Contacts of the strand formed by residues 775 - 782 (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 LEU 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770A GLN* 3.5 2.8 + - - -
771A ILE* 3.3 14.9 + - + +
772A THR* 3.2 38.5 + - + +
774A LYS* 1.3 81.2 - - + +
776A SER* 1.3 64.9 + - - +
811A THR* 3.6 28.5 - - + -
812A ARG 3.5 6.3 - - - +
813A TRP* 4.5 18.6 - - + -
1817A N8E 4.6 3.6 - - - +
285B ALA* 3.7 25.4 - - + -
291B TYR* 4.4 20.2 - - + +
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Residues in contact with SER 776 (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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768A ARG* 3.9 18.4 - - - -
769A TYR 3.5 14.8 - - - -
770A GLN* 3.3 27.8 + - - +
771A ILE* 4.4 0.9 - - - +
775A LEU* 1.3 75.3 - - - +
777A ALA* 1.3 60.7 + - - +
778A SER* 4.9 1.6 + - - -
811A THR* 3.0 12.0 - - - +
812A ARG* 3.0 51.9 + - - +
814A ASP* 5.5 0.9 + - - -
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Residues in contact with ALA 777 (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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767A ALA 4.2 0.2 - - - +
768A ARG* 3.4 1.8 - - - -
769A TYR* 2.9 37.8 + - - +
771A ILE* 4.1 7.9 - - + +
776A SER* 1.3 73.1 - - - +
778A SER* 1.3 62.7 + - - +
810A SER 3.5 6.7 - - - +
811A THR* 4.1 4.5 - - + -
1817A N8E 3.6 28.3 - - - +
809B PHE* 3.9 25.0 - - + -
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Residues in contact with SER 778 (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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766A MET* 5.5 2.7 - - - -
767A ALA 3.2 10.5 - - - -
768A ARG* 3.2 30.3 + - - +
776A SER* 4.9 1.9 + - - -
777A ALA* 1.3 73.3 + - - +
779A VAL* 1.3 63.7 + - - +
780A ASN* 4.6 9.0 - - - -
808A MET 4.5 0.4 - - - -
809A PHE* 3.7 7.1 - - - -
810A SER* 3.0 41.9 + - - +
811A THR* 6.0 0.2 - - - -
1817A N8E 4.9 5.9 - - - +
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Residues in contact with VAL 779 (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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766A MET* 3.4 4.8 - - - +
767A ALA* 2.9 50.0 + - + +
778A SER* 1.3 75.8 - - - +
780A ASN* 1.3 77.6 + - - +
781A VAL* 4.2 13.7 - - + -
807A LEU* 4.9 0.9 - - + -
808A MET 3.3 8.3 - - - +
809A PHE* 3.5 36.3 - - + -
1817A N8E 4.9 16.4 - - - +
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Residues in contact with ASN 780 (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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178A ASP 5.3 0.5 - - - +
179A ASP 2.8 28.5 + - - +
180A PHE* 3.2 27.8 + - - +
181A GLY* 4.4 6.3 + - - -
765A LEU 3.7 5.3 + - - +
766A MET* 4.0 9.6 - - - +
778A SER* 4.6 8.8 - - - -
779A VAL* 1.3 81.1 + - - +
781A VAL* 1.3 65.0 + - - +
782A ASN* 4.1 17.5 + - - +
806A ASN 3.7 0.6 - - - +
807A LEU* 3.1 6.9 - - - +
808A MET* 2.8 49.3 + - + +
810A SER* 5.2 2.6 + - - -
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Residues in contact with VAL 781 (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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764A ASP* 3.7 2.4 - - - -
765A LEU* 3.0 43.1 + - + +
779A VAL* 4.2 14.8 - - + -
780A ASN* 1.3 79.2 - - - +
782A ASN* 1.3 64.1 + - - +
784A VAL* 3.9 21.5 - - + +
805A ARG* 4.5 14.8 - - + -
806A ASN 3.5 3.6 - - - +
807A LEU* 4.0 29.8 - - + -
1817A N8E 4.7 16.6 - - + +
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Residues in contact with ASN 782 (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* 5.0 9.1 + - - +
191A HIS* 5.4 1.7 - - - -
764A ASP* 3.1 26.5 - - - +
765A LEU 5.4 0.3 - - - +
780A ASN* 4.4 17.6 + - - +
781A VAL* 1.3 75.7 - - - +
783A ASN* 1.3 73.0 + - + +
784A VAL 3.4 1.6 - - - -
805A ARG* 3.3 3.1 - - - +
806A ASN* 2.8 60.7 + - - +
808A MET* 5.5 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