Contacts of the strand formed by residues 760 - 769 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735B ARG* 4.0 1.1 + - - +
736B TRP* 3.4 8.8 - - - -
737B GLN* 3.2 70.2 + - + -
738B GLY 5.5 0.9 - - - -
757B GLN* 4.1 20.2 - - + +
758B GLU 3.4 15.0 - - - +
759B ASP* 1.3 77.0 + - - +
761B TRP* 1.3 70.2 + - - +
762B LEU* 4.1 14.0 - - + +
787B LYS* 3.9 25.4 - - + +
789B TYR* 3.3 50.7 - + + -
790B TYR 4.6 4.3 + - - -
791B THR* 5.8 0.2 - - - +
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Residues in contact with TRP 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B LEU* 3.5 28.0 - - + -
734B ALA* 4.1 24.0 - - + -
735B ARG 3.5 12.1 - - - -
736B TRP* 3.4 41.2 - + + +
759B ASP* 5.1 2.8 + - - -
760B TYR* 1.3 77.1 - - - +
762B LEU* 1.3 72.0 + - - +
763B VAL* 4.2 10.5 + - + -
785B PHE* 6.1 0.5 - - - +
787B LYS* 3.8 17.8 - - - +
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Residues in contact with LEU 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ARG* 6.3 2.5 - - - -
716B TYR* 5.3 1.2 + - - -
733B GLY 4.6 0.2 - - - -
734B ALA* 3.3 3.5 - - - -
735B ARG* 2.8 54.2 + - + +
760B TYR* 4.1 13.0 + - + +
761B TRP* 1.3 79.9 - - - +
763B VAL* 1.3 61.9 + - - +
764B ASP* 5.2 1.7 - - - +
783B ASN* 3.5 34.5 - - + +
787B LYS* 4.1 2.2 - - + -
789B TYR* 3.3 49.6 - - + +
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Residues in contact with VAL 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B GLY 3.4 10.1 - - - +
734B ALA* 4.4 13.5 - - + -
761B TRP* 5.0 12.3 - - + -
762B LEU* 1.3 77.9 - - - +
764B ASP* 1.3 71.8 + - - +
765B LEU* 4.9 8.3 - - + -
783B ASN* 3.0 10.0 + - - +
784B VAL* 2.8 36.5 + - + +
785B PHE* 3.9 37.2 - - + +
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Residues in contact with ASP 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE* 4.5 7.8 - - + -
191B HIS* 4.0 18.7 - - - -
716B TYR* 3.7 21.6 + - - -
732B GLY* 3.1 4.0 - - - -
733B GLY* 2.9 42.3 + - - +
762B LEU* 4.2 1.7 + - - +
763B VAL* 1.3 75.5 - - - +
765B LEU* 1.3 65.7 + - - +
781B VAL 2.8 21.3 - - - +
782B ASN* 3.3 27.2 - - - +
783B ASN 4.4 1.0 + - - -
784B VAL* 3.7 1.8 - - - -
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Residues in contact with LEU 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE* 5.7 0.6 - - - -
731B GLY 3.6 12.1 - - - +
732B GLY* 4.3 4.0 - - - -
763B VAL* 4.9 8.1 - - + -
764B ASP* 1.3 84.1 - - - +
766B MET* 1.3 63.5 + - - +
780B ASN* 3.6 4.3 + - - +
781B VAL* 2.9 41.4 + - + +
784B VAL* 4.0 27.1 - - + +
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Residues in contact with MET 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ASP* 3.3 39.3 - - + +
180B PHE* 4.4 12.3 - - + -
718B SER* 5.1 2.9 - - - -
729B THR* 4.3 10.1 - - + +
730B VAL* 3.6 5.2 - - - +
731B GLY* 2.7 56.3 + - - +
765B LEU* 1.3 79.1 - - - +
767B ALA* 1.3 81.7 + - - +
768B ARG* 3.6 32.8 - - + +
778B SER* 5.0 5.6 - - - -
779B VAL* 3.4 8.5 - - - +
780B ASN* 3.7 10.3 - - - +
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Residues in contact with ALA 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1817A N8E 4.2 15.8 - - - +
728B LEU* 4.7 3.8 - - + -
729B THR 3.3 11.0 - - - +
730B VAL* 4.6 9.2 - - + -
766B MET* 1.3 80.8 - - - +
768B ARG* 1.4 59.0 + - - +
777B ALA 4.0 0.8 - - - +
778B SER* 3.1 4.3 - - - -
779B VAL* 2.8 52.6 + - + +
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Residues in contact with ARG 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1817A N8E 5.1 0.7 - - - -
175B GLN* 4.0 10.3 - - - +
178B ASP* 4.8 4.2 + - - +
179B ASP* 2.8 36.3 + - - +
720B LYS* 5.9 1.2 - - - +
727B LYS 3.6 1.5 - - - +
728B LEU* 3.2 5.7 - - - +
729B THR* 2.7 63.2 + - - +
766B MET* 3.6 24.0 - - + +
767B ALA* 1.4 71.5 - - - +
769B TYR* 1.3 63.8 + - - +
770B GLN* 5.0 6.5 + - + +
776B SER* 4.1 24.9 - - - -
777B ALA 3.5 6.1 - - - +
778B SER* 3.2 22.8 + - - +
812B ARG* 6.4 0.9 - - - +
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Residues in contact with TYR 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A LEU* 3.8 18.8 - - + +
809A PHE* 3.8 30.7 - + + -
1817A N8E 3.3 66.4 + - + +
725B LEU* 5.6 1.7 - - + -
727B LYS* 3.2 28.0 - - + +
728B LEU* 3.9 26.5 - - + -
768B ARG* 1.3 74.3 - - - +
770B GLN* 1.3 58.6 + - - +
771B ILE* 3.1 31.5 + - + +
776B SER* 4.3 2.0 - - - -
777B ALA* 3.1 30.5 + - - +
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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