Contacts of the strand formed by residues 430 - 436 (chain A) in PDB entry 2WNT
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 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A VAL* 3.6 3.3 - - - +
427A GLY* 2.7 46.9 + - - +
429A TYR* 1.3 84.1 + - - +
431A GLU* 1.3 61.7 + - - +
447A LYS* 3.4 38.3 - - - +
448A VAL 3.1 14.6 - - - -
449A ILE* 4.2 2.7 - - - -
450A ASP 5.1 0.2 - - - +
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Residues in contact with GLU 431 (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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423A THR* 4.9 8.6 + - + +
425A GLY 3.7 10.5 - - - +
426A VAL* 4.1 11.8 - - + +
430A SER* 1.3 77.7 - - - +
432A CYS* 1.3 60.5 + - - +
433A LYS* 3.9 23.7 + - - +
447A LYS* 4.6 1.1 - - - -
448A VAL* 2.9 62.4 + - + +
484A HIS* 5.6 2.3 + - - -
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Residues in contact with CYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A THR* 3.5 3.2 - - - +
424A ILE* 2.7 50.3 + - - -
425A GLY* 2.9 26.8 + - - +
426A VAL* 4.6 0.8 - - - +
430A SER* 5.4 0.2 + - - -
431A GLU* 1.3 72.3 - - - +
433A LYS* 1.3 56.6 + - - +
445A ALA* 4.4 13.5 - - - -
446A VAL 3.4 12.3 - - - -
447A LYS* 4.3 11.9 - - + +
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Residues in contact with LYS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 3.5 28.2 - - + +
421A LYS 4.5 1.6 + - - +
422A GLU 2.9 20.0 - - - +
423A THR* 3.4 22.1 + - - +
424A ILE* 3.4 8.9 - - - +
431A GLU* 4.1 32.2 + - - +
432A CYS* 1.3 76.3 - - - +
434A ARG* 1.3 60.5 + - - +
445A ALA* 3.6 1.7 - - - -
446A VAL* 2.8 51.9 + - + +
448A VAL* 4.5 10.5 - - + -
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Residues in contact with ARG 434 (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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420A VAL* 4.2 0.2 - - - -
421A LYS* 2.7 59.9 + - - +
422A GLU* 2.9 51.2 + - - +
424A ILE* 3.3 16.4 - - + +
433A LYS* 1.3 71.7 - - - +
435A CYS* 1.3 56.2 + - - +
436A VAL* 4.0 12.3 - - - +
443A GLU* 3.2 43.6 + - + +
444A TYR 3.6 12.1 - - - +
491A LEU* 3.7 18.2 - - + -
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Residues in contact with CYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A TYR* 3.7 31.0 - - + -
419A VAL 3.3 13.5 - - - +
420A VAL* 4.0 11.7 - - + -
421A LYS* 4.0 0.9 - - - +
433A LYS 3.7 0.2 + - - -
434A ARG* 1.3 77.2 - - - +
436A VAL* 1.3 64.3 + - - +
443A GLU* 3.6 2.9 - - - -
444A TYR* 2.8 49.9 + - - +
445A ALA 4.5 0.4 - - - -
446A VAL* 4.1 28.9 - - + -
488A VAL* 4.5 3.4 - - - -
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A TYR* 3.4 3.5 - - - -
419A VAL* 2.8 44.7 + - + +
421A LYS* 3.9 30.7 - - + -
434A ARG* 4.0 14.8 - - - +
435A CYS* 1.3 79.6 - - - +
437A HIS* 1.3 77.0 + - - +
438A LYS* 3.2 1.8 + - - -
441A ASN* 4.0 16.4 - - + +
442A MET 3.6 10.1 - - - +
443A GLU* 4.2 8.5 - - + +
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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