Contacts of the helix formed by residues 589 - 594 (chain B) in PDB entry 2WSC
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 TRP 589 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1812A CLA 2.8 57.4 - + + -
519B VAL* 4.1 14.0 - - + +
522B ALA* 2.9 31.0 - - + +
523B ILE* 4.8 2.9 - - + -
525B LEU* 3.5 26.2 - - + -
526B GLY* 5.5 1.3 - - - -
582B TRP* 4.7 1.6 - + - -
585B ASN* 3.2 33.1 + - - +
586B THR* 2.4 15.6 + - - +
588B GLY* 1.3 70.2 - - - +
590B VAL* 1.3 64.8 - - - +
592B PHE* 3.2 4.8 - + - +
593B TYR* 3.0 23.9 + - - +
1785B CLA 3.2 80.4 - - + +
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Residues in contact with VAL 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B TYR* 3.5 12.1 + - - +
376B GLN* 3.4 22.0 - - - +
523B ILE* 4.0 25.8 - - + +
586B THR* 3.0 20.5 + - + +
587B ILE* 3.4 28.3 - - + +
589B TRP* 1.3 80.5 - - - +
591B THR* 1.3 68.1 + - - +
593B TYR* 3.1 15.8 - - - +
594B TRP 3.5 3.8 + - - -
1755B CLA 4.2 7.4 - - + -
1767B CLA 3.6 28.3 - - + +
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Residues in contact with THR 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B TYR* 4.4 15.5 - - - -
373B THR* 3.2 31.2 + - - +
376B GLN* 5.0 5.2 - - - -
377B TYR* 3.8 16.2 - - + +
587B ILE 3.2 24.5 - - - +
588B GLY* 3.5 6.9 + - - -
590B VAL* 1.3 79.0 - - - +
592B PHE* 1.3 62.7 + - + +
593B TYR 3.0 1.0 + - - -
594B TRP* 2.5 35.5 + - - +
595B HIS* 4.4 0.2 - - - +
721B TYR* 3.8 19.7 + - + -
725B LEU* 6.2 0.2 - - - +
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B GLY* 2.5 37.3 + - - +
589B TRP* 3.2 7.9 - + - +
591B THR* 1.3 74.7 - - + +
593B TYR* 1.3 53.5 + - - +
594B TRP 3.5 0.4 - - - +
595B HIS 2.4 28.9 - - - +
619B TRP* 3.5 34.3 - + + -
623B TYR* 3.8 7.8 + + - -
624B LEU* 3.5 25.4 - - + -
717B TYR* 5.7 0.7 - - - -
721B TYR* 2.9 36.2 + + - -
1785B CLA 3.4 80.8 - + + -
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Residues in contact with TYR 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B ILE* 5.0 1.0 - - - +
516B ASP* 3.2 12.9 + - + +
519B VAL* 3.7 27.8 - - + -
520B HIS* 3.4 33.2 + + - -
523B ILE* 4.1 10.5 - - + -
589B TRP 3.0 9.5 + - - +
590B VAL 3.1 8.3 - - - +
591B THR 3.0 1.0 + - - -
592B PHE* 1.3 74.3 - - - +
594B TRP* 1.3 54.5 + - - +
595B HIS 2.7 4.3 - - - +
596B TRP* 2.2 33.4 - - - +
597B LYS* 2.9 26.2 + - + -
609B PHE* 3.4 34.5 - + - -
619B TRP* 3.9 9.3 - + - -
1767B CLA 3.3 44.0 - + + +
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Residues in contact with TRP 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B TYR* 2.7 63.7 - + + -
368B GLN* 3.5 34.1 - - + -
369B ALA* 3.9 18.5 - - + +
372B TYR* 3.5 38.4 - + + -
590B VAL 3.5 2.2 + - - -
591B THR 2.5 25.9 + - - +
593B TYR* 1.3 77.1 - - - +
595B HIS* 1.3 86.6 + - + +
596B TRP 3.9 0.2 - - - -
598B HIS* 2.9 44.5 - + + +
602B TRP* 4.5 4.7 - + - -
1767B CLA 3.8 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