Contacts of the helix formed by residues 729 - 736 (chain A) in PDB entry 6WCW
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 ASP 729 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A ARG 4.2 0.6 + - - -
728A THR* 1.3 73.0 + - - +
730A PRO* 1.3 76.2 - - - +
731A ASP* 3.1 22.7 + - - +
732A TYR* 3.0 52.0 + - + +
733A ILE* 3.7 8.3 + - - +
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Residues in contact with PRO 730 (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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706A PRO* 4.8 2.9 - - - +
711A LYS* 3.7 17.2 + - - +
719A TYR* 3.5 47.6 - - + +
728A THR 3.2 7.2 - - - +
729A ASP* 1.3 90.1 - - - +
731A ASP* 1.3 63.8 + - - +
732A TYR 3.2 1.5 + - - -
733A ILE* 3.5 15.6 + - + +
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Residues in contact with ASP 731 (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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701A ILE 3.8 0.9 - - - +
702A PHE* 3.2 43.2 - - + -
703A ASN* 3.1 37.9 + - - +
704A VAL* 5.2 3.3 - - - -
706A PRO* 6.4 0.7 - - - -
729A ASP* 3.1 15.8 + - - +
730A PRO* 1.3 80.8 - - - +
732A TYR* 1.3 60.4 - - + +
733A ILE 3.8 0.7 - - - -
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Residues in contact with TYR 732 (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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701A ILE* 3.8 26.9 - - + +
702A PHE* 3.8 41.1 - + + +
728A THR* 6.3 0.9 - - - -
729A ASP* 3.0 45.4 + - + +
731A ASP* 1.3 80.8 - - + +
733A ILE* 1.3 58.1 + - - +
734A LYS 2.8 12.6 + - - -
735A ARG* 3.0 39.5 + - + +
736A LEU* 5.2 0.2 - - - +
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Residues in contact with ILE 733 (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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706A PRO* 3.7 31.2 - - + -
710A ARG* 2.6 44.8 + - + +
711A LYS* 3.7 39.0 - - + +
714A VAL* 3.8 31.2 - - + -
719A TYR* 3.8 11.0 - - + -
728A THR* 4.6 2.2 - - - +
729A ASP 3.8 7.6 - - - +
730A PRO 3.5 14.8 - - - +
731A ASP 3.8 0.8 - - - -
732A TYR* 1.3 73.9 - - - +
734A LYS* 1.3 53.3 + - - +
735A ARG 3.1 1.4 + - - -
736A LEU* 3.3 20.3 + - + +
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Residues in contact with LYS 734 (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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699A GLN* 4.6 11.1 - - - +
700A ILE* 2.8 29.9 + - - +
701A ILE* 4.1 32.3 - - + +
703A ASN* 5.2 13.0 - - + +
706A PRO* 6.5 0.9 - - + -
710A ARG* 3.3 21.2 + - - +
732A TYR 2.8 2.0 + - - -
733A ILE* 1.3 80.9 - - + +
735A ARG* 1.3 60.6 + - - +
736A LEU 3.5 2.9 - - - +
748A GLN* 5.1 0.7 + - - -
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Residues in contact with ARG 735 (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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699A GLN* 6.1 0.4 - - - +
701A ILE* 3.7 41.8 - - + +
732A TYR* 3.0 32.6 + - - +
734A LYS* 1.3 78.4 - - - +
736A LEU* 1.3 65.8 + - + +
737A ARG* 4.1 0.9 - - - +
748A GLN* 2.5 54.8 + - + +
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Residues in contact with LEU 736 (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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710A ARG* 2.8 23.6 + - - -
714A VAL* 3.6 40.2 - - + -
721A CYS* 5.6 2.7 - - + -
728A THR* 4.0 29.6 - - + +
733A ILE* 3.6 21.1 - - + +
734A LYS 3.2 4.0 - - - +
735A ARG* 1.3 86.0 - - + +
737A ARG* 1.3 62.1 + - - +
745A TYR* 3.9 18.6 - - + -
746A PHE 3.3 23.6 - - - +
747A CYS* 3.9 11.2 - - + +
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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