Contacts of the helix formed by residues 135 - 159 (chain A) in PDB entry 2B6V
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 VAL 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LYS* 4.3 34.1 - - + +
58A ILE* 5.2 4.9 - - + -
134A SER* 1.4 86.5 + - - +
136A SER* 1.4 75.8 + - - +
137A TYR 3.2 2.7 - - - +
138A SER* 2.8 29.5 + - - +
139A LYS* 3.1 14.5 + - + +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 3.6 12.7 + - - -
135A VAL* 1.4 84.2 - - - +
137A TYR* 1.4 72.4 + - - +
139A LYS* 3.2 9.3 + - - +
140A LEU* 3.1 25.5 + - - +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.8 19.8 + - + -
133A GLN* 3.9 19.3 - - + -
134A SER* 3.7 31.4 - - - +
136A SER* 1.4 82.7 - - - +
138A SER* 1.4 60.2 + - - +
140A LEU* 3.0 21.1 + - + +
141A LEU* 2.9 46.6 + - + +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.5 39.8 - - - +
59A TYR* 4.6 17.3 - - - -
135A VAL* 2.8 31.4 + - - +
137A TYR* 1.4 77.4 - - - +
139A LYS* 1.4 57.4 + - - +
141A LEU* 3.8 13.0 - - - +
142A SER* 3.1 30.3 + - - -
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 5.2 6.9 - - + +
135A VAL* 3.1 14.1 + - + +
136A SER* 3.5 11.0 - - - +
137A TYR 3.1 1.0 - - - -
138A SER* 1.4 75.4 - - - +
140A LEU* 1.4 60.2 + - + +
142A SER* 3.3 5.5 + - - -
143A VAL* 2.8 59.2 + - + +
146A TRP* 3.8 27.5 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 3.1 13.2 + - - +
137A TYR* 3.0 23.6 + - + +
139A LYS* 1.4 75.7 - - + +
141A LEU* 1.3 64.9 + - + +
143A VAL* 3.1 11.0 + - + +
144A ILE* 2.9 40.4 + - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.3 41.5 - - + +
114A LEU* 3.5 28.0 - - + +
117A PHE* 4.1 25.8 - - + -
118A ASP* 5.5 2.0 - - + +
133A GLN* 6.2 2.5 - - + +
137A TYR* 2.9 37.3 + - + +
138A SER* 3.8 5.2 - - - +
139A LYS 3.2 0.2 - - - -
140A LEU* 1.3 84.0 - - + +
142A SER* 1.4 58.1 + - - +
144A ILE* 5.8 0.9 - - + -
145A VAL* 3.0 32.3 + - - +
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.3 7.8 + - - +
59A TYR* 4.5 8.0 - - - -
62A ASN* 2.8 41.6 + - - -
111A PHE* 5.8 2.3 - - - +
138A SER 3.1 17.9 + - - -
139A LYS* 3.8 7.4 - - - -
141A LEU* 1.4 75.4 - - - +
143A VAL* 1.3 59.6 + - - +
145A VAL* 3.2 7.8 + - - +
146A TRP* 2.8 43.1 + - - -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LYS* 2.8 53.8 + - + +
140A LEU* 3.1 13.2 + - + +
142A SER* 1.3 72.6 - - - +
144A ILE* 1.4 63.6 + - + +
146A TRP* 3.3 21.3 + - + +
147A MET* 2.9 32.8 + - + +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.7 23.1 - - + -
140A LEU* 2.9 25.2 + - + +
141A LEU* 3.8 4.9 - - + +
143A VAL* 1.4 77.4 - - + +
145A VAL* 1.3 59.2 + - - +
147A MET* 3.1 13.8 + - - +
148A LEU* 2.9 54.8 + - + +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 6.4 0.2 - - + -
62A ASN* 6.0 0.4 - - + -
107A VAL* 3.7 39.0 - - + +
110A VAL* 3.9 11.7 - - + +
111A PHE* 3.5 44.4 - - + +
114A LEU* 3.9 14.6 - - + -
141A LEU 3.0 18.8 + - - +
142A SER* 3.2 9.8 + - - +
144A ILE* 1.3 75.8 - - - +
146A TRP* 1.4 57.2 + - + +
147A MET 3.0 0.5 + - - -
148A LEU* 3.2 1.4 + - - +
149A MET* 2.8 35.9 + - - +
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Residues in contact with TRP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 6.1 0.9 - - + -
62A ASN* 2.9 37.3 + - + +
65A ILE* 5.8 7.2 - - + +
107A VAL* 5.2 5.2 - - + -
139A LYS* 3.8 30.5 - - + -
142A SER* 2.8 39.0 + - - -
143A VAL* 3.5 17.5 - - + +
145A VAL* 1.4 76.6 - - + +
147A MET* 1.4 56.8 - - - +
149A MET* 3.6 17.3 - - + +
150A LEU* 3.0 42.5 + - + +
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Residues in contact with MET 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL* 2.9 20.8 + - + +
144A ILE* 3.4 17.0 - - - +
145A VAL 3.1 0.2 - - - -
146A TRP* 1.4 79.1 - - - +
148A LEU* 1.3 61.9 + - + +
150A LEU* 3.6 7.2 - - - +
151A LEU* 2.8 42.8 + - + +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 4.9 1.4 - - - +
110A VAL* 3.6 30.1 - - + -
114A LEU* 5.5 1.3 - - + -
144A ILE* 2.9 36.7 + - + +
145A VAL 3.8 2.5 - - - +
147A MET* 1.3 86.5 - - + +
149A MET* 1.4 64.2 + - - +
151A LEU* 3.6 9.2 + - + -
152A LEU* 3.3 26.5 - - - +
194A ILE* 3.8 25.6 - - + +
198A VAL* 5.6 1.6 - - + -
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Residues in contact with MET 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA* 5.1 2.5 - - - -
103A VAL* 3.0 50.5 - - + +
106A TYR* 4.0 17.7 - - + +
107A VAL* 3.5 33.4 - - - +
110A VAL* 5.0 0.4 - - - +
145A VAL 2.8 18.6 + - - +
146A TRP* 3.6 26.2 - - + +
148A LEU* 1.4 74.9 - - - +
150A LEU* 1.4 84.3 - - + +
151A LEU 3.2 0.7 + - - -
152A LEU* 3.3 5.9 + - - +
153A ALA* 3.1 19.4 + - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A VAL* 5.4 4.3 - - + -
146A TRP* 3.0 27.1 + - + +
147A MET* 3.6 6.3 - - - +
149A MET* 1.4 93.9 - - + +
151A LEU* 1.3 59.9 + - - +
153A ALA* 2.9 7.6 + - + -
154A VAL* 2.8 57.7 + - + +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A MET* 2.8 30.0 + - + +
148A LEU* 3.7 14.4 - - + +
149A MET 3.1 0.8 - - - -
150A LEU* 1.3 72.3 - - - +
152A LEU* 1.4 78.0 + - + +
154A VAL* 4.6 4.7 - - + +
155A PRO* 2.8 25.5 - - + +
189A TYR* 4.0 16.6 - - + +
193A ALA* 6.0 2.7 - - + -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 6.0 0.3 - - - +
106A TYR* 3.8 23.6 - - + -
148A LEU* 3.3 11.2 - - - +
149A MET 3.3 1.6 + - - -
150A LEU 3.1 0.2 - - - -
151A LEU* 1.4 87.5 - - + +
153A ALA* 1.3 67.1 + - - +
155A PRO* 3.5 9.7 - - + +
156A ASN* 4.6 6.1 + - - +
161A ASN* 5.5 1.6 + - - +
174A GLU* 4.7 8.0 - - - +
189A TYR* 3.4 37.7 - - + +
190A ILE* 3.5 39.6 - - + +
193A ALA* 5.1 2.2 - - + -
194A ILE* 3.3 38.4 - - + +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.0 18.5 - - + +
102A TYR* 5.1 7.9 - - - -
103A VAL* 3.2 39.7 - - + +
106A TYR* 5.0 1.0 - - - -
149A MET 3.1 15.4 + - - +
150A LEU* 2.9 8.6 + - + +
152A LEU* 1.3 78.3 - - - +
154A VAL* 1.4 66.0 + - + +
156A ASN* 3.3 19.8 - - - +
157A ILE* 4.2 2.1 - - - +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 2.8 55.0 + - + +
151A LEU* 4.6 4.9 - - + +
153A ALA* 1.4 71.6 - - + +
155A PRO* 1.4 72.1 - - + +
156A ASN 3.2 2.5 - - - -
157A ILE* 2.9 37.7 + - + +
158A ILE* 3.3 22.2 + - + +
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 2.8 30.7 - - + +
152A LEU* 3.5 16.2 - - + +
154A VAL* 1.4 95.3 - - + +
156A ASN* 1.3 53.6 + - - +
158A ILE* 3.0 9.1 + - + +
159A LEU 2.9 30.3 + - - -
160A THR* 2.9 35.5 + - + +
161A ASN* 4.4 4.7 - - - +
189A TYR* 4.1 13.7 - - - +
190A ILE* 6.6 0.2 - - + -
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Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 4.5 3.3 + - - +
98A ALA* 5.3 2.2 - - - +
99A VAL* 4.2 12.2 - - - +
152A LEU 4.6 4.5 - - - +
153A ALA 3.3 18.4 - - - +
155A PRO* 1.3 75.6 - - - +
157A ILE* 1.4 67.3 + - - +
159A LEU* 4.1 2.3 + - - +
160A THR 2.9 12.2 + - - -
161A ASN* 3.1 36.0 - - - +
162A GLN* 3.3 9.4 - - - +
163A SER* 3.0 45.1 + - - +
174A GLU* 3.5 17.2 + - - +
181A ARG* 5.6 1.4 + - - -
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.2 56.0 + - + +
99A VAL* 3.8 34.5 - - + -
153A ALA* 4.2 2.7 - - + +
154A VAL* 2.9 34.4 + - + +
156A ASN* 1.4 75.4 + - - +
158A ILE* 1.4 72.4 + - + +
181A ARG* 5.9 1.2 + - - -
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.6 31.0 - - + +
155A PRO* 3.0 9.2 + - + +
157A ILE* 1.4 87.5 - - + +
159A LEU* 1.4 74.8 + - + +
160A THR* 6.0 0.4 - - - +
181A ARG* 5.5 1.8 + - - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PRO 2.9 9.5 + - - -
156A ASN 4.7 0.7 - - - -
157A ILE 3.7 0.8 - - - -
158A ILE* 1.4 86.5 - - + +
160A THR* 1.3 61.5 + - - +
161A ASN 2.9 19.1 + - - +
181A ARG* 3.1 54.2 + - + +
182A LYS* 4.3 21.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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