Contacts of the strand formed by residues 433 - 438 (chain D) in PDB entry 4OIN
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 433 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D ARG* 3.5 5.9 - - - +
415D VAL* 2.9 38.2 + - - +
431D VAL 3.8 0.8 + - - -
432D TYR* 1.3 74.4 - - - +
434D ARG* 1.3 61.1 + - - -
435D VAL* 5.6 0.2 - - - -
446D VAL* 3.8 11.6 - - - +
447D VAL 3.2 11.9 - - - -
449D SER* 3.2 20.0 + - - +
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Residues in contact with ARG 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D TYR* 4.5 21.7 - - - +
411D THR* 5.9 1.8 - - - +
412D GLY* 3.6 36.1 + - - +
413D ASP 3.6 2.7 - - - +
414D ARG* 3.8 31.9 - - + +
433D GLY* 1.3 73.9 - - - -
435D VAL* 1.3 65.2 + - - +
436D GLU* 3.6 14.9 + - + +
446D VAL* 3.5 3.4 - - - -
447D VAL* 2.9 39.5 + - + +
449D SER* 3.5 11.2 + - - +
135F ILE* 2.8 41.0 + - - +
182F ALA* 5.6 6.9 - - - +
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Residues in contact with VAL 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D VAL* 3.9 24.5 - - + -
410D SER 3.3 20.0 - - - +
411D THR* 3.2 2.4 - - - +
412D GLY* 2.6 31.9 + - - -
413D ASP* 2.8 26.2 + - + +
415D VAL* 4.5 18.8 - - + -
421D LEU* 5.6 1.1 - - + -
433D GLY 5.2 0.4 - - - +
434D ARG* 1.3 73.4 - - - +
436D GLU* 1.3 63.8 + - - +
437D VAL* 3.7 17.7 - - + -
444D VAL* 4.1 12.1 - - + -
445D ARG 4.0 2.7 - - - -
446D VAL* 4.1 16.6 - - + -
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Residues in contact with GLU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLN* 5.3 4.3 - - - +
411D THR* 3.8 13.2 - - + -
434D ARG* 4.6 14.0 + - + +
435D VAL* 1.3 75.9 - - - +
437D VAL* 1.3 62.1 + - - +
438D ASP* 3.6 1.7 + - - +
445D ARG* 2.9 75.3 + - - +
447D VAL* 3.7 24.7 - - + +
179F GLU* 6.0 0.4 - - - +
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Residues in contact with VAL 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D PHE* 4.6 5.4 - - + -
407D VAL* 4.2 16.4 - - + -
409D VAL 3.2 25.8 - - - +
410D SER 3.6 18.6 - - - -
411D THR* 3.4 16.5 + - - +
435D VAL* 3.7 11.0 - - + -
436D GLU* 1.3 69.4 - - - +
438D ASP* 1.3 67.7 + - - +
439D LEU* 3.5 12.8 + - + +
443D VAL 4.3 2.0 - - - -
444D VAL* 4.5 11.7 - - + +
175F HIS* 3.4 29.0 - - + +
179F GLU* 5.4 3.8 - - - +
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Residues in contact with ASP 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D PHE* 3.9 4.0 - - - -
436D GLU 3.6 1.8 + - - -
437D VAL* 1.3 71.0 - - - +
439D LEU* 1.3 57.2 + - - +
440D VAL* 2.9 13.9 + - - +
441D ARG* 2.8 62.5 + - - +
442D ASN* 3.0 5.4 + - - -
443D VAL* 2.9 49.3 + - + +
445D ARG* 3.4 21.3 + - - +
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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