Contacts of the helix formed by residues 162 - 171 (chain B) in PDB entry 1OHV
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 SER 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ALA 3.5 3.8 + - - -
161B PHE* 1.3 76.4 - - - +
163B LYS* 1.3 64.8 + - - +
164B GLU* 3.7 8.3 + - - +
165B GLU* 3.0 42.9 + - - +
166B LEU* 3.2 22.6 + - - +
175B PRO* 5.4 0.3 - - - +
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Residues in contact with LYS 163 (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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161B PHE 3.9 0.6 + - - -
162B SER* 1.3 71.2 - - - +
164B GLU* 1.3 66.3 + - - +
166B LEU* 3.2 13.0 + - - +
167B GLU* 3.1 35.4 + - - +
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Residues in contact with GLU 164 (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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162B SER* 3.3 7.5 + - - +
163B LYS* 1.3 78.0 - - - +
165B GLU* 1.3 51.7 + - - +
167B GLU* 3.2 10.7 + - - +
168B THR* 2.7 46.9 + - + +
175B PRO* 3.8 30.1 - - + +
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Residues in contact with GLU 165 (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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208A ILE* 4.0 12.3 - - + -
152B ARG* 3.1 26.6 + - - +
156B ARG* 3.0 27.1 + - - +
161B PHE* 3.8 4.0 - - - +
162B SER* 3.0 42.0 + - - +
164B GLU* 1.3 76.4 - - - +
166B LEU* 1.3 63.1 + - - +
168B THR* 3.3 6.9 + - - -
169B CYS* 3.0 29.8 + - - +
175B PRO* 4.2 16.6 - - + +
176B GLY* 3.3 16.6 - - - +
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Residues in contact with LEU 166 (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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204A ALA* 3.7 26.5 - - + +
205A ILE* 5.4 1.1 - - - +
208A ILE* 4.2 8.3 - - + -
161B PHE* 4.0 35.0 - - + +
162B SER 3.2 16.6 + - - +
163B LYS* 3.2 11.0 + - - +
165B GLU* 1.3 78.8 - - - +
167B GLU* 1.3 63.4 + - + +
169B CYS* 3.4 17.2 - - - -
170B MET* 3.7 11.4 - - - +
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Residues in contact with GLU 167 (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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163B LYS* 3.1 24.3 + - - +
164B GLU* 3.6 12.8 - - - +
166B LEU* 1.3 77.8 - - + +
168B THR* 1.3 66.9 + - + +
169B CYS 3.4 0.7 + - - -
170B MET* 3.4 18.2 + - - +
171B ILE* 3.9 9.8 + - - +
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Residues in contact with THR 168 (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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164B GLU* 2.7 34.7 + - + +
165B GLU* 3.5 0.5 - - - -
167B GLU* 1.3 75.1 - - + +
169B CYS* 1.3 61.9 + - - +
171B ILE* 3.1 18.7 + - + +
173B GLN* 3.0 46.7 + - + +
174B ALA 3.5 15.5 - - - +
175B PRO* 3.5 7.3 - - + +
176B GLY* 2.9 23.7 + - - -
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Residues in contact with CYS 169 (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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204A ALA* 3.7 35.4 - - - -
207A LYS* 3.1 25.6 - - - -
208A ILE* 3.9 19.3 - - - +
165B GLU 3.0 17.1 + - - +
166B LEU* 3.4 20.0 - - - -
167B GLU 3.3 0.2 - - - -
168B THR* 1.3 77.7 + - - +
170B MET* 1.3 61.5 - - - +
171B ILE 3.4 0.3 + - - -
172B ASN 3.5 5.2 + - - -
176B GLY* 3.8 18.6 - - - +
177B CYS* 3.5 16.2 - - - -
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Residues in contact with MET 170 (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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186A MET* 3.8 23.6 - - + +
201A HIS* 2.9 64.4 + - - +
202A SER 4.0 10.1 - - - +
203A LYS* 3.6 9.2 - - - +
204A ALA* 3.5 31.2 - - + -
207A LYS* 4.5 6.1 - - - +
166B LEU 3.7 16.4 - - - +
167B GLU* 3.4 9.1 + - - +
168B THR 3.1 0.2 - - - -
169B CYS* 1.3 78.9 - - - +
171B ILE* 1.3 61.2 + - + +
172B ASN 3.5 0.7 - - - -
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Residues in contact with ILE 171 (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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186A MET* 4.0 18.2 - - + -
215A TRP 5.6 0.2 - - - +
217A ILE* 3.4 20.7 - - + +
167B GLU 4.0 10.8 - - - +
168B THR* 3.1 14.5 + - + +
170B MET* 1.3 82.9 - - + +
172B ASN* 1.3 71.6 + - - +
173B GLN* 3.2 43.3 + - - +
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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