Contacts of the strand formed by residues 758 - 764 (chain A) in PDB entry 1OY6
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 758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PRO* 5.2 3.2 - - + +
121A GLU* 6.3 0.8 - - - +
124A GLN* 3.2 60.7 - - + +
125A GLN* 4.4 16.4 - - - +
208A LYS* 5.9 0.3 + - - -
757A SER* 1.3 73.2 + - - +
759A VAL* 1.3 63.4 + - - +
760A ASN* 4.3 13.2 - - - -
761A ASP* 2.6 36.0 + - - -
770A LYS* 3.6 36.1 - - + +
771A VAL 4.0 2.2 - - - -
772A TYR* 3.6 35.9 - + + +
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Residues in contact with VAL 759 (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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124A GLN* 5.2 2.3 + - - -
204A ILE* 3.6 28.5 - - + +
207A ILE* 4.2 17.9 - - + -
208A LYS* 3.5 46.5 + - + +
757A SER* 3.2 9.4 + - - +
758A TYR* 1.3 78.5 - - - +
760A ASN* 1.3 63.4 + - + +
771A VAL* 3.3 17.6 + - + +
772A TYR 4.8 0.7 - - - -
773A VAL* 3.3 36.8 - - + +
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Residues in contact with ASN 760 (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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207A ILE* 4.5 8.3 - - + +
208A LYS* 4.6 10.4 - - + +
211A ASN* 2.7 39.5 + - - +
212A ALA* 4.3 5.8 - - - +
239A ARG* 4.2 13.6 + - - +
758A TYR* 3.9 10.5 - - - -
759A VAL* 1.3 85.7 - - + +
761A ASP* 1.3 86.3 + - - +
770A LYS* 4.1 0.3 - - - -
771A VAL* 3.0 28.7 + - + +
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Residues in contact with ASP 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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211A ASN* 3.4 8.5 + - - +
239A ARG* 3.5 34.1 + - - +
758A TYR* 2.6 33.1 + - - -
760A ASN* 1.3 94.5 + - - +
762A PHE* 1.3 61.4 + - - +
768A VAL* 3.7 12.7 - - + +
769A LYS 2.9 21.7 - - - +
770A LYS* 3.7 5.9 - - - +
771A VAL* 3.8 2.5 - - - -
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Residues in contact with PHE 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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183A ALA* 4.4 0.4 - - - -
184A MET* 3.5 29.8 - - + -
211A ASN* 4.0 2.7 - - - +
239A ARG* 4.3 7.9 - - - -
240A LEU 3.4 14.6 - - - +
241A THR 3.7 11.7 - - - -
246A PHE* 3.9 20.2 - + + -
270A LEU* 4.3 11.2 - - + -
761A ASP* 1.3 76.2 - - - +
763A ILE* 1.3 88.2 + - - +
764A ASP* 3.7 22.7 - - + -
768A VAL* 3.5 4.9 - - - +
769A LYS* 3.1 42.4 + - + -
770A LYS 3.2 26.7 - - - -
771A VAL* 3.7 13.7 - - + -
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Residues in contact with ILE 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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213A GLN* 5.1 6.3 - - - +
239A ARG* 4.1 33.3 - - + +
240A LEU 3.3 12.2 + - - +
241A THR* 3.3 25.3 - - + +
762A PHE* 1.3 95.6 - - - +
764A ASP* 1.3 64.9 + - - +
765A ARG 4.6 1.6 - - - +
766A GLY* 4.3 24.9 - - - +
767A ARG 4.4 1.1 - - - -
768A VAL* 4.1 16.6 - - + -
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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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241A THR* 4.5 6.9 - - - +
270A LEU* 3.6 22.2 - - - +
762A PHE* 3.7 18.9 - - + -
763A ILE* 1.3 77.0 - - - +
765A ARG* 1.3 102.6 + - - +
766A GLY 3.3 0.2 - - - -
767A ARG* 3.3 20.3 + - - +
769A LYS* 2.7 42.3 + - + -
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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