Contacts of the helix formed by residues 361 - 365 (chain A) in PDB entry 4P8V
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR 3.3 16.6 - - - -
34A THR* 3.9 11.8 - - - +
268A THR* 2.7 20.8 + - - -
359A ILE* 3.7 5.4 - - - -
360A TRP* 1.3 90.4 + - - +
362A ILE* 1.3 64.8 + - - +
363A ASP* 2.7 24.2 + - - -
364A MET* 2.9 27.7 + - - +
365A ASP 3.5 0.9 + - - -
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Residues in contact with ILE 362 (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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31A CYS* 3.5 33.7 - - + -
32A TYR 2.9 19.2 + - - +
33A PHE* 4.0 11.2 - - + -
46A PHE* 4.2 16.8 - - + -
51A ILE* 4.3 15.5 - - + -
55A LEU* 4.8 7.0 - - + -
56A CYS* 4.5 1.6 - - - -
59A LEU* 4.3 18.6 - - + -
359A ILE* 4.1 8.7 - - + -
361A SER* 1.3 73.2 - - - +
363A ASP* 1.3 59.5 + - - +
364A MET 3.1 0.4 - - - -
365A ASP* 3.2 26.8 + - - +
367A PHE* 4.2 0.9 - - - +
377A TYR* 3.5 31.3 - - + +
380A VAL* 4.0 16.2 - - + -
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Residues in contact with ASP 363 (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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33A PHE* 3.6 7.3 - - - -
34A THR* 2.7 32.5 + - - +
37A SER* 2.6 24.4 + - - +
40A ARG* 4.6 3.8 + - - -
44A GLY 4.7 2.1 - - - +
46A PHE* 3.2 38.2 - - + -
305A TYR* 3.6 9.4 + - - -
361A SER* 2.7 28.7 + - - -
362A ILE* 1.3 74.0 - - - +
364A MET* 1.3 60.2 + - - +
365A ASP 3.6 0.2 - - - -
367A PHE* 3.5 19.3 - - - -
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Residues in contact with MET 364 (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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36A TRP* 6.3 0.4 - - - -
40A ARG* 4.1 18.6 - - - +
268A THR* 3.4 13.9 - - - +
269A TYR* 3.6 32.1 - - + -
301A PHE* 3.9 24.2 - - - -
303A ALA* 3.7 15.5 - - + +
304A TYR* 3.0 25.6 + - - +
305A TYR* 3.8 6.5 - - - -
360A TRP* 3.8 2.2 - - + +
361A SER* 2.9 29.6 + - - +
363A ASP* 1.3 82.3 - - - +
365A ASP* 1.3 63.9 + - - +
2B NAG 3.3 26.9 - - - +
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Residues in contact with ASP 365 (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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268A THR* 3.7 15.6 + - + -
304A TYR* 3.8 4.4 - - - -
305A TYR* 3.5 6.3 - - - -
361A SER 3.5 3.8 + - - -
362A ILE 3.2 15.1 + - - +
364A MET* 1.3 82.7 - - - +
366A ASP* 1.3 73.7 + - - +
367A PHE* 2.8 22.5 + - - -
377A TYR* 3.1 24.3 - - + +
378A PRO* 3.2 14.4 - - - +
379A LEU* 3.2 23.9 + - - +
380A VAL* 2.9 32.5 + - + +
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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