Contacts of the helix formed by residues 117 - 143 (chain A) in PDB entry 2VQQ
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 1.3 73.5 - - - +
118A TRP* 1.3 72.6 + - + +
119A ASN 3.1 0.2 - - - -
120A GLU* 3.1 25.0 + - + +
121A VAL* 3.3 11.7 + - + +
20B LYS* 5.4 0.6 - - - +
168B PHE* 4.0 33.4 - - + -
299B LEU* 3.6 39.9 - - + -
332B HIS* 3.8 45.9 - - + +
1409B TFG 5.1 9.2 - - + +
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Residues in contact with TRP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 4.1 15.3 - - + -
84A LEU* 4.0 26.7 - - + -
112A VAL* 3.7 20.3 - - + +
116A THR* 3.0 19.6 + - + +
117A ILE* 1.3 87.5 - - + +
119A ASN* 1.3 60.3 + - - +
121A VAL* 3.5 30.4 + - + +
122A HIS* 3.0 27.5 + - - +
296B PRO* 3.8 31.2 - - + -
298B PRO* 6.4 0.2 - - + -
299B LEU* 4.5 9.0 - - + -
332B HIS* 4.4 17.4 + + - -
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.3 34.6 + - - +
112A VAL* 4.0 9.7 - - - +
114A SER* 3.3 43.0 - - - +
116A THR 2.9 16.2 + - - +
118A TRP* 1.3 77.7 - - - +
120A GLU* 1.3 72.5 + - - +
122A HIS* 3.4 8.0 + - - +
123A SER* 2.9 35.5 + - - -
114B SER 5.7 0.9 - - - +
115B ASP* 5.1 0.5 - - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR 4.3 5.5 - - - +
117A ILE* 3.1 12.3 + - - +
119A ASN* 1.3 94.1 - - - +
121A VAL* 1.3 66.5 + - - +
123A SER* 3.4 9.9 + - - -
124A ALA* 3.0 23.6 + - - +
170A TYR* 3.5 20.8 + - - +
20B LYS* 6.0 0.3 + - - -
120B GLU* 5.1 7.1 - - - +
168B PHE* 3.7 30.3 - - + -
1409B TFG 3.8 18.1 - - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN* 5.2 1.6 - - - +
83A PRO* 3.6 31.9 - - + -
117A ILE 3.3 10.2 + - - +
118A TRP* 3.6 37.2 - - + +
119A ASN 3.4 0.2 - - - -
120A GLU* 1.3 76.0 - - - +
122A HIS* 1.3 63.4 + - - +
124A ALA* 3.3 5.4 + - - +
125A GLY* 3.1 17.8 + - - -
299B LEU* 4.0 17.0 - - + -
1409B TFG 3.8 29.7 - - + -
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Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.4 21.9 + - - -
19A LEU 2.7 27.6 + - - -
20A LYS* 3.8 15.3 + - - -
22A GLN* 3.6 19.6 + - + +
112A VAL* 5.1 15.6 - - + +
118A TRP 3.0 17.0 + - - +
119A ASN* 3.5 10.5 - - - +
121A VAL* 1.3 76.9 - - - +
123A SER* 1.3 50.6 + - - +
125A GLY* 3.1 4.2 + - - +
126A ALA* 2.7 35.6 + - + +
154A ARG* 3.7 15.5 + - - -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.7 2.9 - - - -
119A ASN* 2.9 27.5 + - - -
120A GLU* 3.7 13.6 + - - -
121A VAL 3.3 0.2 - - - -
122A HIS* 1.3 75.2 - - - +
124A ALA* 1.3 58.0 + - - +
126A ALA* 3.3 3.3 + - - +
127A ALA* 2.9 23.9 + - - +
154A ARG* 3.0 33.2 + - - +
155A PRO* 3.4 11.5 - - - +
170A TYR* 4.2 14.6 - - - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.6 17.4 - - + +
120A GLU 3.0 9.2 + - - +
121A VAL 3.6 2.5 - - - +
123A SER* 1.3 72.7 - - - +
125A GLY* 1.3 63.3 + - - +
127A ALA* 3.3 4.2 + - - +
128A ARG* 3.2 18.4 + - - +
170A TYR* 3.9 29.1 - - + -
171A PHE* 3.8 8.5 - - - -
1409B TFG 3.5 32.3 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 5.8 1.2 - - - +
79A TYR 4.6 2.4 + - - -
80A GLY 6.6 0.2 - - - -
121A VAL 3.1 13.4 + - - -
122A HIS* 3.1 5.6 + - - -
124A ALA* 1.3 74.3 - - - +
126A ALA* 1.3 62.8 + - - +
128A ARG* 3.2 10.0 + - - +
129A LEU* 3.1 20.8 + - - +
1409B TFG 5.4 0.2 - - - -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 4.7 4.7 - - - +
18A MET* 3.8 20.3 - - - +
122A HIS* 2.7 18.3 + - - +
123A SER 3.4 9.4 - - - +
125A GLY* 1.3 71.2 - - - +
127A ALA* 1.3 56.4 + - - +
129A LEU* 3.3 8.5 + - - +
130A ALA* 2.8 29.3 + - - +
154A ARG* 3.5 27.0 - - - +
155A PRO* 3.7 10.5 - - + -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER 2.9 13.6 + - - +
124A ALA 3.4 10.1 - - - +
125A GLY 3.2 0.4 - - - -
126A ALA* 1.3 73.9 - - - +
128A ARG* 1.3 65.3 + - - +
130A ALA* 3.3 4.8 + - - +
131A VAL* 3.0 28.9 + - - +
155A PRO* 3.5 18.3 - - + +
156A PRO 5.9 1.3 - - - +
170A TYR* 3.8 17.9 - - + +
171A PHE* 3.7 22.8 - - + +
173A SER* 4.6 0.3 + - - -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.9 31.8 - - + +
62A ALA* 2.8 52.4 + - - +
63A THR* 4.2 3.0 - - - +
64A LEU* 3.6 27.7 - - - +
67A LEU* 4.3 15.0 - - + -
80A GLY* 2.8 37.7 + - - -
81A THR* 5.0 1.6 - - - +
82A ASN 5.7 0.2 - - - +
124A ALA 3.2 9.6 + - - +
125A GLY* 3.2 12.3 + - - +
127A ALA* 1.3 77.8 - - - +
129A LEU* 1.3 60.5 + - - +
131A VAL* 3.6 2.8 + - - -
132A GLY 3.4 6.8 + - - -
171A PHE* 3.8 16.6 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 4.0 15.5 - - - +
17A LEU* 3.6 37.7 - - + +
18A MET* 3.8 21.5 - - + +
60A ARG* 3.2 35.2 - - - +
61A LYS* 3.9 12.5 - - + +
125A GLY 3.1 12.1 + - - +
126A ALA* 3.5 9.2 - - - +
127A ALA 3.2 0.2 - - - -
128A ARG* 1.3 75.2 - - - +
130A ALA* 1.3 59.7 + - - +
132A GLY 3.2 0.3 + - - -
133A CYS* 2.9 41.8 + - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.9 13.2 - - - -
126A ALA 2.8 20.6 + - - +
127A ALA* 3.5 7.9 - - - +
129A LEU* 1.3 73.5 - - - +
131A VAL* 1.3 61.4 + - - +
133A CYS* 3.4 2.1 + - - +
134A VAL* 3.0 28.9 + - - +
153A VAL* 4.0 15.0 - - + -
154A ARG 3.6 20.2 - - - +
155A PRO 4.3 4.9 - - - +
173A SER* 4.0 9.6 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.6 23.8 - - + -
67A LEU* 3.8 9.0 - - + -
127A ALA 3.0 15.7 + - - +
128A ARG 3.8 1.3 - - - +
129A LEU 3.2 0.4 - - - -
130A ALA* 1.3 74.4 - - - +
132A GLY* 1.3 58.2 + - - +
134A VAL* 3.3 2.4 + - - +
135A VAL* 2.9 30.9 + - + +
171A PHE* 3.6 26.0 - - + -
172A ASN 4.8 0.2 - - - -
173A SER* 3.4 28.0 - - - +
176A VAL* 3.7 33.4 - - + -
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.0 27.3 + - - +
61A LYS 4.1 1.3 - - - -
62A ALA* 3.6 14.9 - - - +
128A ARG 3.4 4.9 + - - -
129A LEU 3.2 3.2 + - - -
131A VAL* 1.3 76.3 - - - +
133A CYS* 1.3 59.3 + - - +
135A VAL* 3.8 6.3 - - - +
136A GLU* 3.0 35.5 + - - +
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Residues in contact with CYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.5 31.2 - - + +
14A TYR 5.2 0.9 - - - -
15A ASP* 4.3 8.1 - - - -
18A MET* 4.3 15.5 - - - -
59A GLY* 3.7 25.6 - - - -
60A ARG 3.5 0.4 + - - -
129A LEU* 2.9 36.5 + - - +
130A ALA 3.6 4.9 - - - +
132A GLY* 1.3 77.3 - - - +
134A VAL* 1.3 62.0 + - - +
136A GLU* 3.8 0.6 - - - +
137A LEU 3.2 17.7 + - - -
153A VAL* 3.9 15.3 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA 3.0 17.6 + - - +
131A VAL 3.8 3.8 - - - +
133A CYS* 1.3 74.1 - - - +
135A VAL* 1.3 59.1 + - - +
137A LEU* 3.3 3.0 + - - +
138A VAL* 2.9 48.4 + - + +
151A ALA* 3.9 26.5 - - + -
153A VAL* 4.0 16.4 - - + -
173A SER* 4.0 32.3 - - - +
174A VAL* 4.6 4.7 - - + +
177A ALA* 4.1 4.3 - - + -
325A VAL* 5.3 2.0 - - + -
327A ALA* 4.2 15.9 - - + -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.6 24.2 - - - +
66A GLU* 4.7 3.4 - - - +
131A VAL* 2.9 23.9 + - + +
132A GLY* 3.8 6.1 - - - +
134A VAL* 1.3 75.7 - - - +
136A GLU* 1.3 59.3 + - - +
138A VAL* 3.4 1.0 + - - +
139A PHE* 2.9 44.5 + - + +
173A SER 5.0 0.2 - - - +
176A VAL* 4.2 8.1 - - + -
177A ALA* 3.9 26.2 - - + +
180A LEU* 3.7 32.5 - - + -
184A ARG* 5.6 1.1 - - - +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.8 11.7 - - + -
58A ARG 4.1 16.4 - - - +
59A GLY* 4.9 0.9 - - - -
60A ARG* 3.0 42.3 + - + +
132A GLY 3.0 21.1 + - - +
133A CYS* 3.8 5.6 - - - +
135A VAL* 1.3 74.8 - - - +
137A LEU* 1.3 63.1 + - - +
139A PHE* 3.5 4.8 + - - +
140A LYS* 3.1 46.6 + - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 4.1 20.0 - - - +
13A VAL* 3.8 19.1 - - + +
57A ILE* 3.5 14.1 - - + +
133A CYS 3.2 14.4 + - - +
134A VAL* 3.8 3.6 - - - +
136A GLU* 1.3 75.5 - - - +
138A VAL* 1.3 65.8 + - - +
140A LYS* 3.3 2.0 + - - +
141A VAL* 3.1 26.2 + - + +
146A LEU* 4.1 19.3 - - + -
149A GLY* 3.8 12.3 - - - -
150A PHE 3.6 41.7 - - - +
151A ALA* 3.9 2.9 - - + +
325A VAL* 3.9 13.2 - - + -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 2.9 26.0 + - + +
135A VAL 3.7 3.6 - - - +
137A LEU* 1.3 75.9 - - - +
139A PHE* 1.3 58.6 + - + +
141A VAL* 3.4 2.6 + - - +
142A ALA* 2.9 28.5 + - + +
177A ALA* 3.9 21.8 - - + -
181A LEU* 3.6 37.5 - - + -
282A VAL* 5.3 1.9 - - + +
284A LEU* 3.8 26.5 - - + -
325A VAL* 3.9 23.6 - - + -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 2.9 37.9 + - + +
136A GLU* 4.0 5.8 - - - +
138A VAL* 1.3 78.5 - - + +
140A LYS* 1.3 56.7 + - + +
142A ALA* 4.4 3.1 - - - -
143A THR* 3.0 40.9 + - + +
177A ALA 4.3 4.3 - - - -
180A LEU* 3.5 45.5 - - + -
181A LEU* 3.8 18.8 - - + -
184A ARG* 4.1 18.6 - - + -
185A LEU* 3.5 32.3 - - + -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 4.1 32.5 - - + +
58A ARG 5.9 0.8 - - - +
136A GLU* 3.1 34.9 + - - +
137A LEU* 3.3 5.1 + - - +
139A PHE* 1.3 76.7 - - + +
141A VAL* 1.3 60.2 - - - +
143A THR* 3.8 5.2 - - - -
144A GLY 3.4 1.0 + - - -
145A GLU* 2.9 67.2 + - + +
146A LEU* 2.9 21.2 + - + -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.1 19.4 + - + +
138A VAL 3.9 3.8 - - - +
140A LYS* 1.3 77.0 - - - +
142A ALA* 1.3 60.4 + - - +
143A THR 3.2 0.4 - - - -
144A GLY* 3.1 15.9 + - - -
146A LEU* 3.4 16.3 - - + +
147A LYS 3.4 19.7 - - - +
148A ASN* 3.4 34.5 - - - +
282A VAL* 5.9 2.5 - - + -
323A ARG* 4.0 19.8 - - + +
324A ILE 3.9 20.9 - - - +
325A VAL* 3.7 13.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 2.9 18.6 + - + +
139A PHE* 3.4 3.3 + - - +
141A VAL* 1.3 76.6 - - - +
143A THR* 1.3 59.6 + - - +
181A LEU* 3.6 28.0 - - + -
185A LEU* 4.4 8.2 - - + +
187A VAL* 5.4 2.5 - - + -
282A VAL* 4.2 17.3 - - + +
323A ARG* 4.4 19.9 + - - +
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 3.0 25.8 + - + +
140A LYS* 3.4 10.2 + - - -
142A ALA* 1.3 77.7 - - - +
144A GLY* 1.3 60.5 + - - +
145A GLU* 3.6 11.1 + - - +
185A LEU* 4.1 26.5 - - + -
----------------------------------------------------------
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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