Contacts of the helix formed by residues 232 - 237 (chain B) in PDB entry 4BVH
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 GLY 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PRO* 5.5 2.0 - - - -
229B ASN 4.8 1.4 + - - -
230B ILE 3.2 6.0 - - - -
231B ASP* 1.3 79.2 + - - +
233B LEU* 1.3 61.6 + - - +
234B GLU* 3.2 11.2 + - - -
235B ARG* 3.3 9.8 + - - +
236B VAL* 3.2 26.3 + - - +
246B GLU* 5.0 10.5 - - - -
250B THR* 5.6 6.1 - - - -
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Residues in contact with LEU 233 (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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149B SER* 3.9 4.5 - - - +
152B SER* 4.1 7.9 - - - +
154B ILE* 4.3 1.8 - - + -
204B TYR* 3.8 30.1 - - + +
205B LYS* 3.7 19.5 - - - +
206B PRO* 3.7 27.6 - - + +
210B HIS* 3.5 35.6 - - + +
231B ASP* 3.0 28.0 + - - +
232B GLY* 1.3 76.1 - - - +
234B GLU* 1.4 62.0 + - - +
236B VAL* 3.7 14.3 - - + +
237B SER* 2.9 30.5 + - - -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 3.7 9.2 - - + +
148B ILE* 4.1 5.2 - - + +
210B HIS* 4.2 11.1 - - + -
213B LEU* 5.3 1.6 - - + -
225B LEU* 3.7 31.2 - - + -
227B THR* 2.7 39.0 + - - +
229B ASN* 3.9 13.2 + - - +
231B ASP* 4.2 5.0 - - - +
232B GLY* 4.0 6.2 + - - -
233B LEU* 1.4 85.1 + - - +
235B ARG* 1.3 61.2 + - - +
237B SER* 2.8 23.3 + - - -
239B ILE* 3.2 18.2 + - + +
244B LEU* 3.6 20.4 - - + +
246B GLU* 5.2 3.5 - - - +
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Residues in contact with ARG 235 (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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232B GLY* 3.3 10.7 + - - +
234B GLU* 1.3 77.1 + - - +
236B VAL* 1.3 67.3 + - + +
238B GLY* 3.0 14.0 + - - -
239B ILE 4.1 13.7 + - - +
241B ALA* 6.4 1.6 - - - -
244B LEU* 3.8 6.7 - - + +
246B GLU* 4.1 19.9 + - - +
252B ALA* 3.9 25.9 - - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 6.2 3.8 - - + -
206B PRO* 3.7 21.8 - - + -
231B ASP 5.3 1.1 - - - +
232B GLY 3.2 18.7 + - - +
233B LEU* 3.8 17.5 - - + +
234B GLU 3.3 0.2 - - - -
235B ARG* 1.3 78.9 - - + +
237B SER* 1.3 58.4 + - - +
238B GLY* 3.1 4.9 + - - -
390B GLU* 5.6 0.3 - - - +
1395B EDO 3.3 43.1 - - - +
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Residues in contact with SER 237 (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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206B PRO* 4.3 11.9 - - - -
210B HIS* 3.9 31.4 + - - +
211B TYR* 4.4 14.9 - - - -
214B ARG* 2.8 27.1 + - - +
233B LEU 2.9 16.1 + - - -
234B GLU* 2.8 20.1 + - - -
235B ARG 3.1 0.4 - - - -
236B VAL* 1.3 74.4 - - - +
238B GLY* 1.3 57.6 + - - +
239B ILE* 3.6 11.8 - - - +
390B GLU* 5.1 1.7 - - - -
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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