Contacts of the helix formed by residues 177 - 199 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN 4.2 0.3 + - - -
107A GLY* 4.2 15.8 - - - -
168B SER* 3.8 29.9 - - - +
171B THR* 3.6 33.3 + - - +
172B VAL* 3.7 7.6 - - - +
174B ALA* 2.9 10.0 + - - +
175B PRO 3.2 0.2 - - - -
176B HIS* 1.3 79.7 + - - +
178B TRP* 1.3 69.8 + - - +
179B PRO* 3.2 2.5 - - - -
180B HIS* 3.0 19.4 + - + +
181B ILE* 3.2 17.9 + - + +
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Residues in contact with TRP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 5.0 4.5 - - + -
96B ILE* 3.6 19.5 - - + +
99B LEU* 4.1 23.3 - - + -
117B LEU* 2.8 32.1 + - + -
118B GLN 3.1 21.1 + - - +
120B PRO* 3.4 30.3 - - + -
125B PHE* 4.6 7.2 - + - -
128B ILE* 5.7 2.7 - - + -
172B VAL 3.2 26.2 + - - +
173B GLY 4.0 7.2 - - - +
174B ALA 3.0 13.4 + - - +
175B PRO* 5.6 0.4 - - + -
177B THR* 1.3 74.8 - - - +
179B PRO* 1.4 70.5 - - + +
181B ILE* 3.0 22.9 + - + +
182B VAL* 2.8 51.4 + - + +
185B LEU* 4.2 10.1 - - + -
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Residues in contact with PRO 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.5 28.1 - - + +
87B ASN* 6.1 0.2 - - - -
92B ILE* 3.6 29.7 - - + +
175B PRO 3.3 22.7 - - - +
176B HIS* 4.0 3.4 - - - -
177B THR 3.4 5.8 - - - +
178B TRP* 1.4 93.8 - - + +
180B HIS* 1.3 63.8 + - + +
182B VAL* 3.4 5.2 - - + +
183B ALA* 3.3 22.2 + - - +
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.4 31.1 - - + +
160B TYR* 4.2 4.0 + - - -
164B LEU* 4.7 7.9 - - + +
168B SER* 6.0 1.1 - - - +
176B HIS 3.5 24.4 + - - -
177B THR* 3.0 10.6 + - + +
179B PRO* 1.3 78.2 - - + +
181B ILE* 1.3 68.6 + - + +
183B ALA* 3.4 6.4 - - - +
184B ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE* 3.4 38.6 - - + -
164B LEU* 4.0 20.4 - - + -
168B SER* 4.1 12.1 - - - +
169B MET* 3.7 25.8 - - + -
172B VAL* 4.2 13.0 - - + +
177B THR* 3.2 25.5 + - + +
178B TRP* 3.0 19.3 + - + +
180B HIS* 1.3 78.0 - - + +
182B VAL* 1.3 60.4 + - - +
184B ALA* 2.9 7.7 + - + +
185B LEU* 2.9 27.3 + - + +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 4.1 15.9 - - + -
95B CYS* 3.9 30.1 - - + +
96B ILE* 4.0 17.5 - - + +
99B LEU* 4.3 9.9 - - + -
178B TRP* 2.8 57.0 + - + +
179B PRO* 3.4 12.3 - - + +
181B ILE* 1.3 69.1 - - - +
183B ALA* 1.3 70.8 + - - +
185B LEU* 3.2 5.0 + - - +
186B VAL* 3.0 25.4 + - + +
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.5 26.2 + - - +
86B LEU* 3.6 24.2 - - + -
91B PHE* 5.1 0.2 - - + -
95B CYS* 4.5 14.6 - - - -
179B PRO 3.3 16.5 + - - +
180B HIS 3.4 6.1 - - - +
182B VAL* 1.3 85.6 - - + +
184B ALA* 1.3 62.1 + - - +
186B VAL* 3.3 3.2 + - - +
187B TRP* 3.0 18.2 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.3 31.0 - - + -
160B TYR* 3.6 28.4 + - + +
164B LEU* 4.3 12.1 - - + -
180B HIS 3.0 13.7 + - - +
181B ILE* 2.9 12.5 + - + +
183B ALA* 1.3 75.9 - - - +
185B LEU* 1.3 57.7 + - - +
187B TRP* 3.2 4.2 + - - +
188B LEU 2.9 23.4 + - - -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.0 22.4 - - + -
125B PHE* 3.7 32.3 - - + -
128B ILE* 3.8 23.6 - - + -
129B PHE* 4.5 13.2 - - + -
132B LEU* 4.0 20.1 - - + +
155B PHE* 4.4 14.4 - - + -
178B TRP* 4.2 16.2 - - + -
181B ILE 2.9 16.0 + - - +
182B VAL* 3.2 6.7 + - - +
184B ALA* 1.3 76.0 - - - +
186B VAL* 1.3 57.4 + - - +
188B LEU* 3.1 9.8 + - + +
189B ILE* 2.9 32.2 + - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B CYS* 3.5 39.7 - - + +
98B GLN* 3.2 32.5 - - + +
99B LEU* 4.4 9.2 - - + +
182B VAL* 3.0 21.1 + - + +
183B ALA* 3.7 6.5 - - - +
185B LEU* 1.3 71.7 - - - +
187B TRP* 1.3 61.5 + - - +
189B ILE* 3.3 12.5 + - + +
190B ASP* 3.0 34.3 + - - +
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Residues in contact with TRP 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 4.3 8.3 - - - +
155B PHE* 4.1 11.7 - + - -
158B LEU* 3.5 28.5 - - + -
159B GLY 3.7 9.6 - - - -
160B TYR* 3.2 67.3 - + + -
161B PRO* 4.8 0.7 - - + -
183B ALA 3.0 12.9 + - - +
184B ALA 3.3 11.0 - - - +
186B VAL* 1.3 74.5 - - - +
188B LEU* 1.3 81.4 + - - +
190B ASP* 3.0 11.6 + - - +
191B CYS* 3.0 41.4 + - - -
78D LEU* 3.0 33.1 + - + -
79D MET* 3.3 29.0 - - + +
82D PHE* 4.3 5.2 - - + -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 4.3 17.9 - - + -
132B LEU* 3.7 33.7 - - + -
133B TYR* 4.3 9.6 - - + +
136B LEU* 4.1 16.6 - - + -
155B PHE* 4.1 21.1 - - + -
158B LEU* 3.6 31.4 - - + -
184B ALA 2.9 12.2 + - - +
185B LEU* 3.1 9.2 + - + +
187B TRP* 1.3 82.5 - - + +
189B ILE* 1.3 62.5 + - - +
191B CYS* 2.9 18.2 + - + +
192B ILE* 3.0 16.5 + - + +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 4.3 4.9 - - + +
99B LEU* 4.0 31.0 - - + +
102B PHE* 3.6 49.8 - - + -
132B LEU* 4.0 17.0 - - + -
185B LEU 2.9 18.7 + - - +
186B VAL* 3.4 16.6 - - + +
188B LEU* 1.3 74.1 - - - +
190B ASP* 1.3 60.1 + - - +
192B ILE* 3.3 12.9 + - - +
193B LYS* 3.0 39.8 + - - +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 5.9 0.7 + - - -
186B VAL* 3.0 22.1 + - - +
187B TRP* 3.0 15.6 + - - +
189B ILE* 1.3 76.3 - - - +
191B CYS* 1.3 63.4 + - - +
193B LYS* 3.1 23.1 + - - +
194B ILE* 2.9 24.6 + - - +
72D GLY 5.0 0.3 - - - +
73D VAL* 3.7 19.9 - - + +
74D MET* 3.6 22.6 + - - +
75D TYR* 4.7 3.3 + - - -
79D MET* 3.9 18.2 - - + +
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Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.7 2.0 - - + -
158B LEU* 5.3 0.4 - - - -
187B TRP* 3.0 40.1 + - - -
188B LEU* 2.9 17.4 + - + +
190B ASP* 1.3 74.1 - - - +
192B ILE* 1.3 53.3 + - - +
194B ILE* 2.9 4.8 + - - +
195B HIS* 2.7 32.6 + - - +
79D MET* 3.6 13.9 - - - +
82D PHE* 3.4 55.6 - - + -
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.1 25.6 - - + -
132B LEU* 3.4 35.7 - - + +
135B PHE* 3.9 36.3 - - + +
136B LEU* 4.4 19.1 - - + -
188B LEU* 3.0 17.0 + - + +
189B ILE* 3.3 17.0 + - - +
191B CYS* 1.3 73.8 - - - +
193B LYS* 1.3 57.6 + - + +
195B HIS* 3.8 0.7 - - - +
196B THR* 2.8 45.4 + - - +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 5.2 11.4 - - + -
189B ILE* 3.0 31.4 + - + +
190B ASP* 3.1 22.5 + - - +
192B ILE* 1.3 75.4 - - + +
194B ILE* 1.3 64.6 + - - +
196B THR* 3.2 5.4 + - - -
197B ALA* 3.0 24.8 + - - +
70D ASN 5.4 0.2 - - - +
71D SER* 3.9 25.3 + - - +
72D GLY 4.6 10.7 + - - +
73D VAL* 4.9 2.0 - - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 2.9 16.9 + - - +
191B CYS 3.4 6.1 - - - +
193B LYS* 1.3 75.0 - - - +
195B HIS* 1.3 58.8 + - - +
197B ALA* 3.3 2.8 + - - +
198B MET* 3.0 28.3 + - + +
67D MET* 4.0 17.3 - - - -
68D PRO* 3.9 13.0 - - + +
71D SER* 4.0 10.1 - - - -
73D VAL* 3.8 15.9 - - + -
79D MET* 3.7 43.3 - - + -
82D PHE* 3.9 14.8 - - + -
83D LEU* 3.9 22.0 - - + -
86D SER* 4.1 8.7 - - - +
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE 4.9 6.5 - - - -
136B LEU* 3.8 30.9 + - + -
191B CYS 2.7 19.1 + - - +
192B ILE 3.8 3.1 - - - +
194B ILE* 1.3 74.8 - - - +
196B THR* 1.3 61.7 + - - +
198B MET* 3.4 5.0 - - + +
199B LYS* 3.0 62.0 + - + +
82D PHE* 4.1 4.9 - + + -
85D PHE* 4.7 2.9 - + - -
86D SER* 3.0 35.5 + - - +
89D VAL* 3.8 24.5 - - + -
90D THR* 4.9 4.3 - - - -
106D THR* 4.3 14.6 - - + +
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 5.8 1.2 - - - -
192B ILE* 2.8 33.5 + - - +
193B LYS* 3.8 5.4 - - - -
195B HIS* 1.3 71.7 - - - +
197B ALA* 1.3 66.1 + - - +
199B LYS* 3.2 22.6 + - + +
200B GLU* 3.1 18.0 - - - +
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS 3.0 15.5 + - - +
194B ILE 3.6 4.7 - - - +
196B THR* 1.3 76.9 - - - +
198B MET* 1.3 58.4 + - - +
200B GLU* 2.9 33.6 + - - +
201B SER 3.5 7.4 + - - +
68D PRO* 3.9 20.0 - - + -
70D ASN* 4.1 27.4 - - + +
71D SER* 4.4 1.8 - - - +
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Residues in contact with MET 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 3.0 16.6 + - + +
195B HIS* 3.4 12.6 - - - +
197B ALA* 1.3 77.2 - - - +
199B LYS* 1.3 57.9 + - + +
200B GLU 3.0 11.1 + - - +
201B SER* 4.1 5.8 + - - -
202B SER* 3.6 23.5 + - - -
66D MET 4.3 1.1 - - - +
68D PRO* 3.6 22.2 - - + +
83D LEU* 4.6 1.8 - - + +
86D SER* 3.1 37.2 - - - +
87D ASN* 3.5 37.0 - - - +
90D THR* 3.1 39.0 - - + +
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Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE 5.8 2.2 - - - -
195B HIS* 3.0 52.0 + - + +
196B THR* 3.2 14.5 + - - +
197B ALA 3.1 1.8 - - - -
198B MET* 1.3 76.4 - - + +
200B GLU* 1.3 73.6 + - - +
89D VAL* 5.1 4.6 - - - +
90D THR* 5.9 1.8 - - - +
93D ASP* 5.3 5.7 + - - -
106D THR* 5.8 0.6 - - - +
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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