Contacts of the helix formed by residues 117 - 143 (chain B) in PDB entry 2VQO
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 ILE 117 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 4.0 31.9 - - + -
299A LEU* 3.7 37.7 - - + -
332A TYR* 4.0 46.8 - - + +
1410A TFG 5.3 9.2 - - + +
116B THR* 1.3 75.4 - - - +
118B TRP* 1.3 75.0 + - + +
119B ASN 3.2 0.2 - - - -
120B GLU* 3.1 23.0 + - + +
121B VAL* 3.3 11.6 + - + +
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Residues in contact with TRP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO* 4.0 24.5 - - + -
299A LEU* 4.5 7.9 - - + -
332A TYR* 4.1 28.0 - + - -
83B PRO* 4.5 20.4 - - + -
113B ASP 5.2 2.9 - - - +
116B THR* 3.1 20.3 - - + +
117B ILE* 1.3 87.7 - - + +
119B ASN* 1.3 61.3 + - - +
120B GLU 3.2 0.2 - - - -
121B VAL* 3.2 30.6 + - + +
122B HIS* 2.9 29.3 + - - +
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER 5.5 1.7 - - - +
115A ASP* 4.6 0.6 + - - -
20B LYS* 4.4 34.6 + - - +
113B ASP 4.2 4.3 + - - -
114B SER* 3.2 48.4 + - - +
116B THR 3.1 9.8 + - - +
118B TRP* 1.3 78.6 - - - +
120B GLU* 1.3 70.3 + - - +
122B HIS* 3.5 8.1 + - - +
123B SER* 3.0 33.8 + - - -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 5.4 7.5 - - - +
168A PHE* 3.7 31.7 - - + -
1410A TFG 3.9 16.8 - - + +
114B SER 5.5 0.3 - - - +
116B THR 4.2 5.9 - - - +
117B ILE* 3.1 11.7 + - - +
119B ASN* 1.3 93.9 - - - +
121B VAL* 1.3 63.9 + - - +
123B SER* 3.7 10.6 + - - -
124B ALA* 3.2 23.4 + - - +
170B TYR* 3.5 21.7 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 4.0 11.4 - - + -
1410A TFG 3.9 35.9 - - + -
82B ASN* 5.4 3.6 - - - +
83B PRO* 4.1 22.9 - - + -
117B ILE 3.3 9.4 + - - +
118B TRP* 3.2 36.7 + - + +
120B GLU* 1.3 75.3 - - - +
122B HIS* 1.3 64.2 + - - +
124B ALA* 3.5 3.8 + - - +
125B GLY* 3.1 18.7 + - - -
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.7 24.9 + - + -
18B MET 4.3 0.4 + - - -
19B LEU 2.8 24.4 + - - -
20B LYS* 3.6 19.2 + - - -
21B HIS 5.6 0.4 - - - -
118B TRP 2.9 16.2 + - - +
119B ASN* 3.7 11.4 - - - +
121B VAL* 1.3 78.5 - - - +
123B SER* 1.3 51.4 + - - +
125B GLY* 3.2 2.6 + - - -
126B ALA* 2.7 34.4 + - + +
154B ARG* 3.8 16.5 + - - -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 5.2 1.6 - - - -
119B ASN* 3.0 24.4 + - - -
120B GLU* 3.7 15.0 + - - -
121B VAL 3.3 0.4 - - - -
122B HIS* 1.3 74.7 - - - +
124B ALA* 1.3 59.9 + - - +
126B ALA* 3.3 2.9 + - - +
127B ALA* 2.9 27.7 + - - +
154B ARG* 3.3 32.1 + - - +
155B PRO* 3.6 8.6 - - - +
170B TYR* 4.1 14.8 - - - -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410A TFG 3.7 26.5 - - + -
79B TYR* 3.6 21.9 - - + +
120B GLU 3.2 8.0 + - - +
121B VAL 3.9 0.2 - - - +
122B HIS 3.4 0.2 - - - -
123B SER* 1.3 77.8 - - - +
125B GLY* 1.3 61.4 + - - +
127B ALA* 3.3 4.4 + - - +
128B ARG* 3.2 17.3 + - - +
170B TYR* 3.9 31.1 - - + -
171B PHE* 3.7 8.3 - - - -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410A TFG 5.5 0.2 - - - -
61B LYS* 5.9 0.7 - - - +
79B TYR 4.7 1.8 + - - -
80B GLY 6.0 1.6 - - - -
121B VAL 3.1 14.7 + - - -
122B HIS* 3.2 5.1 + - - -
124B ALA* 1.3 73.9 - - - +
126B ALA* 1.3 63.8 + - - +
128B ARG* 3.2 9.9 + - - +
129B LEU* 3.2 19.8 + - - +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU 4.5 5.8 - - - +
18B MET* 4.0 20.7 - - - +
122B HIS* 2.7 20.1 + - - +
123B SER 3.3 6.0 + - - +
125B GLY* 1.3 72.2 - - - +
127B ALA* 1.3 51.7 + - - +
129B LEU* 3.3 8.8 + - - +
130B ALA* 2.8 34.3 + - - +
154B ARG* 3.5 27.1 - - - +
155B PRO* 3.9 9.2 - - + -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER 2.9 12.8 + - - +
124B ALA 3.3 10.8 - - - +
125B GLY 3.2 0.4 - - - -
126B ALA* 1.3 74.5 - - - +
128B ARG* 1.3 64.9 + - - +
130B ALA* 3.2 5.0 + - - +
131B VAL* 3.0 28.9 + - - +
155B PRO* 3.7 17.7 - - + +
156B PRO 5.9 0.7 - - - +
170B TYR* 3.7 17.5 - - + +
171B PHE* 3.6 23.1 - - + +
173B SER* 4.7 0.2 + - - -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 3.9 28.7 - - + +
62B ALA* 2.8 53.9 + - - +
63B THR* 4.3 6.1 - - - +
64B LEU* 3.3 28.4 - - - +
67B LEU* 4.4 8.5 - - + -
80B GLY* 3.0 31.5 + - - +
81B THR* 4.7 5.9 - - - +
82B ASN 5.6 0.4 - - - +
124B ALA 3.2 9.6 + - - +
125B GLY* 3.2 10.7 + - - +
127B ALA* 1.3 79.4 - - - +
129B LEU* 1.3 61.3 + - - +
131B VAL* 3.5 3.2 + - - -
132B GLY 3.5 6.9 + - - -
171B PHE* 3.8 13.8 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 4.1 15.7 - - - +
17B LEU* 3.5 39.3 - - + +
18B MET* 3.9 21.3 - - + +
60B ARG* 3.2 37.9 - - - +
61B LYS* 3.9 12.9 - - + +
125B GLY 3.2 9.5 + - - +
126B ALA* 3.6 7.9 - - - +
127B ALA 3.2 0.2 - - - -
128B ARG* 1.3 77.4 - - - +
130B ALA* 1.3 63.8 + - - +
133B CYS* 3.1 31.6 + - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 4.0 14.1 - - - -
126B ALA 2.8 19.8 + - - +
127B ALA* 3.2 9.4 + - - +
129B LEU* 1.3 69.5 - - - +
131B VAL* 1.3 64.9 + - - +
133B CYS* 3.5 1.9 + - - +
134B VAL* 3.2 29.3 + - - +
153B VAL* 4.1 12.7 - - + +
154B ARG 3.6 20.0 - - - +
155B PRO 4.4 4.9 - - - +
173B SER* 4.0 10.3 - - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.7 21.8 - - + -
67B LEU* 3.9 8.3 - - + -
127B ALA 3.0 15.5 + - - +
128B ARG 3.8 1.6 - - - +
129B LEU 3.3 0.6 - - - -
130B ALA* 1.3 76.6 - - - +
132B GLY* 1.3 55.9 + - - +
134B VAL* 3.3 2.9 + - - +
135B VAL* 2.9 36.5 + - + +
171B PHE* 3.7 25.8 - - + +
172B ASN 4.8 0.4 - - - -
173B SER* 3.5 26.5 - - - +
176B VAL* 3.5 36.6 - - + -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.1 27.9 - - - +
61B LYS 4.2 0.2 - - - -
62B ALA* 3.8 15.0 - - - +
128B ARG 3.5 5.1 + - - -
129B LEU 3.4 2.8 + - - -
130B ALA 3.3 0.4 - - - -
131B VAL* 1.3 76.6 - - - +
133B CYS* 1.3 60.4 + - - +
135B VAL* 3.9 6.1 - - - +
136B GLU* 3.0 35.5 + - - +
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Residues in contact with CYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.6 26.9 - - + +
14B TYR 5.2 0.4 - - - -
15B ASP* 4.4 14.1 - - - -
18B MET* 4.5 9.6 - - - -
59B GLY* 3.8 24.2 - - - -
60B ARG 3.5 0.6 + - - -
129B LEU* 3.1 39.2 + - - +
130B ALA 3.7 5.4 - - - +
132B GLY* 1.3 77.1 - - - +
134B VAL* 1.3 61.0 + - - +
136B GLU* 3.6 2.4 + - - +
137B LEU* 3.2 22.7 + - - +
153B VAL* 3.9 13.2 - - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 3.2 14.2 + - - +
131B VAL 3.7 6.5 - - - +
132B GLY 3.3 0.2 - - - -
133B CYS* 1.3 74.8 - - - +
135B VAL* 1.3 59.9 + - - +
137B LEU* 3.2 6.1 + - - +
138B VAL* 2.8 49.1 + - + +
151B ALA* 4.1 14.6 - - + -
153B VAL* 4.1 21.3 - - + -
173B SER* 4.0 26.2 - - - +
174B VAL* 4.6 5.4 - - + -
177B ALA* 4.1 11.9 - - + -
325B VAL* 5.4 2.2 - - + -
327B ALA* 4.4 14.4 - - + -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.6 22.9 - - - +
66B GLU* 5.4 2.7 - - - +
131B VAL* 2.9 24.9 + - + +
132B GLY* 3.9 7.0 - - - +
134B VAL* 1.3 74.1 - - - +
136B GLU* 1.3 58.2 + - - +
138B VAL* 3.8 0.4 - - - +
139B PHE* 3.0 45.4 + - + +
173B SER 5.1 0.2 - - - +
176B VAL* 4.1 16.4 - - + -
177B ALA* 4.1 18.6 - - + +
180B LEU* 3.8 31.6 - - + -
184B ARG* 5.7 1.1 - - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.0 11.8 - - + +
58B ARG* 4.2 24.5 + - - +
59B GLY* 4.7 0.9 - - - -
60B ARG* 3.2 39.3 + - + +
132B GLY 3.0 23.0 + - - +
133B CYS* 3.7 5.8 - - - +
134B VAL 3.3 0.2 - - - -
135B VAL* 1.3 77.0 - - - +
137B LEU* 1.3 61.6 + - - +
139B PHE* 3.6 5.0 + - - +
140B LYS* 3.2 46.4 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY* 4.0 27.8 - - - +
12B LEU 4.3 1.6 - - - +
13B VAL* 3.7 13.0 - - + -
57B ILE* 3.8 20.8 - - + +
133B CYS 3.2 13.6 + - - +
134B VAL* 3.2 5.5 + - - +
136B GLU* 1.3 75.5 - - - +
138B VAL* 1.3 66.8 + - - +
140B LYS* 3.3 2.8 + - - +
141B VAL* 3.1 29.6 + - + +
146B LEU* 4.4 7.6 - - + -
149B GLY* 4.3 6.1 - - - -
150B PHE 3.5 40.4 - - - +
151B ALA* 3.7 8.5 - - + +
325B VAL* 3.9 14.8 - - + -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 2.8 30.0 + - + +
135B VAL 3.8 3.6 - - - +
137B LEU* 1.3 76.0 - - - +
139B PHE* 1.3 58.9 + - + +
141B VAL* 3.4 2.6 + - - +
142B ALA* 2.8 27.4 + - + +
177B ALA* 3.9 22.4 - - + -
181B LEU* 3.4 38.6 - - + -
282B VAL* 5.3 2.1 - - + +
284B LEU* 3.7 26.0 - - + -
325B VAL* 4.0 18.3 - - + +
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.0 38.9 + - + +
136B GLU* 4.1 5.6 - - - +
138B VAL* 1.3 77.6 - - + +
140B LYS* 1.3 58.6 + - + +
142B ALA* 4.3 3.1 - - - -
143B THR* 2.8 41.3 + - + +
177B ALA 4.4 2.7 - - - -
180B LEU* 3.6 45.3 - - + -
181B LEU* 3.8 19.5 - - + -
184B ARG* 4.1 19.7 - - + -
185B LEU* 3.8 31.0 - - + -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.2 33.2 - - + +
58B ARG* 5.1 12.1 + - - +
136B GLU* 3.2 34.7 + - - +
137B LEU* 3.3 5.1 + - - +
139B PHE* 1.3 76.0 - - + +
141B VAL* 1.3 58.4 + - - +
143B THR* 3.8 4.7 - - - -
144B GLY 3.5 0.7 + - - -
145B GLU* 2.9 51.1 + - + +
146B LEU* 2.8 39.7 + - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.1 19.7 + - + +
138B VAL 3.7 4.0 - - - +
140B LYS* 1.3 75.3 - - - +
142B ALA* 1.3 63.7 + - - +
143B THR 3.2 0.2 - - - -
144B GLY* 3.2 11.3 + - - -
146B LEU* 3.5 16.7 - - + +
147B LYS 3.4 19.3 - - - +
148B ASN* 3.7 26.9 - - - +
149B GLY* 4.1 2.0 - - - +
282B VAL* 5.6 3.1 - - + -
323B ARG* 4.0 31.1 + - + +
324B ILE 4.0 7.6 - - - +
325B VAL* 3.6 21.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 2.8 22.4 + - + +
139B PHE 3.4 2.0 + - - +
141B VAL* 1.3 74.6 - - - +
143B THR* 1.3 60.0 + - - +
144B GLY 3.8 0.2 + - - -
181B LEU* 3.6 27.8 - - + -
185B LEU* 3.9 12.2 - - + +
187B VAL* 5.4 2.0 - - + -
282B VAL* 4.5 15.6 - - + +
323B ARG* 4.3 20.3 + - - +
----------------------------------------------------------
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 2.8 27.3 + - + +
140B LYS* 3.5 9.4 + - - -
142B ALA* 1.3 76.5 - - - +
144B GLY* 1.3 60.2 + - - +
145B GLU* 3.4 11.7 + - - +
185B LEU* 3.9 28.9 - - + -
----------------------------------------------------------
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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