Contacts of the strand formed by residues 760 - 769 (chain A) in PDB entry 2W77
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 TYR 760 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735A ARG* 3.9 2.8 - - + +
736A TRP* 3.3 10.4 - - - -
737A GLN* 3.1 68.6 + - + -
738A GLY 5.3 1.3 - - - -
757A GLN* 3.6 23.8 - - + +
758A GLU 3.5 14.4 - - - +
759A ASP* 1.3 76.9 - - - +
761A TRP* 1.3 69.2 + - - +
762A LEU* 4.1 18.3 - - + +
787A LYS* 3.6 25.8 - - + +
789A TYR* 3.3 46.0 - + + -
790A TYR 4.5 4.0 + - - -
791A THR* 5.8 0.2 - - - +
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Residues in contact with TRP 761 (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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713A LEU* 3.8 27.1 - - + -
734A ALA* 4.0 25.4 - - + -
735A ARG 3.4 10.1 - - - -
736A TRP* 3.5 42.6 - + + +
759A ASP* 5.6 0.9 + - - -
760A TYR* 1.3 75.2 - - - +
762A LEU* 1.3 73.0 + - - +
763A VAL* 4.4 10.0 + - + -
785A PHE* 6.5 0.4 - - + -
787A LYS* 3.9 17.4 - - - +
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Residues in contact with LEU 762 (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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716A TYR* 5.1 2.6 + - - +
734A ALA* 3.1 4.2 - - - +
735A ARG* 2.8 56.8 + - + +
760A TYR* 4.1 15.0 + - + +
761A TRP* 1.3 81.6 - - - +
763A VAL* 1.3 62.6 + - - +
764A ASP* 4.2 3.6 + - - +
783A ASN* 3.2 37.0 - - + +
787A LYS* 4.2 3.8 - - + -
789A TYR* 3.6 44.9 - - + +
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Residues in contact with VAL 763 (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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733A GLY 3.3 7.9 - - - +
734A ALA* 4.4 13.2 - - + -
761A TRP* 4.2 13.2 - - + -
762A LEU* 1.3 77.6 - - - +
764A ASP* 1.3 70.3 + - - +
765A LEU* 4.8 8.1 - - + -
783A ASN* 3.2 10.4 + - - +
784A VAL* 2.9 42.7 + - + +
785A PHE* 4.1 34.4 - - + +
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Residues in contact with ASP 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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180A PHE* 4.8 9.7 - - + -
191A HIS* 3.4 29.5 + - - -
716A TYR* 3.6 18.9 + - + -
732A GLY* 3.1 3.2 - - - -
733A GLY 2.6 39.2 + - - +
762A LEU* 4.2 3.4 + - - +
763A VAL* 1.3 75.4 - - - +
765A LEU* 1.3 69.0 + - - +
781A VAL 3.7 2.0 - - - -
782A ASN* 3.1 28.0 - - - +
783A ASN* 3.2 19.8 + - - -
784A VAL* 4.6 0.2 - - - -
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Residues in contact with LEU 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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180A PHE* 5.7 0.4 - - - -
731A GLY 3.4 11.7 - - - +
732A GLY* 4.0 6.1 - - - -
763A VAL* 4.8 8.1 - - + -
764A ASP* 1.3 82.8 - - - +
766A MET* 1.3 64.6 - - - +
780A ASN* 3.7 4.2 + - - +
781A VAL* 3.0 40.3 + - + +
782A ASN* 5.4 0.2 - - - +
784A VAL* 3.8 28.2 - - + +
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Residues in contact with MET 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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179A ASP* 3.3 38.8 - - + +
180A PHE* 4.4 11.2 - - + -
718A SER* 4.7 4.5 - - - -
729A THR* 4.1 6.3 - - + +
730A VAL* 3.6 7.2 - - - +
731A GLY* 2.8 56.0 + - - +
765A LEU* 1.3 79.3 - - - +
767A ALA* 1.3 66.7 + - - +
768A ARG* 3.7 48.2 - - + +
778A SER* 5.5 2.5 - - - +
779A VAL* 3.4 11.2 - - - +
780A ASN* 4.0 8.7 - - - +
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Residues in contact with ALA 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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728A LEU* 4.9 7.0 - - + -
729A THR 3.3 10.5 - - - +
730A VAL* 4.2 13.0 - - + -
766A MET* 1.3 80.6 - - - +
768A ARG* 1.3 60.2 + - - +
777A ALA 4.2 0.2 - - - +
778A SER* 3.2 3.8 - - - -
779A VAL* 2.9 47.6 + - + +
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Residues in contact with ARG 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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175A GLN* 3.8 13.2 - - - +
178A ASP* 4.4 7.1 + - - +
179A ASP* 2.6 42.6 + - - +
727A LYS 4.3 0.7 - - - -
728A LEU* 3.5 7.2 - - - +
729A THR* 2.8 59.1 + - - +
766A MET* 3.7 9.4 - - + +
767A ALA* 1.3 74.5 - - - +
769A TYR* 1.3 64.9 + - - +
770A GLN* 4.8 6.9 + - - +
776A SER* 3.9 24.7 - - - +
777A ALA 3.4 7.2 - - - +
778A SER* 3.2 23.8 + - - +
812A ARG* 6.4 0.7 - - - +
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Residues in contact with TYR 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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724A ALA 5.6 1.4 + - - -
725A LEU* 5.9 3.8 - - + -
727A LYS* 3.2 35.5 - - + +
728A LEU* 3.9 26.2 - - + -
768A ARG* 1.3 75.5 - - - +
770A GLN* 1.3 63.8 + - - +
771A ILE* 3.1 30.4 + - + +
776A SER* 3.5 2.6 - - - -
777A ALA 2.9 31.8 + - - +
287B SER* 5.3 2.2 + - - -
807B LEU* 3.7 36.7 - - + +
809B PHE* 3.8 33.7 - + + -
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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