Contacts of the helix formed by residues 177 - 201 (chain A) in PDB entry 2VE7
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 THR 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A SER* 3.6 36.7 - - - +
171A THR* 3.1 38.5 + - - +
172A VAL* 3.5 8.7 - - - +
174A ALA* 2.8 11.0 + - - +
175A PRO 3.3 0.4 - - - -
176A HIS* 1.3 82.3 + - - +
178A TRP* 1.3 66.6 + - - +
179A PRO* 3.2 3.6 - - - -
180A HIS* 2.9 20.1 + - + +
181A ILE* 3.2 13.2 + - + -
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Residues in contact with TRP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 5.2 2.9 - - + -
96A ILE* 3.5 18.7 - - + +
99A LEU* 4.1 10.8 - - + -
117A LEU* 2.7 31.5 + - + -
118A GLN 3.0 20.6 + - - +
120A PRO* 3.5 28.9 - - + -
125A PHE* 4.5 6.5 - + - -
128A ILE* 5.9 1.3 - - + -
172A VAL 3.1 30.3 + - - +
173A GLY* 4.1 9.0 - - - +
174A ALA 3.0 11.7 + - - +
175A PRO* 5.5 0.9 - - + -
177A THR* 1.3 73.6 - - - +
179A PRO* 1.4 69.8 - - + +
181A ILE* 3.0 24.4 + - + +
182A VAL* 2.8 47.3 + - + +
185A LEU* 3.8 23.8 - - + -
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.9 22.1 - - + +
92A ILE* 3.7 35.7 - - + +
175A PRO 3.6 20.9 - - - +
176A HIS* 4.1 3.1 - - - -
177A THR 3.3 6.7 - - - +
178A TRP* 1.4 95.2 - - + +
180A HIS* 1.3 64.5 + - + +
182A VAL* 3.6 5.8 - - + +
183A ALA* 3.3 21.8 + - - +
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Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 5.5 0.2 + - - -
86A LEU* 3.5 30.8 - - + +
160A TYR* 4.5 2.8 + - - -
164A LEU* 4.7 7.8 - - + +
168A SER* 6.1 1.8 - - - -
176A HIS 3.7 22.4 + - - -
177A THR* 2.9 12.7 + - + +
179A PRO* 1.3 76.3 - - + +
181A ILE* 1.3 73.7 + - + +
183A ALA* 3.6 4.4 + - - +
184A ALA* 3.2 19.8 + - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.4 36.6 - - + -
164A LEU* 3.9 19.7 - - + -
168A SER* 4.2 12.8 - - - +
169A MET* 3.9 25.8 - - + -
172A VAL* 4.1 12.1 - - + +
177A THR* 3.2 24.4 + - + +
178A TRP* 3.0 20.8 + - + -
180A HIS* 1.3 76.5 - - + +
182A VAL* 1.3 61.5 + - - +
184A ALA* 2.8 23.8 + - + +
185A LEU* 2.8 14.1 + - + +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 4.1 26.2 - - + -
95A CYS* 4.1 14.8 - - + +
96A ILE* 3.9 23.1 - - + +
99A LEU* 3.9 19.5 - - + -
178A TRP* 2.8 52.2 + - + +
179A PRO 3.6 7.0 - - - +
181A ILE* 1.3 72.3 - - - +
183A ALA* 1.3 66.4 + - - +
185A LEU* 3.0 6.8 + - - +
186A VAL* 2.8 26.4 + - - +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.4 35.4 + - - +
86A LEU* 3.8 15.5 - - + -
92A ILE* 5.5 0.2 - - + -
95A CYS* 4.9 10.1 - - - -
179A PRO 3.3 14.6 + - - +
180A HIS* 3.6 6.7 - - - +
181A ILE 3.2 0.2 - - - -
182A VAL* 1.3 84.1 - - + +
184A ALA* 1.3 56.8 + - - +
186A VAL* 3.2 8.0 + - - +
187A TRP* 2.8 28.8 + - - +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.3 31.9 - - + -
160A TYR* 3.6 27.1 + - + +
164A LEU* 4.2 12.6 - - + -
180A HIS 3.2 10.1 + - - +
181A ILE* 2.8 17.4 + - + +
183A ALA* 1.3 74.3 - - - +
185A LEU* 1.3 57.9 + - - +
187A TRP* 3.1 3.1 + - - +
188A LEU 2.8 23.9 + - - -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.9 27.6 - - + -
125A PHE* 3.9 32.5 - - + -
128A ILE* 4.5 9.6 - - + -
129A PHE* 4.7 13.5 - - + -
132A LEU* 4.2 17.3 - - + +
155A PHE* 4.6 13.2 - - + -
178A TRP* 3.8 30.7 - - + -
181A ILE* 2.8 14.0 + - + +
182A VAL* 3.0 7.2 + - - +
184A ALA* 1.3 76.7 - - - +
186A VAL* 1.3 50.5 + - - +
188A LEU* 2.9 8.7 + - + +
189A ILE* 2.8 40.4 + - - +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 6.2 0.2 - - - +
95A CYS* 3.4 39.3 - - + +
98A GLN* 4.0 16.4 - - + +
99A LEU* 4.4 6.7 - - + +
182A VAL 2.8 16.9 + - - +
183A ALA* 3.6 6.7 - - - +
185A LEU* 1.3 76.7 - - - +
187A TRP* 1.3 61.9 + - - +
189A ILE* 3.5 11.7 + - + +
190A ASP* 3.2 25.4 + - - +
74C MET* 3.3 36.1 - - + -
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Residues in contact with TRP 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 4.6 3.8 - - - +
155A PHE* 4.2 11.0 - + - -
158A LEU* 3.5 29.2 - - + -
159A GLY 3.8 7.6 - - - -
160A TYR* 3.2 70.5 - + + -
161A PRO* 4.1 1.2 - - + +
183A ALA 2.8 11.7 + - - +
184A ALA 3.1 6.5 + - - +
186A VAL* 1.3 74.5 - - - +
188A LEU* 1.3 74.2 + - - +
190A ASP* 3.3 7.9 + - - +
191A CYS* 3.1 46.0 + - - -
78C LEU* 2.7 37.7 + - + +
79C MET* 3.4 23.0 - - + +
82C PHE* 4.2 7.6 - - + -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE* 4.1 26.5 - - + -
132A LEU* 3.5 36.1 - - + -
133A TYR* 4.2 9.0 - - + +
136A LEU* 4.1 14.1 - - + -
155A PHE* 4.1 12.3 - - + -
158A LEU* 3.6 30.5 - - + -
184A ALA 2.8 13.0 + - - +
185A LEU* 3.3 10.3 - - + +
187A TRP* 1.3 85.9 - - + +
189A ILE* 1.3 61.5 + - - +
191A CYS* 3.2 8.0 + - + +
192A ILE* 3.1 27.7 + - + +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 4.4 5.4 - - + +
99A LEU* 3.6 45.5 - - + +
102A PHE* 3.5 38.4 - - + -
132A LEU* 4.0 21.1 - - + -
185A LEU 2.8 21.5 + - - +
186A VAL* 3.7 16.2 - - + +
188A LEU* 1.3 69.9 - - - +
190A ASP* 1.3 61.6 + - - +
192A ILE* 3.2 9.8 + - - +
193A LYS* 2.8 40.6 + - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 5.9 0.2 + - - -
186A VAL* 3.2 16.9 + - - +
187A TRP* 3.3 9.0 + - - +
189A ILE* 1.3 76.1 - - - +
191A CYS* 1.3 67.4 + - - +
193A LYS* 3.0 21.5 + - - +
194A ILE* 2.8 28.1 + - - +
72C GLY 4.6 0.2 - - - +
73C VAL* 3.3 27.8 - - + +
74C MET* 2.8 38.8 + - - +
79C MET* 4.2 16.1 - - + +
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Residues in contact with CYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 4.4 7.9 - - + -
158A LEU* 5.1 0.7 - - - -
187A TRP* 3.1 50.7 + - - -
188A LEU* 3.2 11.4 + - + +
190A ASP* 1.3 76.7 - - - +
192A ILE* 1.3 51.3 + - - +
194A ILE* 3.1 6.2 + - - +
195A HIS* 2.8 31.7 + - - +
79C MET* 4.8 3.7 - - - -
82C PHE* 3.4 54.3 - - + -
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 3.8 16.8 - - + -
132A LEU* 3.2 53.4 - - + +
135A PHE* 3.6 37.0 - - + -
136A LEU* 4.1 21.5 - - + -
188A LEU* 3.1 17.9 - - + +
189A ILE* 3.4 10.1 - - - +
191A CYS* 1.3 73.2 - - - +
193A LYS* 1.3 58.2 + - - +
195A HIS* 3.2 0.7 + - + +
196A THR* 2.7 43.3 + - - +
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Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 6.2 2.0 - - - -
102A PHE* 4.6 14.8 - - + -
189A ILE* 2.8 31.5 + - + +
190A ASP* 3.0 25.6 + - - +
192A ILE* 1.3 76.3 - - - +
194A ILE* 1.3 60.9 + - - +
196A THR* 3.6 8.7 + - - +
197A ALA* 3.0 25.3 + - - +
71C SER 4.5 17.2 - - - +
72C GLY* 3.4 25.7 + - - +
73C VAL* 5.0 1.6 - - + -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP 2.8 20.3 + - - +
191A CYS 3.3 6.5 - - - +
193A LYS* 1.3 72.6 - - - +
195A HIS* 1.3 63.3 + - - +
197A ALA* 3.2 8.1 + - - +
198A MET* 3.0 51.1 + - + +
67C MET* 3.9 21.1 - - - -
68C PRO* 4.6 6.2 - - + +
71C SER* 4.7 4.9 + - - +
73C VAL* 4.0 11.9 - - + -
79C MET* 3.5 33.9 - - + -
82C PHE* 4.0 21.1 - - + -
83C LEU* 4.1 11.7 - - + -
86C SER* 4.2 2.7 - - - +
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Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE 3.7 22.9 + - - -
136A LEU* 3.9 22.8 + - + -
191A CYS 2.8 18.6 + - - +
192A ILE* 3.6 3.8 - - + +
194A ILE* 1.3 73.0 - - - +
196A THR* 1.3 64.6 + - - +
198A MET* 3.0 22.7 + - - +
199A LYS* 3.5 35.0 + - + +
82C PHE* 4.4 3.1 - - + -
85C PHE* 4.1 20.0 - + - -
86C SER* 3.2 37.0 + - - +
89C VAL* 4.6 16.5 - - + +
90C THR* 5.5 2.2 - - - -
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 6.3 0.4 - - - +
135A PHE* 4.4 3.8 - - - +
192A ILE* 2.7 33.1 + - - +
193A LYS* 3.7 7.9 - - - +
195A HIS* 1.3 73.4 - - - +
197A ALA* 1.3 65.9 + - + +
199A LYS* 3.4 22.2 - - - +
200A GLU* 3.5 22.4 + - - +
2225B GOL 3.7 25.9 + - - +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS 3.0 18.3 + - - +
194A ILE* 3.5 6.1 - - - +
195A HIS 3.1 0.2 - - - -
196A THR* 1.3 75.3 - - + +
198A MET* 1.3 53.5 + - - +
199A LYS 2.8 15.5 + - - -
200A GLU* 3.3 5.1 + - - +
201A SER* 3.3 24.3 + - - -
68C PRO* 4.7 16.6 - - + +
69C VAL* 6.4 0.9 - - + -
71C SER* 6.1 3.1 - - - +
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Residues in contact with MET 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.0 44.1 + - + +
195A HIS* 3.0 5.9 + - - +
197A ALA* 1.3 72.2 - - - +
199A LYS* 1.3 61.5 + - - +
201A SER* 4.2 11.2 - - - +
202A SER* 4.8 2.3 + - - -
66C MET* 4.0 12.3 - - - +
68C PRO* 3.6 35.2 - - + -
83C LEU* 4.2 4.7 - - + -
86C SER* 3.8 12.1 + - - +
87C ASN* 3.2 35.2 - - - +
90C THR* 4.3 14.4 + - - +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE 4.9 4.0 + - - -
138A PRO* 6.1 0.8 - - - +
195A HIS* 3.6 43.0 - - + +
196A THR* 3.4 12.8 - - - +
197A ALA 2.8 0.6 + - - -
198A MET* 1.3 77.5 - - - +
200A GLU* 1.3 69.3 + - - +
201A SER 3.5 0.2 - - - -
202A SER* 3.4 15.2 + - - -
119B ALA* 3.2 31.8 + - - +
120B PRO 5.1 0.4 + - - -
121B SER* 4.0 18.0 + - - +
123B LYS* 5.6 0.7 - - - +
2225B GOL 3.3 32.8 + - - +
90C THR* 5.7 4.5 - - + +
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 3.5 21.3 + - - +
197A ALA* 3.3 7.6 + - - +
199A LYS* 1.3 81.6 - - - +
201A SER* 1.3 62.4 + - - +
202A SER* 3.4 3.6 + - - -
121B SER* 3.1 13.3 - - - -
122B VAL* 2.4 48.3 + - + +
123B LYS* 3.4 36.3 - - + +
170B TYR 5.5 0.3 - - - +
2225B GOL 3.7 14.3 + - - -
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ALA 3.3 10.7 + - - -
198A MET* 4.2 7.0 - - - +
199A LYS 4.2 8.0 + - - -
200A GLU* 1.3 79.1 - - - +
202A SER* 1.4 66.5 + - - +
123B LYS* 6.1 0.2 - - - +
----------------------------------------------------------
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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