Contacts of the helix formed by residues 100 - 127 (chain B) in PDB entry 6AHU
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 LYS 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 1.3 63.0 + - - +
102B ILE* 3.4 7.2 - - - +
103B THR* 3.4 21.3 + - + +
104B ALA* 2.9 29.2 + - + +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 1.3 77.0 - - - +
102B ILE* 1.3 68.9 + - + +
104B ALA* 4.4 7.2 - - + +
105B SER* 2.9 52.2 + - - -
18E PRO* 3.5 41.9 - - + +
21E ARG* 2.4 38.6 + - + -
22E LEU* 6.5 1.6 - - + -
61E TYR 6.1 0.4 - - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 4.9 3.8 - - - -
101B TYR* 1.3 88.2 - - + +
103B THR* 1.3 82.4 + - - +
105B SER* 4.0 5.2 + - - -
106B THR* 2.9 23.4 + - - -
129E CYS* 5.3 7.9 - - - -
131E ASP* 3.6 19.1 - - - +
134E GLU* 3.2 41.2 - - + +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 3.4 24.3 + - + +
101B TYR 3.2 0.6 - - - -
102B ILE* 1.3 92.5 - - - +
104B ALA* 1.3 64.0 + - - +
106B THR* 3.1 17.2 + - - -
107B PHE* 3.2 35.0 - - + -
131E ASP* 5.4 0.3 + - - -
133E GLY 5.4 5.6 + - - +
134E GLU* 5.1 8.7 + - - +
137E ALA* 5.3 8.7 - - + -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 2.9 19.0 + - + +
101B TYR* 4.1 9.4 - - + +
103B THR* 1.3 76.3 - - - +
105B SER* 1.3 61.7 + - - +
106B THR 3.4 0.3 + - - -
107B PHE* 3.5 21.3 + - - +
108B ALA* 3.6 10.6 + - - +
61E TYR* 5.8 5.5 - - + -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 2.9 49.4 + - - -
102B ILE* 4.3 6.5 - - - -
103B THR 3.3 0.4 - - - -
104B ALA* 1.3 76.0 - - - +
106B THR* 1.3 63.2 + - - +
107B PHE 3.4 0.2 - - - -
108B ALA* 3.6 6.5 + - - +
109B GLN* 3.2 41.0 + - - +
21E ARG* 4.8 5.2 + - - -
61E TYR 5.2 6.6 + - - -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE 2.9 17.5 + - - -
103B THR 3.1 10.1 + - - -
105B SER* 1.3 77.5 - - - +
107B PHE* 1.3 60.0 + - + +
109B GLN* 3.8 5.5 - - - +
110B ALA* 2.9 30.5 + - + +
122E LEU* 5.2 6.1 - - + +
125E LEU* 5.3 2.1 - - - +
134E GLU* 3.8 14.6 + - - +
137E ALA* 3.7 37.9 - - + +
138E ILE* 3.8 21.5 - - + +
141E SER* 5.2 2.2 - - - -
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 3.2 45.8 - - + -
104B ALA* 3.5 13.7 + - - +
105B SER 3.4 0.2 - - - -
106B THR* 1.3 78.2 - - + +
108B ALA* 1.3 62.0 + - - +
110B ALA* 4.1 5.1 - - + +
111B ARG* 3.3 44.6 + - - +
137E ALA* 5.3 11.0 - - + -
140E LYS* 5.4 17.5 - - + -
144E ARG* 5.5 10.3 - - - -
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA 3.6 9.8 + - - +
105B SER* 3.6 8.2 + - - +
106B THR 3.2 0.4 - - - -
107B PHE* 1.3 80.6 - - - +
109B GLN* 1.3 58.2 + - + +
111B ARG* 3.4 6.3 + - - +
112B ALA* 2.9 27.4 + - - +
61E TYR* 3.7 31.9 - - + +
62E THR* 3.6 19.7 + - - +
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.2 27.5 + - - +
106B THR* 4.2 4.8 - - - +
108B ALA* 1.3 75.9 - - + +
110B ALA* 1.3 63.0 + - - +
112B ALA* 4.0 6.7 - - - -
113B ALA* 3.4 2.4 + - - +
21E ARG* 5.6 5.9 - - - +
62E THR* 4.8 16.9 + - + +
118E ASN* 2.5 40.3 + - - +
121E GLN* 3.1 37.5 + - - +
122E LEU* 3.3 27.0 - - + +
125E LEU* 4.5 12.2 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 2.9 19.5 + - + +
107B PHE* 4.1 5.6 - - + +
109B GLN* 1.3 76.8 - - - +
111B ARG* 1.3 59.4 + - + +
113B ALA* 3.2 8.7 + - - +
114B GLU* 3.1 36.5 + - - +
122E LEU* 5.4 2.3 - - - +
137E ALA 5.7 0.2 - - - +
140E LYS 5.7 0.2 - - - +
141E SER* 3.8 32.5 - - - -
144E ARG* 6.4 1.1 - - - +
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.3 31.5 + - - +
108B ALA* 3.9 4.9 - - - +
110B ALA* 1.3 75.2 - - + +
112B ALA* 1.3 60.1 + - - +
113B ALA 3.2 0.2 - - - -
114B GLU* 3.5 19.7 - - - +
115B ILE* 2.9 50.2 + - + +
144E ARG* 5.9 5.6 - - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 2.9 17.0 + - - +
109B GLN* 3.7 4.0 - - - +
110B ALA 3.2 0.2 - - - -
111B ARG* 1.3 78.5 - - - +
113B ALA* 1.3 56.0 + - - +
115B ILE* 5.2 1.6 - - - -
116B SER* 3.1 31.1 + - - +
57E TYR* 4.9 10.1 - - - +
59E ASN* 5.2 3.6 - - - +
62E THR* 4.4 18.6 - - + +
114E LEU* 3.9 14.4 - - + +
115E ILE* 5.2 0.2 - - - +
118E ASN* 3.5 18.4 - - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLN 4.0 1.8 - - - +
110B ALA* 3.2 11.8 + - - +
112B ALA* 1.3 77.0 - - - +
114B GLU* 1.3 60.1 + - + +
116B SER* 5.1 1.1 - - - -
117B ALA* 3.3 24.9 + - - +
115E ILE* 5.0 16.8 - - + +
118E ASN* 3.2 23.7 - - + +
119E ARG* 5.8 6.3 - - + +
145E SER* 5.6 9.4 - - - -
148E LEU* 3.7 5.2 - - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 3.1 24.9 + - - +
111B ARG* 3.2 22.4 + - - +
113B ALA* 1.3 79.2 - - + +
115B ILE* 1.3 60.9 + - + +
116B SER 3.4 0.4 - - - -
117B ALA* 3.3 2.4 + - - +
118B MET* 2.9 48.8 + - + +
141E SER* 5.9 0.6 - - - +
144E ARG* 3.3 43.2 + - + +
145E SER* 5.5 1.6 - - - +
148E LEU* 3.8 23.5 - - + +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ARG* 2.9 37.9 + - + +
112B ALA* 5.1 2.0 - - - +
114B GLU* 1.3 73.9 - - + +
116B SER* 1.3 59.4 + - - +
118B MET* 3.3 17.0 + - + +
119B LEU* 2.8 39.9 + - + +
57E TYR* 5.4 13.7 - - + +
59E ASN* 6.0 5.4 - - - +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 3.1 21.1 + - - -
114B GLU 3.4 0.2 - - - -
115B ILE* 1.3 78.7 - - - +
117B ALA* 1.3 60.1 + - - +
119B LEU* 3.9 4.4 + - - +
120B LYS* 3.4 24.3 + - - +
57E TYR* 4.0 7.6 + - - -
111E GLN* 2.9 37.6 + - - +
114E LEU* 3.4 15.0 - - - +
115E ILE* 4.0 19.5 - - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 3.3 21.0 + - - +
114B GLU 3.3 4.4 + - - +
115B ILE 3.2 0.4 - - - -
116B SER* 1.3 80.0 - - - +
118B MET* 1.3 58.6 + - - +
120B LYS* 3.3 10.8 - - + +
121B ALA* 3.2 27.9 + - - +
115E ILE* 4.2 10.7 - - + +
119E ARG* 6.4 0.4 - - - +
148E LEU* 3.8 20.4 - - + -
60G ALA* 5.8 6.6 - - + +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.9 41.4 + - + +
115B ILE* 3.3 15.0 + - + +
117B ALA* 1.3 75.1 - - - +
119B LEU* 1.3 64.2 + - - +
120B LYS 3.2 0.9 - - - -
121B ALA* 3.9 5.4 - - + +
122B VAL* 3.3 35.4 + - + +
148E LEU* 4.1 21.1 - - + -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A C 5.1 18.2 - - + +
115B ILE* 2.8 27.0 + - + +
116B SER* 4.2 6.1 - - - +
117B ALA 3.3 0.4 - - - -
118B MET* 1.3 79.4 - - - +
120B LYS* 1.3 55.4 + - + +
123B THR* 2.5 32.7 + - + +
57E TYR* 5.9 7.2 - - + -
107E ILE* 4.6 13.9 - - + -
108E ARG* 6.2 2.2 - - + -
111E GLN* 4.2 30.1 - - + +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER 3.4 15.8 + - - +
117B ALA* 3.3 16.4 - - + +
119B LEU* 1.3 82.0 - - + +
121B ALA* 1.3 59.8 + - - +
122B VAL 3.7 0.2 - - - -
123B THR* 4.2 2.5 - - - -
124B GLN* 3.3 42.4 + - - +
108E ARG* 3.8 24.4 + - + +
111E GLN* 5.4 3.4 - - + -
112E LYS* 3.7 39.9 - - + +
115E ILE* 3.9 19.7 - - + -
59G GLY 4.1 4.3 + - - +
60G ALA* 3.2 40.5 + - + +
61G ARG* 4.8 2.3 - - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 3.2 18.3 + - - +
118B MET* 3.7 4.7 + - - -
119B LEU 3.6 0.2 - - - -
120B LYS* 1.3 80.3 - - + +
122B VAL* 1.3 65.8 + - + +
123B THR 3.3 0.6 + - - -
124B GLN* 3.6 9.3 + - - +
125B LYS* 3.6 26.9 + - - +
60G ALA* 5.5 10.1 - - + -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 3.3 26.5 + - + +
121B ALA* 1.3 78.9 - - + +
123B THR* 1.3 53.4 + - - +
125B LYS* 3.0 10.6 + - + +
126B SER* 2.7 38.4 + - - -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A U 5.8 0.2 - - - -
273A C 3.8 21.5 - - - +
119B LEU* 2.5 31.0 + - + +
120B LYS 4.6 0.2 - - - -
121B ALA 3.3 0.6 - - - -
122B VAL* 1.3 79.8 - - - +
124B GLN* 1.3 60.7 + - - +
126B SER* 4.1 9.0 - - - -
127B SER* 3.1 22.1 + - - +
128B ASN 6.0 1.3 - - - +
108E ARG* 3.4 31.4 + - - +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A U 4.8 16.2 - - + +
120B LYS* 3.3 34.0 + - - +
121B ALA* 3.6 10.2 + - - +
122B VAL 3.3 0.4 - - - -
123B THR* 1.3 79.0 - - - +
125B LYS* 1.3 60.3 + - + +
126B SER 3.7 0.2 + - - -
127B SER* 4.4 8.8 + - - -
134B THR* 5.4 3.8 - - - +
108E ARG* 3.4 22.6 - - - +
112E LYS* 5.4 7.7 - - - +
60G ALA 5.1 5.7 + - - +
61G ARG* 6.1 2.0 - - - +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ALA* 3.6 14.5 + - - +
122B VAL* 3.0 12.1 + - + +
124B GLN* 1.3 78.3 - - + +
126B SER* 1.3 62.6 + - - +
127B SER* 5.1 0.2 - - - -
134B THR* 3.5 27.5 + - + +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 2.7 24.2 + - - -
123B THR* 3.4 11.4 + - - -
125B LYS* 1.3 76.5 - - - +
127B SER* 1.3 70.9 + - - +
128B ASN* 4.0 2.1 + - - -
129B SER* 3.1 25.2 + - - +
130B LEU 3.3 22.2 + - - +
134B THR* 3.9 0.2 + - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A U 4.7 21.3 + - - +
273A C 6.0 0.7 - - - -
123B THR* 3.1 13.3 + - - -
124B GLN 4.5 9.4 - - - -
126B SER* 1.3 81.2 - - - +
128B ASN* 1.3 70.5 + - - +
130B LEU* 3.3 15.9 + - - +
133B GLN* 3.3 44.7 + - - +
134B THR* 4.7 2.2 - - - -
108E ARG* 5.7 2.2 - - - +
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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