Contacts of the strand formed by residues 769 - 773 (chain A) in PDB entry 5EPG
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 MET 769 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760A VAL* 3.2 34.5 - - + -
761A VAL 3.7 2.5 - - - -
762A PRO* 3.6 32.3 - - + -
767A GLN* 3.4 10.7 + - - +
768A GLU* 1.3 77.0 - - - +
770A ASP* 1.3 64.8 + - - +
771A VAL* 4.2 11.2 - - + -
785A VAL* 4.9 0.9 - - + -
789A LEU* 3.6 22.2 - - + -
795A LYS 3.1 8.9 + - - +
796A VAL* 3.6 10.0 - - + -
797A MET* 3.1 24.9 + - - +
822A ALA* 3.9 7.6 - - + +
825A ALA* 3.7 20.0 - - + -
826A ASN* 4.0 22.2 - - - +
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Residues in contact with ASP 770 (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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759A LEU 4.0 1.2 - - - +
760A VAL* 3.6 0.7 - - - +
761A VAL* 2.8 44.3 + - + +
763A LYS* 3.7 28.9 - - - +
768A GLU* 5.3 2.5 - - - +
769A MET* 1.3 77.6 - - - +
771A VAL* 1.3 63.1 + - - +
772A TYR* 3.5 29.7 + - + +
797A MET* 3.5 9.3 - - - +
799A HIS* 3.0 22.2 + - - +
1078A GLU* 4.6 3.8 - - - +
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Residues in contact with VAL 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A MET* 5.3 0.9 - - + -
759A LEU 3.8 2.5 - - - +
760A VAL* 4.1 31.4 - - + -
769A MET* 4.6 2.9 - - + -
770A ASP* 1.3 78.0 - - - +
772A TYR* 1.3 63.2 + - - +
773A VAL* 3.9 13.5 - - + -
781A ILE* 3.8 23.8 - - + -
785A VAL* 4.3 14.1 - - + -
796A VAL* 4.3 18.8 - - + -
797A MET 2.9 14.3 + - - +
798A CYS* 3.4 7.9 - - + -
799A HIS* 2.9 29.0 + - - +
818A ALA* 4.7 7.9 - - + -
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Residues in contact with TYR 772 (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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600A CYS* 3.3 4.9 - - - -
603A MET* 3.3 33.9 - - + -
758A MET* 3.2 3.1 - - - +
759A LEU* 2.7 61.8 + - + +
761A VAL* 4.1 16.8 - - + +
770A ASP* 3.5 38.2 + - + +
771A VAL* 1.3 69.4 - - - +
773A VAL* 1.3 59.3 + - - +
799A HIS* 3.6 36.5 + + + +
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Residues in contact with VAL 773 (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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600A CYS* 3.8 5.1 - - - -
757A SER 3.7 10.3 - - - +
758A MET* 3.7 16.8 - - + -
771A VAL* 3.9 13.7 - - + -
772A TYR* 1.3 76.3 - - - +
774A SER* 1.3 64.2 + - - +
775A THR* 3.2 10.6 + - + +
781A ILE* 4.1 8.1 - - + -
798A CYS* 3.4 32.1 - - - -
799A HIS 3.7 4.7 + - - +
800A VAL* 3.0 30.5 - - - +
814A THR* 3.6 31.6 - - + -
818A ALA* 5.2 0.2 - - + -
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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