Contacts of the strand formed by residues 763 - 769 (chain A) in PDB entry 1HXK
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 VAL 763 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712A PHE* 4.1 26.0 - - + -
760A LEU* 2.8 39.2 + - + +
761A PRO 3.1 7.9 - - - +
762A SER* 1.3 95.9 - - - +
764A VAL* 1.3 74.7 + - - +
765A HIS* 3.5 3.7 + - + +
778A ASN* 3.9 31.0 - - + +
779A LEU 3.3 6.1 - - - +
780A VAL* 4.3 16.4 - - + -
790A ILE* 4.4 13.2 - - + -
866A GLN* 5.6 0.2 - - + -
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Residues in contact with VAL 764 (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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598A TRP* 3.7 56.1 - - + +
607A ILE* 4.7 6.7 - - + -
758A VAL 3.4 8.1 - - - +
759A GLY* 4.6 6.5 - - - -
760A LEU 5.6 0.4 - - - +
763A VAL* 1.3 74.3 - - - +
765A HIS* 1.3 58.8 + - - +
766A GLN* 3.4 25.6 + - + +
778A ASN* 3.5 1.9 - - - -
779A LEU* 2.9 55.5 + - + +
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Residues in contact with HIS 765 (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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692A GLY 4.2 10.4 + - - -
693A LEU* 3.4 28.1 - - + +
694A LEU 5.0 0.4 - - - -
710A PHE* 3.9 22.8 - + + -
712A PHE* 3.5 28.3 - + + -
756A VAL 3.8 1.4 + - - +
757A SER* 3.2 2.8 - - - -
758A VAL* 2.8 48.1 + - + +
760A LEU* 4.2 4.9 - - + -
763A VAL* 3.5 1.5 + - + -
764A VAL* 1.3 72.2 - - - +
766A GLN* 1.3 63.5 + - - +
767A THR* 3.9 19.2 + - - -
776A ILE* 3.6 20.5 - - + +
778A ASN* 2.8 28.5 - - - +
792A MET* 4.3 1.0 - - - -
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Residues in contact with GLN 766 (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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534A SER 5.8 0.4 + - - -
598A TRP* 5.8 1.8 - - - -
755A SER* 5.9 0.4 - - - -
756A VAL 3.4 3.4 - - - -
757A SER* 3.4 24.4 + - - +
764A VAL* 3.4 30.8 + - + +
765A HIS* 1.3 80.2 - - - +
767A THR* 1.3 63.2 + - - +
768A ILE* 4.0 12.3 - - + +
775A GLU 3.8 0.3 - - - +
776A ILE* 3.2 9.7 - - - +
777A ARG* 2.8 69.5 + - + +
779A LEU* 4.2 4.4 - - - +
889A LEU* 4.2 14.0 - - - +
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Residues in contact with THR 767 (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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686A LEU* 3.9 18.4 - - + -
688A PHE* 3.6 37.8 - - + -
694A LEU* 5.2 5.5 - - + +
710A PHE* 5.1 2.4 - - - -
755A SER* 3.1 5.2 - - - -
756A VAL 2.9 31.2 + - - -
765A HIS* 3.9 15.2 + - - -
766A GLN* 1.3 73.3 - - - +
768A ILE* 1.3 63.4 + - - +
769A MET* 4.1 3.5 - - + +
774A PRO* 4.0 6.5 - - + -
775A GLU 3.5 2.7 - - - -
776A ILE* 3.7 23.4 - - + +
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Residues in contact with ILE 768 (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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753A GLU* 3.5 37.2 - - + +
754A SER 3.5 4.9 - - - +
755A SER* 4.1 10.5 - - - -
766A GLN* 4.7 12.1 - - + +
767A THR* 1.3 81.2 - - - +
769A MET* 1.3 63.6 + - - +
770A ARG* 4.1 12.3 + - + +
774A PRO* 3.3 5.9 - - - +
775A GLU* 2.7 51.2 + - + +
777A ARG* 3.5 50.3 - - + +
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Residues in contact with MET 769 (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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678A LEU* 3.3 53.2 - - + +
679A ARG* 4.8 2.2 - - - -
680A VAL* 3.5 20.9 - - + +
684A PRO* 5.4 4.0 - - + +
686A LEU* 3.7 36.8 - - + -
688A PHE* 3.9 16.4 - - + -
753A GLU* 3.3 5.9 - - - -
754A SER* 2.8 48.4 + - - +
755A SER* 4.1 2.5 - - - -
756A VAL* 4.3 0.2 - - + -
767A THR* 4.1 10.1 - - + +
768A ILE* 1.3 76.3 - - - +
770A ARG* 1.3 63.8 + - - +
771A GLY 3.7 1.6 - - - +
772A GLY 5.5 3.4 - - - +
774A PRO* 4.4 5.8 - - + -
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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