Contacts of the helix formed by residues 95 - 122 (chain B) 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 MET 95 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B MET* 3.7 37.0 - - + -
35B ARG 3.5 33.6 + - - +
36B GLY* 4.5 1.6 - - - +
38B ASN* 3.9 16.8 - - + +
39B PHE* 3.8 30.7 - - - +
42B LEU* 3.6 27.8 - - + -
93B LYS 4.0 0.4 + - - -
94B THR* 1.3 77.0 - - + +
96B ASP* 1.3 54.6 + - - +
98B LEU* 2.7 12.2 + - - +
99B MET* 2.6 42.5 + - + +
149B PHE* 4.1 11.2 - - + -
37J HIS* 5.6 1.6 - - + -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 3.1 13.9 - - + +
95B MET* 1.3 77.7 - - - +
97B GLN* 1.3 64.0 + - + +
99B MET* 3.9 0.8 - - - +
100B GLU* 2.8 37.0 + - - +
149B PHE* 3.8 10.2 - - - -
150B LEU* 3.8 23.8 - - + +
37J HIS* 2.9 39.4 + - - -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO 4.8 1.1 + - - +
93B LYS* 3.3 46.1 - - + +
94B THR* 2.8 41.5 + - - +
96B ASP* 1.3 79.4 - - + +
98B LEU* 1.3 62.8 + - - +
100B GLU* 3.4 14.1 + - - +
101B ASP* 3.1 21.7 + - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 5.2 5.4 - - + +
30B ILE* 3.8 37.8 - - + +
33B TYR* 4.6 3.4 - - + +
34B MET* 3.8 36.6 - - + +
35B ARG 5.2 0.7 - - - +
89B TYR* 4.3 16.4 - - + -
93B LYS* 4.3 30.5 - - + +
94B THR 2.8 20.2 + - - +
95B MET* 2.7 10.6 + - - +
97B GLN* 1.3 74.3 - - - +
99B MET* 1.3 70.8 + - + +
101B ASP* 3.0 11.3 + - + +
102B LEU* 2.8 21.1 + - - +
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Residues in contact with MET 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.6 30.1 - - + -
34B MET* 4.8 0.4 - - + -
42B LEU* 4.1 16.8 - - + -
46B MET* 4.3 11.4 - - + -
95B MET* 2.6 27.6 + - + +
96B ASP 3.9 2.9 - - - +
98B LEU* 1.3 77.8 - - + +
100B GLU* 1.3 52.4 + - - +
102B LEU* 2.9 10.1 + - + +
103B VAL* 2.7 36.3 + - + +
146B PHE* 3.8 33.4 - - + -
149B PHE* 3.4 27.4 - - + -
150B LEU* 4.0 20.6 - - + -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP* 2.8 27.7 + - - +
97B GLN* 3.6 15.6 - - - +
99B MET* 1.3 77.0 - - - +
101B ASP* 1.3 61.3 + - - +
103B VAL* 3.9 3.7 - - - +
104B GLY* 3.0 20.8 + - - -
150B LEU* 3.8 26.6 - - + +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 3.3 39.2 + - - +
29B GLN* 4.7 9.7 + - - -
30B ILE* 5.2 3.7 - - + +
93B LYS* 5.8 6.5 - - - -
97B GLN 3.1 12.8 + - - +
98B LEU* 3.0 15.0 + - + +
100B GLU* 1.3 72.6 - - - +
102B LEU* 1.3 68.2 + - - +
104B GLY* 3.2 2.4 + - - -
105B THR* 3.0 23.6 + - - -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.4 33.9 - - + -
26B LYS* 5.2 1.3 - - - -
27B ILE* 4.8 3.6 - - + -
30B ILE* 4.1 19.6 - - + +
46B MET* 4.0 9.0 - - + -
49B LEU* 3.8 15.0 - - + -
98B LEU 2.8 12.1 + - - +
99B MET* 3.0 13.0 - - + +
101B ASP* 1.3 77.4 - - - +
103B VAL* 1.3 64.2 + - - +
105B THR* 3.0 5.9 + - - -
106B LEU* 2.9 25.6 + - + +
146B PHE* 3.7 48.9 - - + -
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MET 2.7 20.1 + - - +
100B GLU* 3.9 6.5 - - - +
102B LEU* 1.3 74.8 - - - +
104B GLY* 1.3 54.3 + - - +
106B LEU* 3.1 11.0 + - + +
107B GLU* 2.7 53.8 + - + +
143B ILE* 5.0 7.2 - - + +
146B PHE* 3.4 36.3 - - + -
147B LYS* 3.9 22.9 - - + +
150B LEU* 4.2 13.7 - - + -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU 3.0 15.6 + - - -
101B ASP* 3.7 3.8 - - - -
102B LEU 3.2 0.2 - - - -
103B VAL* 1.3 76.6 - - - +
105B THR* 1.3 58.5 + - - +
107B GLU* 3.1 14.6 + - - +
108B LEU* 2.8 27.7 + - - +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.3 37.2 - - + -
26B LYS* 3.5 18.4 - - - -
84B VAL* 3.8 30.1 - - + +
85B GLU 5.7 0.2 + - - -
101B ASP* 3.0 15.4 + - - -
102B LEU 3.6 6.5 - - - -
104B GLY* 1.3 77.2 - - - +
106B LEU* 1.3 62.8 + - - +
108B LEU* 3.0 9.1 + - + +
109B LEU* 3.0 24.7 + - + +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.7 24.5 - - + -
49B LEU* 5.6 1.8 - - + -
53B PHE* 3.9 24.7 - - + -
102B LEU* 2.9 24.1 + - + +
103B VAL* 3.2 15.9 - - + +
105B THR* 1.3 75.7 - - - +
107B GLU* 1.3 66.2 + - - +
109B LEU* 3.1 7.0 + - + +
110B ARG* 2.8 23.7 + - - +
139B ILE* 3.7 12.9 - - + +
142B HIS* 3.9 26.2 - - + -
143B ILE* 3.7 22.4 - - + +
146B PHE* 4.2 16.8 - - + -
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 2.7 33.9 + - + +
104B GLY* 3.1 13.7 + - - +
106B LEU* 1.3 73.5 - - - +
108B LEU* 1.3 63.5 + - - +
110B ARG* 3.1 27.9 + - - +
111B ASP* 2.9 30.7 + - - +
143B ILE* 3.9 19.1 - - + +
147B LYS* 3.5 27.4 + - - -
154B PRO 4.3 6.6 - - - +
155B LEU* 5.7 0.9 - - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN* 4.2 0.2 - - - +
83B SER* 3.7 27.4 - - - +
84B VAL* 4.0 28.5 - - + -
85B GLU* 5.1 1.1 - - + +
104B GLY 2.8 13.2 + - - +
105B THR* 3.0 11.2 + - - +
107B GLU* 1.3 78.4 - - - +
109B LEU* 1.3 66.1 + - + +
111B ASP* 3.3 5.4 + - - +
112B GLU* 2.9 61.8 + - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.7 23.3 - - - +
19B ASN* 4.1 17.7 - - + -
20B LEU* 4.2 13.5 - - + -
23B PHE* 3.6 40.4 - - + -
53B PHE* 4.6 7.4 - - + -
84B VAL* 4.4 0.9 - - + -
105B THR* 3.0 18.6 + - + +
106B LEU* 3.6 7.2 - - + +
108B LEU* 1.3 82.7 - - + +
110B ARG* 1.3 57.0 + - - +
112B GLU* 3.1 2.0 + - - -
113B TYR* 2.7 50.2 + - + +
139B ILE* 4.2 13.0 - - + -
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 2.8 12.7 + - - +
107B GLU* 3.2 30.0 + - - +
109B LEU* 1.3 78.5 - - - +
111B ASP* 1.3 91.1 + - - +
113B TYR* 3.1 5.8 + - - +
114B LYS* 2.9 22.8 + - + +
136B LYS* 4.2 19.9 - - + +
139B ILE* 3.9 16.3 - - + +
140B ASP* 3.2 26.8 + - - +
143B ILE* 3.8 23.2 - - - +
154B PRO 5.2 0.2 + - - -
155B LEU* 3.8 26.9 - - - +
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 2.9 19.4 + - - +
108B LEU* 3.9 4.9 - - - +
110B ARG* 1.3 112.7 + - - +
112B GLU* 1.3 63.4 + - + +
114B LYS* 3.2 16.6 + - - +
115B GLN* 2.9 29.2 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.1 12.5 - - + -
15B HIS* 3.1 10.1 + - - -
16B GLN* 3.0 29.2 + - - +
19B ASN* 3.0 10.6 + - - -
83B SER* 2.6 28.6 + - - -
108B LEU* 2.9 37.4 + - + +
109B LEU* 3.8 4.0 - - - +
111B ASP* 1.3 73.9 - - + +
113B TYR* 1.3 66.8 + - - +
115B GLN* 3.0 15.3 + - + +
116B GLY 2.9 17.2 + - - -
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.9 12.7 - + - -
16B GLN* 3.6 30.2 - - + +
20B LEU* 3.4 24.9 - - - +
56B GLN* 2.9 19.0 + - - -
60B VAL* 4.9 0.6 - - + +
109B LEU* 2.7 34.7 + - + +
110B ARG* 3.5 5.6 - - - +
112B GLU* 1.3 73.2 - - - +
114B LYS* 1.3 52.2 + - - +
116B GLY* 2.8 2.9 + - - -
117B ILE* 2.5 39.7 + - - +
132B LEU* 4.0 23.1 - - + +
135B PHE* 3.3 41.7 - + + -
136B LYS* 4.2 12.1 - - + -
139B ILE* 3.8 18.3 - - + +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 2.9 14.1 + - + +
111B ASP* 3.3 14.4 - - - +
113B TYR* 1.3 75.5 - - - +
115B GLN* 1.3 66.9 + - - +
117B ILE* 3.0 14.4 + - + +
118B GLU* 2.8 53.8 + - - +
136B LYS* 4.6 13.8 - - + +
124L GLY* 3.8 12.2 + - - -
126L ASP* 2.5 33.8 + - - +
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.7 5.4 - - + -
111B ASP* 2.9 28.3 + - - +
112B GLU* 3.0 16.6 + - + +
114B LYS* 1.3 80.1 - - - +
116B GLY* 1.3 67.0 + - - +
118B GLU* 2.8 24.8 + - - +
119B LEU* 2.9 16.7 + - + +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.5 36.8 - - - -
112B GLU 2.9 7.7 + - - -
113B TYR 2.8 10.1 + - - -
115B GLN* 1.3 72.7 - - - +
117B ILE* 1.3 53.5 + - - +
119B LEU* 4.0 5.2 - - - -
120B THR* 2.6 43.9 + - - +
132B LEU* 4.0 4.3 - - - -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR 2.5 18.3 + - - +
114B LYS* 3.2 19.3 - - - +
115B GLN 2.9 0.2 - - - -
116B GLY* 1.3 74.1 - - - +
118B GLU* 1.3 60.4 + - + +
120B THR* 2.7 23.7 - - - +
121B ASP* 3.2 5.0 + - - +
129B ASN* 3.2 18.7 + - - +
132B LEU* 3.7 21.8 - - + +
133B ILE* 3.3 37.0 - - + +
136B LYS* 4.3 21.8 - - + -
126L ASP* 3.6 33.7 - - + +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 2.8 57.9 + - - +
115B GLN* 2.8 17.2 + - - +
117B ILE* 1.3 80.2 - - + +
119B LEU* 1.3 57.0 + - - +
121B ASP* 3.2 6.9 + - - +
122B LYS* 2.9 41.9 + - - +
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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
----------------------------------------------------------
7B VAL* 3.8 27.8 - - + +
8B ASP* 4.0 11.0 - - - +
9B THR* 4.1 5.8 - - - +
12B PHE* 3.6 38.8 - - + -
115B GLN 2.9 15.8 + - - +
116B GLY* 3.4 6.1 - - - +
118B GLU* 1.3 72.5 - - - +
120B THR* 1.3 68.5 + - - +
121B ASP 3.0 3.1 + - - -
122B LYS* 3.1 26.5 + - - +
123B GLU* 2.8 52.5 - - - +
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 4.1 16.6 + - - -
12B PHE* 6.4 0.2 - - - -
116B GLY* 2.6 25.5 + - - +
117B ILE* 2.7 24.5 - - - +
119B LEU* 1.3 78.9 - - - +
121B ASP* 1.3 56.5 + - - +
123B GLU* 3.7 1.3 + - - +
124B GLY 3.0 5.2 + - - -
125B ASP* 2.9 36.9 + - - +
128B THR* 3.4 17.7 - - - +
129B ASN* 3.2 41.5 + - - +
132B LEU* 4.4 6.1 - - + -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE 3.6 9.2 - - - +
118B GLU* 3.2 8.9 + - - +
119B LEU 3.0 0.8 - - - -
120B THR* 1.3 82.6 - - - +
122B LYS* 1.3 68.2 - - - +
123B GLU 3.1 1.6 - - - -
124B GLY* 2.9 13.9 + - - +
129B ASN* 4.0 17.8 + - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 2.9 21.7 + - + +
119B LEU* 3.1 35.8 + - - +
121B ASP* 1.3 79.0 - - - +
123B GLU* 1.3 66.9 + - + +
124B GLY* 3.2 0.5 + - - -
----------------------------------------------------------
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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