Contacts of the helix formed by residues 659 - 663 (chain A) in PDB entry 2WKP
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 LYS 659 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A ALA* 2.9 28.7 + - - +
557A VAL 3.5 17.3 - - - +
626A SER* 3.6 19.5 + - - +
627A LEU* 4.8 2.9 - - - +
628A VAL* 4.3 6.8 - - + +
658A THR* 1.3 80.7 - - - +
660A LEU* 1.3 66.5 + - - +
661A ASP* 3.1 5.8 - - - -
662A LEU* 2.9 42.1 + - + +
663A ARG 3.8 2.6 + - - -
700A CYS 3.2 4.2 + - - -
701A SER* 4.6 0.2 - - - +
702A ALA 5.2 0.2 - - - +
1724A GTP 3.3 60.7 + - + +
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Residues in contact with LEU 660 (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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627A LEU* 3.8 16.2 - - + -
658A THR 3.2 1.2 - - - -
659A LYS* 1.3 76.8 - - - +
661A ASP* 1.3 61.3 + - - +
663A ARG* 3.2 50.4 + - - +
664A ASP* 4.5 3.0 + - - +
699A GLU* 3.9 21.3 - - + +
700A CYS* 3.0 27.9 + - - +
701A SER* 4.0 1.6 - - - +
706A ARG* 3.3 43.9 + - + +
707A GLY* 5.9 0.2 - - - -
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Residues in contact with ASP 661 (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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659A LYS 3.7 3.3 - - - -
660A LEU* 1.3 78.4 - - - +
662A LEU* 1.3 67.1 + - - +
663A ARG 3.7 0.2 + - - -
664A ASP* 4.1 5.2 + - - +
665A ASP* 4.0 12.1 + - - +
701A SER* 2.7 25.2 + - - +
703A LEU* 3.5 14.5 - - + +
704A THR* 4.0 11.0 - - + -
706A ARG* 3.8 19.3 - - - +
1724A GTP 2.7 47.9 + - - +
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Residues in contact with LEU 662 (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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628A VAL* 3.6 23.3 - - + +
659A LYS* 2.9 35.3 + - + +
661A ASP* 1.3 81.6 - - - +
663A ARG* 1.3 64.8 + - - +
664A ASP 3.1 3.6 - - - -
665A ASP* 3.0 29.7 + - + +
668A THR* 3.6 29.7 - - + +
669A ILE* 4.8 0.7 - - - +
1724A GTP 3.4 34.1 - - + +
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Residues in contact with ARG 663 (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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627A LEU* 3.7 13.3 - - + +
628A VAL* 3.9 12.3 - - + +
659A LYS 3.8 2.6 + - - -
660A LEU* 3.2 34.3 + - + +
662A LEU* 1.3 78.7 - - - +
664A ASP* 1.3 66.9 + - - +
669A ILE* 3.6 18.6 - - - +
679A PRO* 3.7 19.6 - - + +
680A ILE 2.9 30.3 + - - -
681A THR* 4.5 3.8 - - - +
682A TYR* 3.4 18.6 - - - +
699A GLU* 2.8 43.0 + - - -
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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