ALA* 1.3 60.6 + - - +
137J ASN* 4.3 2.8 - - - +
138J GLN* 4.1 14.6 + - - +
629K TYR* 6.0 1.1 - - + -
630K CYS* 3.0 34.8 - - + +
633K THR* 4.5 14.8 - - + +
634K ILE* 3.4 16.9 - - + +
637K ASN* 4.4 3.3 + - - -
----------------------------------------------------------
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Residues in contact with ALA 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J LEU* 2.7 24.5 + - + +
132J ASP* 3.8 1.8 - - - +
134J ILE* 1.3 72.5 - - - +
136J GLU* 1.3 68.5 + - + +
137J ASN 3.1 1.3 - - - -
138J GLN* 2.8 27.5 + - - +
139J ALA* 3.9 1.0 + - - +
504K LYS* 4.7 16.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J TYR* 5.4 2.6 - - - -
132J ASP* 2.6 56.7 + - - +
133J THR* 3.4 5.3 + - - +
135J ALA* 1.3 73.6 - - + +
137J ASN* 1.3 61.5 + - - +
139J ALA* 3.0 25.4 + - - +
140J LYS* 4.0 1.0 + - - +
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Residues in contact with ASN 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J THR* 3.1 25.1 + - - +
134J ILE* 4.3 3.1 - - - +
135J ALA 3.1 0.4 - - - -
136J GLU* 1.3 77.9 - - - +
138J GLN* 1.3 64.8 + - - +
140J LYS* 2.9 22.8 + - - +
141J ASN* 3.2 6.6 + - - +
634K ILE* 3.9 4.6 + - - +
637K ASN* 2.7 38.2 + - + +
638K GLN* 3.4 39.4 - - - +
641K ASN* 3.6 9.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J ILE 4.1 9.2 + - - +
135J ALA* 2.8 17.5 + - - +
137J ASN* 1.3 75.2 - - - +
139J ALA* 1.3 49.9 + - - +
141J ASN* 2.9 16.2 + - - +
142J GLU* 2.6 58.9 + - - +
633K THR* 5.9 2.5 - - + +
637K ASN* 3.1 28.3 - - - +
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Residues in contact with ALA 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J ALA 3.9 0.4 + - - -
136J GLU* 3.0 16.8 + - - +
138J GLN* 1.3 77.8 - - - +
140J LYS* 1.3 63.0 + - - +
142J GLU* 2.9 15.1 + - - +
143J HIS* 2.9 28.4 + - - +
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Residues in contact with LYS 140 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J GLU 4.0 0.6 + - - -
137J ASN* 2.9 19.2 + - - +
139J ALA* 1.3 79.5 - - - +
141J ASN* 1.3 63.4 + - - +
142J GLU 3.2 0.7 + - - -
143J HIS* 3.3 12.8 + - - +
144J LEU* 3.4 20.0 + - + +
638K GLN* 4.7 7.0 + - + -
641K ASN* 3.7 26.9 + - + +
642K GLU* 3.9 12.9 + - - -
645K GLN* 3.9 16.8 + - - -
----------------------------------------------------------
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Residues in contact with ASN 141 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J ASN 3.2 1.4 + - - -
138J GLN* 2.9 17.6 + - - +
140J LYS* 1.3 79.0 - - - +
142J GLU* 1.3 58.5 + - - +
144J LEU* 5.3 0.2 - - - -
145J GLN* 3.1 30.7 + - - +
637K ASN* 4.1 23.8 + - - +
640K LYS* 3.4 47.1 + - - +
641K ASN* 3.4 18.1 - - + +
644K LEU* 3.9 8.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU 142 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J GLN* 2.6 44.7 + - - +
139J ALA* 2.9 16.1 + - - +
141J ASN* 1.3 74.2 - - - +
143J HIS* 1.3 66.4 + - - +
145J GLN* 3.3 4.7 + - - +
146J LYS* 3.0 53.6 + - + +
----------------------------------------------------------
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Residues in contact with HIS 143 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J ALA* 2.9 14.2 + - - +
140J LYS* 3.3 9.8 + - - +
142J GLU* 1.3 75.5 - - - +
144J LEU* 1.3 54.6 + - + +
146J LYS* 3.0 7.3 + - - +
147J GLU* 2.7 54.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J LYS* 3.4 18.3 + - + +
141J ASN 4.6 0.4 - - - +
143J HIS* 1.3 79.6 - - + +
145J GLN* 1.3 55.5 + - - +
147J GLU* 4.1 6.1 - - + -
148J ASN* 2.6 38.3 + - - +
641K ASN* 3.3 29.8 - - + +
644K LEU* 4.1 14.4 - - + -
645K GLN* 3.7 42.4 - - - +
648K ASN* 3.2 29.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J ASN* 3.1 26.5 + - - +
142J GLU* 3.3 7.2 + - - +
143J HIS 3.1 0.2 - - - -
144J LEU* 1.3 80.1 - - - +
146J LYS* 1.3 73.8 + - + +
148J ASN* 3.7 4.3 - - - +
149J GLU* 3.0 36.0 + - - +
644K LEU* 3.8 22.8 - - + +
----------------------------------------------------------
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Residues in contact with LYS 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J GLU* 3.0 50.4 + - - +
143J HIS* 3.6 7.4 - - - +
145J GLN* 1.3 89.4 - - + +
147J GLU* 1.3 72.0 + - - +
149J GLU* 3.3 32.2 + - - +
150J ARG* 3.4 10.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 147 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J HIS* 2.7 42.7 + - + +
144J LEU* 3.8 6.7 - - + +
146J LYS* 1.3 74.6 - - - +
148J ASN* 1.3 66.8 + - - +
150J ARG* 3.0 26.9 + - - +
151J LEU* 3.0 28.4 + - - +
648K ASN* 4.1 13.5 - - - +
----------------------------------------------------------
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Residues in contact with ASN 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J LEU 2.6 22.4 + - - +
145J GLN* 3.7 8.5 - - - +
147J GLU* 1.3 73.4 - - - +
149J GLU* 1.3 67.7 + - - +
151J LEU* 3.7 6.0 - - - +
152J LEU* 3.0 28.8 + - - +
644K LEU* 3.6 23.3 - - + +
647K GLU* 3.8 25.9 + - - +
648K ASN* 3.3 23.7 + - - +
651K LEU* 4.8 8.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J GLN* 3.0 38.9 - - - +
146J LYS* 3.4 20.3 - - - +
147J GLU 3.2 0.2 - - - -
148J ASN* 1.3 77.5 - - + +
150J ARG* 1.3 57.8 + - - +
152J LEU* 2.7 35.0 + - - +
153J ARG* 3.6 11.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J LYS 3.4 11.0 + - - +
147J GLU* 3.0 44.6 + - - +
149J GLU* 1.3 75.3 - - - +
151J LEU* 1.3 73.5 + - - +
153J ARG* 2.8 43.4 + - - +
154J ASP* 2.6 36.3 + - - +
652K LEU* 5.4 2.8 - - - +
655K TRP* 5.8 1.4 - - - -
----------------------------------------------------------
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLU 3.0 20.2 + - - +
148J ASN 3.7 2.7 - - - +
150J ARG* 1.3 91.4 - - - +
152J LEU* 1.3 56.6 + - - +
153J ARG 3.0 2.2 + - - -
154J ASP* 3.2 21.2 - - - +
155J TRP* 3.0 28.5 - - + +
648K ASN* 4.4 22.0 - - - +
651K LEU* 3.8 31.4 - - + -
652K LEU* 3.4 37.9 - - + +
655K TRP* 4.4 16.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 152 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J ASN* 3.0 21.1 + - - +
149J GLU* 2.7 20.5 + - - +
151J LEU* 1.3 71.2 - - - +
153J ARG* 1.3 61.7 + - + +
155J TRP* 4.0 21.3 - - + -
156J ASN* 3.1 23.2 - - - +
650K ARG* 5.5 2.2 - - - +
651K LEU* 3.6 24.5 - - + -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il