Contacts of the strand formed by residues 775 - 782 (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 LEU 775 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ALA* 3.5 31.6 - - + -
291A TYR* 4.6 12.8 - - + -
770B GLN* 3.8 2.9 - - - -
771B ILE* 3.2 22.4 + - + +
772B THR* 2.8 45.1 + - + +
774B LYS* 1.3 79.3 - - + +
776B SER* 1.3 60.4 + - - +
811B THR* 4.0 22.0 - - + -
812B ARG 3.5 4.5 - - - +
813B TRP* 3.7 31.4 - - + -
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Residues in contact with SER 776 (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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768B ARG* 4.1 22.3 - - - -
769B TYR 3.4 11.9 - - - -
770B GLN* 3.6 27.9 + - - +
771B ILE* 4.2 2.5 - - - -
775B LEU* 1.3 73.7 - - - +
777B ALA* 1.3 59.9 + - - +
778B SER* 4.9 1.3 + - - -
811B THR* 3.5 7.2 - - - +
812B ARG* 3.0 46.0 + - - +
814B ASP* 5.4 1.1 + - - -
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Residues in contact with ALA 777 (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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809A PHE* 4.4 12.1 - - + -
1817A N8E 3.7 37.7 - - - +
768B ARG* 3.5 1.8 - - - -
769B TYR* 3.1 30.2 + - - +
771B ILE* 4.1 17.0 - - + +
776B SER* 1.3 74.0 - - - +
778B SER* 1.3 63.2 + - - +
810B SER 3.4 5.2 - - - +
811B THR* 4.8 5.8 - - + -
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Residues in contact with SER 778 (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 3.5 14.5 - - - +
179B ASP 5.9 0.4 - - - -
282B GLU* 5.6 0.7 + - - -
766B MET* 5.0 4.9 - - - -
767B ALA 3.1 11.0 - - - -
768B ARG* 3.2 30.4 + - - +
776B SER* 4.9 0.9 + - - -
777B ALA* 1.3 73.6 + - - +
779B VAL* 1.3 61.3 + - - +
780B ASN* 4.6 9.0 - - - -
808B MET 4.4 0.2 - - - -
809B PHE* 3.7 1.2 - - - -
810B SER* 2.8 46.5 + - - +
812B ARG 5.8 0.2 - - - +
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Residues in contact with VAL 779 (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 3.7 23.8 - - - -
765B LEU 4.1 0.2 - - - +
766B MET* 3.4 5.1 - - - +
767B ALA* 2.8 45.2 + - + +
778B SER* 1.3 76.0 - - - +
780B ASN* 1.3 74.9 + - - +
781B VAL* 4.3 13.9 - - + -
807B LEU* 4.6 1.3 - - + -
808B MET 3.3 7.6 - - - +
809B PHE* 3.7 34.3 - - + -
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Residues in contact with ASN 780 (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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178B ASP 5.4 0.5 - - - +
179B ASP 3.0 28.5 + - - +
180B PHE* 3.4 29.6 + - - +
181B GLY* 4.7 3.7 + - - -
765B LEU 3.6 4.6 + - - +
766B MET* 3.7 13.4 - - - +
778B SER* 4.6 7.1 - - - -
779B VAL* 1.3 80.3 + - - +
781B VAL* 1.3 62.7 + - - +
782B ASN* 4.1 15.1 + - - +
806B ASN 3.8 0.5 - - - +
807B LEU* 3.0 7.6 - - - +
808B MET* 2.7 50.3 + - + +
810B SER* 5.7 1.6 - - - -
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Residues in contact with VAL 781 (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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764B ASP* 2.8 22.1 - - - +
765B LEU* 2.9 27.6 + - + +
779B VAL* 4.3 11.4 - - + +
780B ASN* 1.3 76.5 - - - +
782B ASN* 1.3 63.9 + - - +
784B VAL* 4.4 18.6 - - + -
805B ARG* 4.3 20.4 - - + -
806B ASN 3.4 8.1 - - - +
807B LEU* 4.0 26.9 - - + -
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Residues in contact with ASN 782 (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* 5.2 7.8 + - - +
191B HIS* 5.8 1.9 - - - -
764B ASP* 3.3 23.5 - - - +
780B ASN* 4.2 18.4 + - - +
781B VAL* 1.3 80.5 - - - +
783B ASN* 1.3 74.1 + - + +
784B VAL* 3.3 1.3 - - - -
805B ARG* 3.2 1.4 - - - +
806B ASN* 2.7 61.1 + - - +
808B MET* 5.8 4.0 - - - +
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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