Contacts of the helix formed by residues 664 - 669 (chain A) in PDB entry 6WG4
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 ARG 664 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A LYS* 5.7 3.4 - - - +
531A GLN* 5.2 2.2 - - - -
660A LYS* 3.2 9.7 + - + +
661A ALA* 2.6 44.1 + - - +
662A LYS* 5.8 0.6 - - - +
663A ALA* 1.3 75.0 - - - +
665A ARG* 1.3 62.8 + - + +
666A TRP 3.1 0.4 - - - -
667A ASP* 3.2 18.2 + - + +
668A GLU* 3.2 33.1 + - - +
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Residues in contact with ARG 665 (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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518A ARG* 4.9 3.4 - - - +
520A ILE* 3.8 26.3 - - + +
542A MET* 3.5 23.4 - - - +
543A ASP* 2.6 41.7 + - - -
661A ALA 5.7 0.2 - - - +
662A LYS* 3.4 27.3 + - - +
663A ALA 3.0 0.4 - - - -
664A ARG* 1.3 82.6 - - + +
666A TRP* 1.3 60.9 + - - +
667A ASP 3.4 0.7 + - - -
668A GLU* 3.6 23.8 - - + +
669A LYS* 3.2 28.6 + - + +
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Residues in contact with TRP 666 (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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520A ILE* 3.5 29.8 - - + -
523A CYS* 3.1 44.4 - - - -
524A GLN* 3.5 20.2 + - - +
525A PRO* 3.4 23.4 - - + +
531A GLN* 3.5 36.8 + - + +
534A VAL* 3.8 18.2 - - + -
535A THR* 3.1 25.6 + - - +
538A LEU* 4.0 5.6 - - + -
542A MET* 3.5 26.1 - - + +
662A LYS 4.7 1.8 - - - -
663A ALA* 3.0 23.9 + - - +
665A ARG* 1.3 78.4 - - - +
667A ASP* 1.3 59.2 + - - +
669A LYS* 3.3 23.6 - - - +
670A ALA* 4.4 2.6 + - - +
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Residues in contact with ASP 667 (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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524A GLN* 3.9 6.4 + - - -
528A LYS* 3.5 30.5 + - - +
531A GLN* 3.2 24.6 + - - +
663A ALA 5.3 0.6 - - - +
664A ARG* 3.2 10.4 + - + +
666A TRP* 1.3 81.1 - - - +
668A GLU* 1.3 61.0 + - - +
669A LYS 3.4 0.9 - - - -
670A ALA* 3.3 22.0 - - - +
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Residues in contact with GLU 668 (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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664A ARG* 3.2 33.3 + - + +
665A ARG* 3.5 38.3 - - + +
667A ASP* 1.3 76.4 - - - +
669A LYS* 1.3 66.8 + - + +
670A ALA 3.2 8.9 - - - +
672A ASP* 5.6 0.3 + - - -
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Residues in contact with LYS 669 (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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520A ILE* 3.2 33.0 + - + +
521A ASP* 3.7 32.1 + - - +
523A CYS 3.9 4.2 + - - -
524A GLN* 3.3 19.2 + - - +
601A GLU* 5.9 0.8 + - - -
665A ARG* 3.2 17.9 - - + +
666A TRP* 3.3 24.2 - - - +
668A GLU* 1.3 78.3 - - + +
670A ALA* 1.3 75.4 + - - +
671A VAL* 3.4 4.0 + - - -
672A ASP 5.2 0.2 + - - -
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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