Contacts of the helix formed by residues 126 - 149 (chain K) in PDB entry 1QGH
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 ASP 126 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 2.4 36.1 + - - +
117D ILE* 3.8 22.6 - - + +
133D ILE* 3.6 28.6 - - + +
136D LYS* 5.2 4.5 - - - +
121K ASP* 5.0 8.0 - - - +
124K GLY* 3.2 7.8 - - - +
125K ASP* 1.3 72.1 + - - +
127K VAL* 1.3 66.2 + - + +
129K ASN* 3.0 10.7 + - - +
130K ASP* 2.8 23.0 + - - +
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Residues in contact with VAL 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 5.8 0.2 - - + -
133D ILE* 3.5 33.4 - - + +
136D LYS* 3.7 25.7 - - + +
137D ALA* 3.6 30.7 - - + +
140D ASP* 4.3 0.7 - - - +
63K ARG* 3.2 41.7 - - - +
125K ASP* 3.3 1.0 + - - -
126K ASP* 1.3 81.3 - - + +
128K THR* 1.3 62.1 - - - +
130K ASP* 3.1 2.8 + - - +
131K MET* 3.0 24.5 + - + +
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Residues in contact with THR 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K THR* 3.9 6.6 - - + +
13K LEU* 3.7 32.6 - - + +
63K ARG* 2.9 21.1 + - - +
67K ILE* 4.6 0.3 - - - +
120K THR* 3.7 17.3 - - - +
125K ASP* 2.6 36.8 + - - -
127K VAL* 1.3 71.6 - - - +
129K ASN* 1.3 67.4 + - - +
131K MET* 3.2 13.5 + - + +
132K LEU* 3.0 24.3 + - + +
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Residues in contact with ASN 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ILE* 6.2 0.2 - - - +
126F ASP* 5.8 0.2 + - - -
117K ILE* 3.0 40.6 + - - +
120K THR* 3.0 22.9 - - + +
121K ASP* 3.9 18.3 - - - +
125K ASP 3.0 8.4 + - - +
126K ASP* 3.0 14.2 + - - +
128K THR* 1.3 80.0 - - - +
130K ASP* 1.3 68.2 + - - +
132K LEU* 3.2 5.0 + - - +
133K ILE* 3.0 39.3 + - - +
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Residues in contact with ASP 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP* 3.4 25.7 - - - +
133D ILE* 3.8 26.1 - - + +
134D ALA* 5.4 1.2 + - - +
130F ASP* 3.3 27.8 - - - +
126K ASP 2.8 10.8 + - - +
127K VAL* 3.8 5.8 - - - +
129K ASN* 1.3 81.8 - - - +
131K MET* 1.3 67.3 + - - +
133K ILE* 3.1 8.1 + - - +
134K ALA* 3.0 21.7 + - - +
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Residues in contact with MET 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ALA* 6.5 0.2 - - + -
13K LEU* 4.3 4.7 - - + -
59K GLU* 4.1 16.8 - - - +
60K VAL* 4.1 16.2 - - + -
63K ARG* 4.0 30.3 - - + -
127K VAL* 3.0 19.3 + - + +
128K THR* 3.2 22.2 + - + +
130K ASP* 1.3 78.8 - - - +
132K LEU* 1.3 88.0 + - + +
134K ALA* 3.2 5.3 + - - +
135K PHE* 3.0 49.5 + - + -
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Residues in contact with LEU 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K PHE* 3.8 33.9 - - + -
13K LEU* 4.4 3.4 - - + -
16K GLN* 5.9 0.9 - - + -
60K VAL* 5.2 2.5 - - + -
113K TYR* 4.1 17.1 - - + +
116K GLY 4.1 11.2 - - - +
117K ILE* 3.5 19.9 - - + +
120K THR* 4.0 13.0 - - - +
128K THR* 3.0 28.5 + - + +
129K ASN* 3.5 3.8 - - - +
131K MET* 1.3 97.2 - - + +
133K ILE* 1.3 67.8 + - - +
135K PHE* 3.2 15.6 + - + +
136K LYS* 2.8 24.1 + - - +
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Residues in contact with ILE 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ASP* 3.6 26.9 - - + +
127F VAL* 3.6 29.1 - - + +
130F ASP* 4.0 20.9 - - + +
117K ILE* 3.1 24.9 - - + -
129K ASN* 3.0 34.1 + - - +
130K ASP* 3.1 17.0 + - - +
132K LEU* 1.3 76.3 - - - +
134K ALA* 1.3 64.9 + - - +
136K LYS* 2.9 5.2 + - - +
137K ALA* 2.9 20.7 + - + +
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Residues in contact with ALA 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ASP* 5.6 0.6 + - - +
130K ASP 3.0 12.1 + - - +
131K MET* 3.6 9.4 - - - +
133K ILE* 1.3 79.2 - - - +
135K PHE* 1.3 66.5 + - + +
137K ALA* 3.3 21.4 + - - +
138K SER* 3.4 7.1 + - - -
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Residues in contact with PHE 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K GLN* 3.4 50.8 + - + +
59K GLU* 3.7 31.4 - - + -
60K VAL* 3.4 27.6 - - + -
113K TYR* 3.4 24.9 - + + -
131K MET* 3.0 40.5 + - + -
132K LEU* 3.7 9.0 - - + +
134K ALA* 1.3 80.2 - - + +
136K LYS* 1.3 63.1 + - - +
138K SER* 3.2 7.0 + - - -
139K ILE* 3.0 24.8 + - - +
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Residues in contact with LYS 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F ARG* 4.4 7.2 - - - +
125F ASP* 5.5 0.6 + - - -
126F ASP* 5.3 4.5 - - - +
127F VAL* 3.7 21.3 - - + +
110K ARG* 4.2 39.7 - - + +
113K TYR* 4.3 6.5 - - + -
114K LYS* 4.7 21.4 - - + +
117K ILE* 4.6 13.7 - - + -
132K LEU 2.8 14.0 + - - +
133K ILE* 3.4 9.2 - - - +
135K PHE* 1.3 75.5 - - - +
137K ALA* 1.3 67.5 + - - +
139K ILE* 3.0 8.6 + - + +
140K ASP* 2.8 48.9 + - - +
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Residues in contact with ALA 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F ARG* 5.0 0.5 + - - -
127F VAL* 3.6 29.5 - - + +
133K ILE* 2.9 12.2 + - + +
134K ALA* 3.3 14.8 - - - +
136K LYS* 1.3 78.5 - - - +
138K SER* 1.3 61.8 + - - +
140K ASP* 3.2 6.1 + - - +
141K LYS* 3.2 19.6 + - - +
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Residues in contact with SER 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K GLU* 2.6 28.0 + - - -
53K PHE* 5.1 0.3 - - - -
56K GLN* 4.7 3.2 + - - -
134K ALA 3.4 6.7 + - - -
135K PHE* 3.2 12.7 + - - -
136K LYS 3.0 0.4 - - - -
137K ALA* 1.3 78.9 - - - +
139K ILE* 1.3 65.7 + - - +
141K LYS* 3.0 10.0 + - - +
142K HIS* 2.9 33.7 + - - -
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Residues in contact with ILE 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K PHE* 4.0 27.8 - - + -
56K GLN* 4.4 1.6 - - - +
106K LEU* 3.5 31.0 - - + +
109K LEU* 4.2 15.7 - - + -
110K ARG* 3.9 13.0 - - + +
113K TYR* 3.8 31.6 - - + -
135K PHE 3.0 16.4 + - - +
136K LYS* 3.0 9.2 + - - +
138K SER* 1.3 76.2 - - - +
140K ASP* 1.3 54.1 + - - +
142K HIS* 3.1 8.3 + - - +
143K ILE* 2.7 51.9 + - + +
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Residues in contact with ASP 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F ARG* 2.7 31.8 + - - +
66F ALA* 4.0 15.6 - - + +
127F VAL* 4.3 0.3 - - - +
110K ARG* 3.2 33.3 - - - +
136K LYS* 2.8 38.7 + - - +
137K ALA 3.4 9.0 - - - +
139K ILE* 1.3 79.6 - - - +
141K LYS* 1.3 56.7 + - - +
143K ILE* 3.4 7.4 + - - +
144K TRP* 3.0 26.5 + - - +
154K PRO* 5.9 0.2 - - - +
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Residues in contact with LYS 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLU* 2.8 32.1 + - + +
66F ALA* 4.9 4.5 - - + -
43H HIS* 5.4 2.2 + - - -
137K ALA 3.2 9.0 + - - +
138K SER* 3.0 11.9 + - - +
140K ASP* 1.3 78.1 - - - +
142K HIS* 1.3 66.9 + - + +
144K TRP* 3.1 23.8 + - + +
145K MET* 3.0 47.1 + - + +
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Residues in contact with HIS 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K LYS* 4.4 6.6 + - - -
49K LEU* 3.7 23.5 - - + +
52K GLU* 2.8 28.0 + - - -
53K PHE* 4.0 20.8 - + - -
106K LEU* 4.0 17.0 - - + -
138K SER* 2.9 35.3 + - - -
139K ILE* 3.5 6.5 - - - +
141K LYS* 1.3 80.2 - - + +
143K ILE* 1.3 58.9 + - - +
145K MET* 3.1 21.1 + - + +
146K PHE* 2.8 43.8 + - + +
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Residues in contact with ILE 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K VAL* 5.0 4.5 - - + +
106K LEU* 3.7 31.4 - - + +
107K GLU* 4.0 15.5 - - + +
110K ARG* 3.8 37.0 - - - +
139K ILE* 2.7 40.0 + - + +
140K ASP* 3.5 7.6 - - - +
141K LYS 3.2 0.2 - - - -
142K HIS* 1.3 74.3 - - - +
144K TRP* 1.3 61.9 + - - +
146K PHE* 4.6 1.7 - - - +
147K LYS* 3.1 29.2 + - + +
154K PRO* 4.0 23.3 - - + +
155K LEU* 5.3 1.8 - - + -
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Residues in contact with TRP 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F GLU* 3.8 41.7 - - + -
65F LEU* 3.8 31.3 - - + +
66F ALA* 4.1 20.0 - - + -
31H HIS 4.6 0.7 - - - -
32H TRP* 3.9 13.5 + - - -
34H MET 5.4 0.6 + - - -
39H PHE* 4.0 18.1 - + - -
43H HIS* 3.6 27.4 - + - -
140K ASP 3.0 15.0 + - - +
141K LYS* 3.1 20.8 + - + +
143K ILE* 1.3 76.6 - - - +
145K MET* 1.3 78.1 + - + +
147K LYS* 3.8 1.4 - - - +
148K ALA* 2.9 36.0 + - + +
152K LYS 5.1 0.4 - - - +
154K PRO* 3.9 29.0 - - + +
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Residues in contact with MET 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H PHE* 3.4 36.9 - - + -
40H PHE* 3.8 13.8 - - + -
43H HIS* 4.7 10.3 - - - -
45K LYS* 4.0 15.5 - - - +
141K LYS* 3.0 41.2 + - + +
142K HIS* 3.9 26.2 - - + +
144K TRP* 1.3 98.8 - - + +
146K PHE* 1.3 66.8 + - + +
148K ALA* 3.4 2.4 + - - +
149K PHE* 2.9 21.0 + - - +
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Residues in contact with PHE 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.5 32.3 - + - -
42K LEU* 4.6 1.3 - - + -
45K LYS* 3.8 15.3 - - + -
46K MET* 3.5 24.7 - - + -
49K LEU* 4.0 11.0 - - + -
99K MET* 3.7 34.3 - - + +
102K LEU* 3.6 19.1 - - + -
103K VAL* 3.4 23.8 - - + -
106K LEU* 4.2 5.4 - - + -
142K HIS* 2.8 48.6 + - + +
145K MET* 1.3 73.3 - - - +
147K LYS* 1.3 63.6 + - - +
149K PHE* 3.1 6.5 + - + +
150K LEU* 2.9 26.1 + - + +
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Residues in contact with LYS 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K VAL* 3.8 23.1 - - + -
107K GLU* 3.5 25.5 + - - -
143K ILE* 3.1 21.7 + - + +
144K TRP 3.9 2.0 - - - +
146K PHE* 1.3 74.9 - - - +
148K ALA* 1.3 68.6 + - - +
150K LEU* 2.7 22.0 + - + +
151K GLY 2.8 9.7 + - - -
152K LYS* 2.9 29.6 + - + +
153K ALA 3.1 22.9 - - - +
154K PRO* 3.2 11.9 - - + +
156K GLU* 3.3 35.2 + - - +
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Residues in contact with ALA 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H MET 3.8 11.2 - - - +
35H ARG* 3.5 9.3 - - + +
36H GLY 2.7 24.1 + - - -
39H PHE* 3.6 31.4 - - + -
144K TRP* 2.9 24.9 + - + +
145K MET 3.7 2.9 - - - +
147K LYS* 1.3 77.6 - - - +
149K PHE* 1.3 56.7 + - - +
151K GLY* 2.7 12.8 + - - -
152K LYS 3.5 10.2 + - - +
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Residues in contact with PHE 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLY* 3.1 27.8 - - - -
37H HIS* 3.2 62.7 + - + -
39H PHE* 4.0 4.2 - - + +
40H PHE* 3.9 27.8 - + + -
38K ASN* 4.0 6.7 - - + -
42K LEU* 3.5 28.0 - - + -
95K MET* 4.1 4.3 - - + -
96K ASP* 3.6 20.2 - - - -
99K MET* 3.6 28.3 - - + -
145K MET 2.9 15.7 + - - +
146K PHE* 3.1 9.2 + + - +
148K ALA* 1.3 75.5 - - - +
150K LEU* 1.3 68.1 + - + +
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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