Contacts of the helix formed by residues 595 - 600 (chain B) 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 CYS 595 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B ARG* 5.4 10.1 - - + +
591B TYR* 3.2 21.2 + - - -
592B ASP* 3.1 16.8 + - - +
594B GLY* 1.3 75.0 - - - +
596B ASP* 1.3 65.3 + - - +
598B TRP* 3.3 8.2 + - - +
599B SER* 3.0 27.4 + - - -
660B PRO* 6.1 1.6 - - - -
663B ARG* 4.4 6.5 - - - +
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Residues in contact with ASP 596 (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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523B VAL* 4.4 4.3 - - + +
527B HIS* 2.9 29.0 + - + +
532B VAL* 3.7 4.7 - - - +
533B HIS* 3.0 27.7 + - - +
534B ARG* 2.8 31.0 + - - -
535B ASP 4.4 0.2 + - - -
536B LEU* 3.8 23.5 - - + +
592B ASP 3.2 6.4 + - - -
593B GLU 2.9 9.3 + - - +
595B CYS* 1.3 78.4 - - - +
597B ILE* 1.3 63.8 + - - +
599B SER* 3.5 5.5 + - - -
600B LEU* 3.1 22.1 + - - +
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Residues in contact with ILE 597 (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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523B VAL* 4.6 0.9 - - + -
527B HIS* 4.3 9.0 - - + -
593B GLU* 3.0 16.9 + - + +
594B GLY* 3.7 9.0 - - - +
596B ASP* 1.3 76.5 - - - +
598B TRP* 1.3 60.7 + - - +
600B LEU* 3.1 19.0 + - + +
601B GLY* 2.8 26.0 + - - -
655B MET* 3.8 33.6 - - + +
663B ARG* 4.6 3.8 - - + -
664B LEU 3.4 26.9 - - - +
665B THR* 4.5 1.6 - - - +
666B ALA* 3.7 36.6 - - + +
669B VAL* 4.5 4.9 - - + -
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Residues in contact with TRP 598 (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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594B GLY 2.9 18.7 + - - +
595B CYS* 3.3 7.4 + - - +
597B ILE* 1.3 77.1 - - - +
599B SER* 1.3 70.0 + - - +
601B GLY* 2.9 11.6 + - - -
602B ILE* 3.0 40.3 + - + +
614B PHE* 3.5 30.7 - + - -
629B ILE* 4.1 23.4 - - + +
655B MET 3.8 8.0 + - - -
656B LEU* 3.5 28.5 + - + +
663B ARG* 3.5 34.9 - - - +
701B THR* 4.5 2.5 - - + -
702B TYR* 4.4 5.2 - + - -
705B LEU* 3.4 35.4 - - + -
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Residues in contact with SER 599 (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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534B ARG 5.9 0.7 - - - -
536B LEU* 3.2 37.8 + - - +
538B PRO* 5.7 0.5 - - - +
595B CYS 3.0 13.9 + - - -
596B ASP 3.6 8.3 - - - -
598B TRP* 1.3 83.0 - - - +
600B LEU* 1.3 63.6 + - - +
602B ILE* 3.2 7.2 + - - +
603B LEU* 3.2 22.2 + - - +
702B TYR* 2.9 27.5 + - - -
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Residues in contact with LEU 600 (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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516B LEU* 4.3 15.7 - - + +
519B ILE* 3.8 18.8 - - + -
520B GLY* 4.2 23.6 - - - -
523B VAL* 4.2 13.7 - - + -
536B LEU* 3.5 29.2 - - + +
541B ILE* 5.4 4.3 - - + -
596B ASP 3.1 13.1 + - - +
597B ILE* 3.3 24.7 - - + +
599B SER* 1.3 76.5 - - - +
601B GLY* 1.3 57.2 + - - +
603B LEU* 3.3 11.1 + - + +
604B LEU* 2.9 29.6 + - - +
655B MET* 3.4 16.4 - - + +
666B ALA* 5.9 0.9 - - + -
669B VAL* 6.1 2.5 - - + -
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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