Contacts of the strand formed by residues 765 - 769 (chain A) in PDB entry 3IAY
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 SER 765 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A CA 4.3 3.6 - - - -
606A THR* 4.6 11.9 - - - -
607A LEU 3.0 13.9 - - - -
608A ASP* 3.6 11.9 - - - -
735A ILE* 3.4 9.2 - - - +
738A THR* 6.1 0.4 - - - -
761A GLY* 3.1 19.6 - - - -
762A ASP* 3.1 27.1 + - - +
763A THR 3.8 0.4 - - - -
764A ASP* 1.3 83.0 - - - +
766A VAL* 1.3 68.4 + - - +
767A MET* 4.3 7.8 - - - +
799A LEU* 5.8 0.4 - - - -
802A GLU* 5.5 0.7 - - - -
12P DOC 5.3 3.3 + - - -
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Residues in contact with VAL 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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593A ILE* 4.2 9.9 - - + -
605A ALA 3.4 3.5 - - - +
606A THR* 3.5 1.7 - - - -
607A LEU* 2.9 49.5 + - + +
735A ILE* 4.4 8.5 - - + -
738A THR* 4.0 29.4 - - + -
739A LYS* 4.5 10.1 - - - +
742A VAL* 5.1 2.5 - - + -
758A VAL* 3.9 24.2 - - + -
760A TYR 3.5 3.1 - - - -
765A SER* 1.3 80.4 - - - +
767A MET* 1.3 64.5 + - - +
768A VAL* 3.9 15.9 - - + -
799A LEU* 5.7 0.7 - - + -
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Residues in contact with MET 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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604A ILE* 3.6 18.4 - - + -
605A ALA 3.5 4.3 - - - -
606A THR* 3.7 32.1 - - + +
758A VAL* 3.4 3.6 - - - -
759A VAL* 2.9 39.4 + - + +
760A TYR* 2.7 46.7 + - + +
761A GLY* 4.0 4.9 - - - -
765A SER* 4.3 9.9 - - - +
766A VAL* 1.3 78.6 - - - +
768A VAL* 1.3 59.4 + - - +
803A LYS* 5.7 0.9 - - - +
805A TYR* 4.7 3.1 - - + -
808A TYR* 3.9 19.7 - - + +
816A TYR* 3.8 22.9 - - + +
12P DOC 4.6 2.9 - - - +
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Residues in contact with VAL 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A PRO 4.2 0.7 - - - +
604A ILE* 3.5 6.0 - - - +
605A ALA* 2.8 44.6 + - - +
607A LEU* 4.5 11.4 - - + -
742A VAL* 3.9 27.8 - - + -
756A ALA* 4.1 6.7 - - + -
757A VAL 3.5 8.5 - - - +
758A VAL* 4.2 6.3 - - + -
766A VAL* 3.9 23.6 - - + -
767A MET* 1.3 74.8 - - - +
769A LYS* 1.3 68.2 + - - +
770A PHE* 3.6 36.4 + - + -
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Residues in contact with LYS 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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600A TYR* 4.2 17.1 - - + -
602A VAL* 3.9 30.3 - - + -
603A PRO 4.4 2.5 - - - +
604A ILE* 3.8 14.5 - - + +
755A ASP 4.3 1.4 - - - +
756A ALA* 3.4 0.9 - - - -
757A VAL* 2.7 61.0 + - - +
759A VAL* 4.0 12.3 - - + +
767A MET 4.1 0.6 + - - -
768A VAL* 1.3 72.5 - - - +
770A PHE* 1.3 66.6 + - - +
771A GLY* 3.9 15.1 - - - +
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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