Contacts of the helix formed by residues 232 - 237 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A PRO* 4.9 4.5 - - - -
229A ASN 4.9 1.2 + - - -
230A ILE* 3.1 6.7 - - - +
231A ASP* 1.3 78.9 + - - +
233A LEU* 1.3 61.9 + - - +
234A GLU* 3.2 11.9 + - - -
235A ARG* 3.3 13.7 + - - +
236A VAL* 3.1 26.4 + - - +
246A GLU* 5.1 8.3 - - - -
250A THR* 5.7 4.7 - - - -
133B ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A SER* 3.8 20.0 - - - +
152A SER* 3.8 29.2 - - - +
154A ILE* 4.0 9.9 - - + -
204A TYR* 3.8 26.2 - - + +
205A LYS 4.0 0.9 - - - +
206A PRO* 3.8 20.3 - - + +
210A HIS* 3.5 21.0 - - + +
231A ASP* 2.9 27.2 + - + +
232A GLY* 1.3 75.2 - - - +
234A GLU* 1.3 59.9 + - - +
236A VAL* 3.7 12.8 - - + +
237A SER* 3.0 28.4 + - - -
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.7 8.8 - - + +
148A ILE* 4.3 3.8 - - + +
210A HIS* 4.3 13.2 - - + -
213A LEU* 5.4 0.9 - - + -
225A LEU* 3.8 25.4 - - + -
227A THR* 2.6 42.5 + - - +
229A ASN* 4.0 12.6 + - - +
231A ASP* 4.2 5.2 - - - +
232A GLY* 4.0 6.6 + - - -
233A LEU* 1.3 84.0 + - - +
235A ARG* 1.3 64.0 + - - +
237A SER* 2.7 24.6 + - - -
239A ILE* 3.2 16.5 + - + +
244A LEU* 3.6 22.4 - - + -
246A GLU* 5.2 3.5 - - - +
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLY* 3.3 11.5 + - - +
234A GLU* 1.3 80.2 + - - +
236A VAL* 1.3 58.5 + - - +
238A GLY* 2.9 17.0 + - - -
239A ILE 4.1 0.9 - - - +
241A ALA* 6.4 0.2 - - - +
244A LEU* 3.8 12.9 - - + +
246A GLU* 4.1 21.9 + - - +
250A THR* 5.1 1.2 + - - +
252A ALA* 3.4 27.9 - - - +
126B GLN* 3.0 25.3 - - - +
130B GLU* 2.6 29.8 + - - +
133B ARG* 3.3 35.8 - - - +
375B GLU 5.2 1.2 + - - -
376B LEU* 3.3 21.2 + - - +
377B LEU 4.7 3.6 - - - -
378B GLY* 4.7 5.5 - - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 5.5 9.0 - - + -
202A GLY 6.2 1.1 - - - +
204A TYR 5.3 3.4 - - - +
206A PRO* 3.5 26.1 - - + +
211A TYR* 4.6 3.6 + - - +
231A ASP 5.3 1.1 - - - +
232A GLY 3.1 21.7 + - - +
233A LEU* 3.7 19.7 - - + +
234A GLU 3.3 0.2 - - - -
235A ARG* 1.3 74.6 - - - +
237A SER* 1.3 57.4 + - - +
238A GLY* 3.1 4.7 + - - -
390A GLU* 5.5 0.7 - - - +
127B ASP* 4.5 4.9 - - - +
130B GLU* 3.6 39.1 - - + +
133B ARG* 4.5 6.5 - - - +
134B ALA* 5.5 10.8 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PRO* 3.8 5.1 - - - +
210A HIS* 3.8 28.3 + - - +
211A TYR* 3.6 27.9 - - - -
214A ARG* 2.9 27.3 + - - +
233A LEU 3.0 15.2 + - - -
234A GLU* 2.7 20.1 + - - -
236A VAL* 1.3 74.3 - - - +
238A GLY* 1.3 58.0 + - - +
239A ILE* 3.5 13.2 - - - +
127B ASP* 4.3 0.7 - - - -
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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