Contacts of the helix formed by residues 175 - 184 (chain B) in PDB entry 2VSH
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 CYS 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B TYR* 5.0 0.7 - - - -
93B ILE* 3.7 26.2 - - + +
96B ILE* 4.3 10.8 - - - -
102B LEU* 3.7 31.0 - - + -
106B ASP* 2.9 20.3 + - - +
107B ILE 4.0 3.1 - - - -
108B VAL* 3.8 32.8 - - - -
173B PHE 3.6 1.0 + - - -
174B ARG* 1.3 71.2 - - - +
176B LYS* 1.3 64.0 + - - +
178B PHE* 3.2 5.4 + - - +
179B MET* 3.1 27.3 + - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.9 7.0 - - + +
103B THR 4.6 5.2 + - - +
104B PRO* 3.7 48.9 + - + +
106B ASP 4.8 0.4 + - - -
174B ARG* 3.3 0.8 - - - +
175B CYS* 1.3 77.5 - - - +
177B ASP* 1.3 62.3 + - - +
179B MET* 3.2 8.2 + - + +
180B ASP* 2.9 60.5 + - - +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PRO 4.5 2.6 - - - +
134B ASP 4.6 2.6 - - - +
174B ARG* 3.2 43.6 + - + +
176B LYS* 1.3 80.1 + - - +
178B PHE* 1.3 65.4 + - - +
180B ASP* 3.3 2.5 + - - +
181B LEU* 3.1 28.6 + - - +
200B PHE* 4.0 14.1 - - + -
1233B P6G 2.7 50.5 + - - +
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ASN* 3.6 37.9 - - - -
89B ILE* 3.8 18.6 - - + -
90B LYS 4.0 3.4 - - - -
93B ILE* 3.7 10.8 - - + -
173B PHE* 3.6 37.0 - + + -
174B ARG 3.1 6.5 + - - -
175B CYS 3.6 6.7 - - - +
177B ASP* 1.3 77.6 - - - +
179B MET* 1.3 80.8 + - + +
181B LEU* 3.8 2.2 - - + +
182B TYR* 2.8 55.4 + + + +
196B ALA* 4.1 11.0 - - + -
199B ILE* 4.1 15.5 - - + -
200B PHE* 3.9 15.9 - + + -
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Residues in contact with MET 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 3.7 34.5 - - + +
93B ILE* 3.6 37.2 - - + -
94B GLU* 4.9 10.1 - - - +
102B LEU* 5.6 1.1 - - + -
175B CYS 3.1 14.9 + - - +
176B LYS* 3.2 9.6 + - + +
178B PHE* 1.3 100.7 - - + +
180B ASP* 1.3 60.1 + - - +
182B TYR* 4.0 9.6 - - + -
183B GLY* 3.0 26.0 + - - -
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LYS* 2.9 49.8 + - - +
177B ASP* 3.7 2.7 - - - +
179B MET* 1.3 80.1 - - - +
181B LEU* 1.3 63.1 + - - +
183B GLY* 4.2 1.2 - - - -
184B SER* 3.5 20.3 + - - -
1233B P6G 3.7 29.1 - - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASP 3.1 14.7 + - - +
178B PHE* 3.9 3.4 - - + +
180B ASP* 1.3 73.5 - - - +
182B TYR* 1.3 66.6 + - - +
184B SER* 2.6 23.5 + - - +
185B LEU* 3.5 11.2 - - - +
199B ILE* 3.9 14.8 - - + -
200B PHE* 3.7 51.8 - - + -
203B LYS* 3.7 27.3 - - + -
205B LYS* 4.2 14.8 - - + -
1233B P6G 3.4 36.3 - - - +
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASP* 4.3 2.4 + - - -
86B ASN* 3.6 26.7 - - + +
87B THR* 3.4 25.8 + - - +
90B LYS* 4.1 27.8 - - + -
178B PHE* 2.8 40.7 + + + +
179B MET* 4.0 19.1 - - + +
181B LEU* 1.3 76.1 - - - +
183B GLY* 1.3 64.0 + - - +
185B LEU* 3.1 22.0 + - + +
190B LYS* 3.3 62.5 + - + +
199B ILE* 4.1 13.4 - - + +
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Residues in contact with GLY 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B MET 3.0 19.2 + - - -
180B ASP 4.2 1.6 - - - -
181B LEU 3.3 0.2 - - - -
182B TYR* 1.3 78.9 - - - +
184B SER* 1.3 57.8 + - - +
185B LEU 3.3 6.5 + - - +
190B LYS* 5.1 4.3 + - - -
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Residues in contact with SER 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ASP 3.5 12.2 + - - -
181B LEU* 2.6 21.8 + - - +
183B GLY* 1.3 77.1 - - - +
185B LEU* 1.3 58.6 + - - +
186B SER 4.0 0.9 + - - -
189B GLU* 4.4 4.7 - - - +
203B LYS* 3.1 31.8 + - - -
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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