Contacts of the helix formed by residues 203 - 208 (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 LYS 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A MET* 3.5 10.3 - - - +
202B SER* 1.3 82.8 + - - +
204B ALA* 1.3 68.4 + - - +
205B ILE* 3.3 22.7 - - + +
206B HIS* 3.0 43.0 + - + +
207B LYS* 3.7 4.3 + - - +
270B GLU 5.7 2.9 - - - -
419B GLU* 5.4 5.1 + - - -
422B ARG* 5.3 3.0 - - - +
440B GLY* 3.3 34.8 + - - +
441B ASP* 4.2 10.1 + - - +
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Residues in contact with ALA 204 (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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166A LEU* 3.8 31.4 - - + +
169A CYS* 3.6 18.9 - - - -
170A MET* 3.5 16.6 - - + +
203B LYS* 1.3 76.4 - - - +
205B ILE* 1.3 64.4 + - - +
207B LYS 2.9 12.8 + - - -
208B ILE* 3.0 16.9 + - - +
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Residues in contact with ILE 205 (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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161A PHE* 3.9 26.9 - - + -
166A LEU* 5.4 2.8 - - + +
346A ALA* 4.4 11.7 - - + -
347A PRO 4.1 8.5 - - - +
348A TYR* 4.4 10.1 - - + +
349A ARG* 3.5 49.8 + - + +
203B LYS* 3.8 19.6 - - + +
204B ALA* 1.3 78.4 - - - +
206B HIS* 1.3 80.0 + - + +
207B LYS 3.5 0.2 + - - -
208B ILE* 4.1 6.8 - - + +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 4.8 5.2 + - - -
348A TYR* 3.3 30.8 - - + +
349A ARG* 4.9 3.9 - - - +
189B PHE* 4.2 8.5 - + + -
192B ARG* 3.3 32.6 + - + +
197B LEU* 3.5 23.6 - - + +
200B THR* 5.1 2.0 - - + -
202B SER* 2.6 31.4 + - - +
203B LYS* 3.0 33.3 + - + +
204B ALA 3.0 0.2 + - - -
205B ILE* 1.3 90.3 - - + +
207B LYS* 1.3 60.3 + - + +
208B ILE 5.4 0.2 - - - -
210B ILE* 4.8 3.5 - - - +
270B GLU* 5.1 9.0 - - + -
500B ACT 5.2 0.7 - - - -
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A CYS* 3.1 40.2 - - - +
170A MET* 4.3 10.5 - - - +
172A ASN* 2.7 25.8 + - - -
176A GLY 4.6 0.2 - - - +
177A CYS* 4.7 4.4 - - - -
197B LEU* 2.7 44.8 + - + +
198B ALA* 3.6 5.3 + - - +
200B THR* 2.8 27.9 + - + +
201B HIS* 4.2 4.5 - - - -
202B SER 5.3 0.2 - - - +
203B LYS 3.9 11.2 - - - +
204B ALA 2.9 5.5 + - - +
206B HIS* 1.3 84.1 - - + +
208B ILE* 1.3 66.1 + - - +
209B ASP 3.5 0.3 + - - -
210B ILE* 3.3 25.1 + - - +
212B SER* 4.1 4.1 + - - -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 3.3 45.1 - - + -
165A GLU* 4.0 19.1 - - + +
166A LEU* 3.8 21.3 - - + +
169A CYS* 3.8 14.4 - - + -
176A GLY 4.1 6.3 - - - +
349A ARG* 3.0 32.4 + - - +
204B ALA 3.0 17.0 + - - +
205B ILE* 4.1 13.3 - - + +
206B HIS 3.8 0.6 - - - -
207B LYS* 1.3 79.9 - - - +
209B ASP* 1.3 78.0 + - - +
210B ILE* 3.2 9.6 + - - +
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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
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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