Contacts of the helix formed by residues 116 - 143 (chain B) in PDB entry 2Q7M
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 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.2 41.4 - - + +
114B PHE 2.3 24.0 + - - +
115B GLY* 1.3 65.0 - - - -
117B ARG* 1.3 58.1 + - + +
119B ILE* 2.8 22.8 - - - +
120B LEU* 2.9 21.3 + - - +
31C GLU* 6.0 1.0 - - - +
501C 2CS 3.1 68.0 - - + +
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Residues in contact with ARG 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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115B GLY* 2.9 3.0 + - - +
116B LYS* 1.3 80.3 - - + +
118B ILE* 1.3 56.7 + - - +
120B LEU* 3.3 8.6 - - + +
121B PHE* 2.8 31.9 + - - +
138F PHE* 3.5 31.9 + - - +
139F PHE* 3.8 26.3 - - + -
141F SER* 3.7 24.9 + - - -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.9 0.4 - - + -
86B ALA* 2.8 37.0 - - + +
89B MET* 3.0 17.3 - - + -
90B TYR* 2.9 53.4 - - + +
93B VAL* 4.5 6.5 - - + -
115B GLY* 2.8 15.7 + - - +
117B ARG* 1.3 72.4 - - - +
119B ILE* 1.3 64.7 + - + +
121B PHE* 2.9 10.7 + - + +
122B LEU* 2.8 41.9 + - + +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR 4.4 4.9 - - - +
67B PHE* 4.1 20.4 - - + -
70B VAL* 3.9 24.8 - - + +
90B TYR* 4.2 14.1 - - + -
115B GLY 2.8 33.2 - - - +
116B LYS* 2.8 27.6 - - - +
118B ILE* 1.3 87.6 - - + +
120B LEU* 1.3 61.5 + - - +
122B LEU* 3.8 1.2 - - - +
123B PHE* 2.8 27.3 + - - +
501C 2CS 3.0 44.9 - - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS 2.9 21.9 + - - +
117B ARG* 3.3 6.7 - - + +
119B ILE* 1.3 79.8 - - - +
121B PHE* 1.3 66.6 + - - +
123B PHE* 3.2 3.0 + - + +
124B LEU* 3.0 51.9 + - + +
501C 2CS 3.1 49.6 - - + +
139F PHE* 3.3 22.2 - - + -
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 4.3 13.0 - - + -
86B ALA* 3.0 37.2 - - + -
117B ARG 2.8 12.3 + - - +
118B ILE* 2.9 10.3 + - + +
120B LEU* 1.3 74.6 - - - +
122B LEU* 1.3 64.5 + - + +
124B LEU* 2.6 31.0 + - + +
125B MET* 3.1 41.3 + - + -
135F LEU* 5.7 4.7 - - + -
139F PHE* 3.0 47.8 - + + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.7 4.3 - - + -
70B VAL* 3.4 36.8 - - + +
71B LEU* 4.1 6.1 - - - -
74B ALA* 2.8 26.9 - - + +
83B ALA* 3.7 14.8 - - + +
86B ALA* 3.9 16.2 - - + -
87B GLY* 4.1 13.9 - - - +
118B ILE* 2.8 37.0 + - + +
121B PHE* 1.3 81.9 - - + +
123B PHE* 1.3 62.3 + - - +
125B MET* 3.0 37.5 + - + -
126B SER* 3.1 2.3 + - - -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.8 15.9 - - + +
119B ILE 2.8 18.9 + - - +
120B LEU 3.2 4.5 - - - +
122B LEU* 1.3 76.4 - - - +
124B LEU* 1.3 77.0 + - + +
126B SER* 3.6 4.6 - - - -
127B VAL* 3.0 34.0 + - + +
17C LEU* 3.3 31.1 - - + +
20C VAL* 3.4 20.0 - - + -
21C VAL* 3.2 28.3 - - + -
501C 2CS 3.7 22.4 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.0 48.2 + - + +
121B PHE* 2.6 21.0 + - + +
123B PHE* 1.3 99.4 - - + +
125B MET* 1.3 58.5 + - - -
127B VAL* 2.9 27.8 - - + +
128B ALA* 2.9 15.1 + - - +
131F PHE* 4.8 5.1 - - + -
135F LEU* 4.3 28.0 - - + +
139F PHE* 4.3 5.4 - - + -
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Residues in contact with MET 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 2.9 35.9 - - + +
77B LEU 3.7 0.2 - - - +
78B CYS* 3.2 25.3 - - + +
79B SER* 4.6 3.1 - - - -
82B PRO* 3.6 20.9 - - - -
83B ALA* 3.0 23.6 - - + -
121B PHE* 3.2 41.1 - - + +
122B LEU* 3.0 23.3 + - + -
124B LEU* 1.3 74.7 - - - +
126B SER* 1.3 63.5 + - - +
128B ALA* 3.0 23.2 + - - +
129B GLY 3.1 7.4 + - - -
135F LEU* 5.9 2.7 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 4.0 3.6 + - - -
73B SER* 2.8 30.3 - - - -
74B ALA* 2.7 29.0 + - - +
77B LEU* 4.1 2.7 - - - +
122B LEU 3.1 7.5 + - - -
123B PHE* 3.6 12.3 - - - -
125B MET* 1.3 74.0 - - - +
127B VAL* 1.3 61.5 + - - +
128B ALA 3.0 4.0 - - - -
130B ILE* 3.0 31.4 + - - +
17C LEU* 4.0 17.0 - - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.0 22.8 + - + +
124B LEU* 2.9 52.5 - - + +
126B SER* 1.3 76.4 - - - +
128B ALA* 1.3 63.2 + - - +
130B ILE* 4.1 10.3 - - + +
131B PHE* 3.5 17.5 + - + +
17C LEU* 4.9 5.3 - - + +
131F PHE* 5.6 4.9 - - + -
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Residues in contact with ALA 128 (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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78B CYS* 4.6 7.9 - - - -
124B LEU 2.9 17.2 + - - +
125B MET* 3.0 15.0 - - - +
126B SER 3.0 1.0 - - - -
127B VAL* 1.3 76.1 - - - +
129B GLY* 1.3 61.2 + - - +
131B PHE* 2.8 28.1 + - - +
132B ASN* 2.8 14.3 + - - +
131F PHE* 4.9 17.0 - - + -
135F LEU* 5.7 1.8 - - + -
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 2.9 25.5 + - - -
78B CYS* 4.5 1.9 - - - +
125B MET 3.1 6.5 + - - -
128B ALA* 1.3 78.6 - - - +
130B ILE* 1.3 54.4 + - - +
132B ASN* 3.4 14.6 - - - +
133B TYR* 2.7 37.0 + - - +
6C VAL* 6.1 0.9 - - - -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.1 29.9 + - + +
126B SER 3.0 17.7 + - - +
127B VAL* 4.1 11.2 - - + +
129B GLY* 1.3 75.6 - - - +
131B PHE* 1.3 63.1 + - + +
133B TYR* 3.9 6.1 - - - +
134B TYR* 3.9 22.5 - - + -
6C VAL* 6.3 0.2 - - - -
10C VAL* 3.5 19.9 - - + +
13C ALA* 3.6 14.4 - - + -
14C ILE* 3.0 43.3 - - + +
17C LEU* 3.9 9.9 - - + -
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.5 11.6 + - + +
128B ALA* 2.8 15.6 + - - +
130B ILE* 1.3 80.8 - - + +
132B ASN* 1.3 75.6 + - + -
133B TYR 2.7 4.7 + - - -
134B TYR* 2.6 40.0 + - + +
135B LEU* 3.4 29.1 + - + -
124F LEU* 4.7 19.5 - - + -
127F VAL* 5.9 2.7 - - + -
128F ALA* 4.7 17.3 - - + -
131F PHE* 5.8 10.8 - + - -
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA 2.8 15.2 + - - +
129B GLY* 3.4 14.4 - - - +
131B PHE* 1.3 96.2 - - + +
133B TYR* 1.3 65.1 + - - +
135B LEU* 3.3 9.3 + - - +
136B ILE* 3.0 40.5 + - - +
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Residues in contact with TYR 133 (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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129B GLY 2.7 16.9 + - - +
130B ILE* 3.9 5.4 - - - +
131B PHE 2.7 1.0 + - - -
132B ASN* 1.3 80.6 + - - +
134B TYR* 1.3 96.3 + + - +
135B LEU 3.0 2.2 - - - -
136B ILE* 3.2 8.3 + - + -
137B PHE* 2.9 40.7 + + + +
3C GLN* 3.1 55.7 + - - -
6C VAL* 3.9 20.0 - - + -
7C GLY* 2.9 28.5 - - - -
10C VAL* 3.9 14.4 - - + -
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 3.9 10.8 - - + -
131B PHE* 2.6 20.5 + - + +
133B TYR* 1.3 105.7 - + - +
135B LEU* 1.3 62.8 + - + +
137B PHE* 3.4 14.7 - + - +
138B PHE* 3.2 37.7 + + + +
10C VAL* 3.1 31.2 - - + +
11C LEU* 4.2 7.6 - - - +
14C ILE* 4.5 7.3 - - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.4 26.0 + - + -
132B ASN* 3.3 16.8 + - - +
133B TYR 3.0 0.4 - - - -
134B TYR* 1.3 80.2 - - + +
136B ILE* 1.3 56.1 + - + +
137B PHE 2.8 5.4 + - - -
138B PHE* 2.8 23.2 + - + -
139B PHE* 3.3 33.8 + - + +
140B GLY* 3.1 12.7 + - - -
121F PHE* 3.7 21.3 - - + -
124F LEU* 4.2 29.4 - - + +
125F MET* 5.8 0.7 - - + -
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASN* 3.0 48.4 + - - +
133B TYR* 3.2 8.7 + - - +
135B LEU* 1.3 76.0 - - + +
137B PHE* 1.3 57.5 + - - +
140B GLY* 3.2 27.2 - - - -
141B SER* 3.7 1.2 + - - -
3C GLN* 3.4 35.2 + - + +
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Residues in contact with PHE 137 (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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133B TYR* 2.9 41.6 + + + +
134B TYR* 3.4 15.5 - + - +
135B LEU 2.8 0.8 + - - -
136B ILE* 1.3 80.9 - - - +
138B PHE* 1.3 93.9 + + - +
141B SER* 3.7 15.2 + - - -
3C GLN* 3.6 12.3 - - - +
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 3.2 23.2 + + + +
135B LEU* 2.8 9.7 + - + -
137B PHE* 1.3 123.1 - + + +
139B PHE* 1.3 76.0 + + + +
140B GLY 2.6 14.6 + - - -
141B SER* 2.7 25.0 + - - -
142B ASP* 3.7 4.5 + - - +
117F ARG* 4.6 14.1 - - - +
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.3 21.2 + - + -
138B PHE* 1.3 85.5 - + + +
140B GLY* 1.3 57.2 + - - +
141B SER 4.4 4.6 - - - +
142B ASP* 4.8 6.9 - - - +
143B PHE* 5.0 5.9 + - - +
117F ARG* 3.8 44.0 - - + -
120F LEU* 3.0 38.6 - - + -
121F PHE* 3.0 62.8 - + + -
124F LEU* 3.6 11.9 - - + -
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 3.1 5.6 + - - -
136B ILE* 3.2 28.7 - - - -
138B PHE 2.6 7.9 + - - -
139B PHE* 1.3 72.8 - - - +
141B SER* 1.3 63.4 + - - +
143B PHE* 4.4 10.4 - - - +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE 3.7 3.9 + - - -
137B PHE 3.7 13.5 + - - -
138B PHE* 2.7 10.9 + - - -
139B PHE 4.4 0.2 - - - +
140B GLY* 1.3 81.0 - - - +
142B ASP* 1.3 93.5 + - - +
143B PHE* 2.6 26.1 + - - +
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.9 7.4 - - - +
139B PHE* 4.8 5.8 - - - -
141B SER* 1.3 87.1 + - - +
143B PHE* 1.3 61.2 + - - +
144B GLU* 2.3 43.8 + - - +
89F MET* 5.9 1.3 - - + -
117F ARG* 2.3 52.0 + - - -
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Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE 5.0 6.8 + - - +
140B GLY 4.4 8.7 - - - +
141B SER* 2.6 27.4 + - - +
142B ASP* 1.3 89.9 - - - +
144B GLU* 1.3 71.1 + - - +
145B ASN* 3.3 33.9 + - - +
85F PHE* 4.1 27.8 - + + -
89F MET* 4.6 10.8 - - - +
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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