Contacts of the helix formed by residues 231 - 236 (chain A) in PDB entry 4H36
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 ALA 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG 5.5 1.0 + - - -
229A TYR 3.7 0.4 + - - -
230A ARG* 1.3 75.8 - - - +
232A PRO* 1.3 77.9 - - + +
233A GLU* 3.3 24.7 - - - +
234A VAL* 3.0 15.9 + - - +
235A ILE* 3.1 11.9 + - - +
244A VAL* 3.5 20.5 + - + +
247A TRP* 3.3 26.4 - - + -
248A SER* 5.2 0.6 + - - -
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Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG 4.3 0.2 - - - +
231A ALA* 1.3 86.7 - - + +
233A GLU* 1.3 59.8 + - - +
234A VAL 3.1 0.2 + - - -
235A ILE* 3.1 13.8 + - + -
236A LEU* 2.7 43.9 + - + +
247A TRP* 3.7 31.6 - - + -
272A TRP* 4.2 15.3 - - + -
275A VAL* 4.8 4.5 - - + -
286A PHE* 4.7 3.1 - - + -
342A ILE* 3.9 41.1 - - + +
347A ARG* 4.0 0.9 - - - +
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Residues in contact with GLU 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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231A ALA* 3.6 9.9 - - - +
232A PRO* 1.3 74.7 - - - +
234A VAL* 1.3 61.1 + - - +
236A LEU 4.1 0.2 - - - -
237A GLY* 3.3 0.5 + - - -
238A MET* 2.8 49.0 + - + -
239A GLY 3.3 24.8 + - - +
240A TYR* 3.7 14.7 - - + +
241A LYS 5.3 0.9 + - - -
243A ASN* 4.7 1.0 - - - +
244A VAL* 3.3 16.9 - - + +
286A PHE* 5.5 0.2 - - - -
344A PRO* 3.4 27.0 - - + +
347A ARG* 2.8 45.3 + - - -
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Residues in contact with VAL 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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188A ARG* 3.6 31.9 - - + +
230A ARG* 3.7 29.8 - - + -
231A ALA 3.0 13.7 + - - +
233A GLU* 1.3 78.0 - - - +
235A ILE* 1.3 60.1 + - - +
237A GLY* 3.1 17.5 + - - -
239A GLY 5.6 0.2 - - - +
240A TYR* 3.7 17.7 - - + -
244A VAL* 3.6 30.5 - - + -
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Residues in contact with ILE 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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227A ARG 5.1 1.3 - - - +
230A ARG* 3.7 23.3 - - + +
231A ALA 3.1 13.5 + - - +
232A PRO* 3.5 16.6 - - + +
234A VAL* 1.3 77.8 - - + +
236A LEU* 1.3 72.7 + - + +
237A GLY 3.2 0.6 + - - -
268A TYR* 3.5 49.1 - - + +
271A GLN* 4.1 23.1 - - + -
272A TRP* 4.5 20.2 - - + +
275A VAL* 5.5 4.3 - - + -
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Residues in contact with LEU 236 (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 PRO 2.7 23.1 + - - +
235A ILE* 1.3 84.9 - - + +
237A GLY* 1.3 65.6 + - - +
238A MET* 3.5 13.8 + - + +
272A TRP* 3.7 49.1 - - + -
286A PHE* 4.0 21.8 - - + -
290A LEU* 4.0 16.0 - - + +
291A GLN* 5.3 2.4 + - - +
294A VAL* 4.5 28.3 - - + +
297A TYR* 6.3 1.1 - - + -
298A VAL* 4.5 14.4 - - + -
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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