Contacts of the strand formed by residues 757 - 762 (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 SER 757 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A CYS* 3.5 18.1 - - - -
601A ASP* 4.5 9.7 - - - +
754A GLU* 4.2 10.9 - - - +
755A THR* 2.6 24.9 + - - -
756A GLN* 1.3 75.6 + - - +
758A MET* 1.3 66.9 + - - +
773A VAL* 3.9 2.9 - - - +
774A SER* 3.1 29.7 + - - +
834A CYS 3.5 6.7 - - - -
835A VAL* 3.8 21.4 - - - +
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Residues in contact with MET 758 (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* 3.6 5.3 - - - -
756A GLN* 5.1 2.9 - - - +
757A SER* 1.3 85.0 - - - +
759A LEU* 1.3 60.7 + - - +
760A VAL* 4.6 4.0 - - + -
771A VAL* 5.3 0.7 - - + -
772A TYR 3.2 13.2 - - - +
773A VAL* 3.7 10.1 - - + -
814A THR* 3.7 30.7 - - + +
817A ILE* 3.4 28.7 - - + +
818A ALA* 3.2 37.7 - - - -
821A THR* 4.3 11.4 - - + -
833A ARG* 3.4 9.6 - - - +
834A CYS* 2.9 46.0 + - + +
835A VAL* 4.7 1.0 - - - +
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Residues in contact with LEU 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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600A CYS* 4.2 0.6 - - - -
603A MET* 4.1 29.4 - - + -
606A VAL* 3.8 18.4 - - + -
609A GLU* 3.6 22.7 - - - +
758A MET* 1.3 74.6 - - - +
760A VAL* 1.3 62.4 + - - +
761A VAL* 3.7 25.6 - - + -
771A VAL* 3.8 1.0 - - - -
772A TYR* 2.7 49.0 + - + +
831A ALA* 4.5 4.5 - - + -
832A VAL 3.6 15.9 - - - +
833A ARG* 3.8 27.4 - - + +
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Residues in contact with VAL 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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758A MET* 4.6 7.0 - - + -
759A LEU* 1.3 76.1 - - - +
761A VAL* 1.3 60.0 + - - +
762A PRO* 3.9 1.4 - - - +
769A MET* 3.2 30.7 - - + -
770A ASP 3.6 2.7 - - - +
771A VAL* 4.1 27.6 - - + -
818A ALA 4.3 4.7 - - - +
821A THR* 3.2 34.5 - - + -
822A ALA* 3.7 20.4 - - + +
825A ALA* 4.1 3.4 - - + +
831A ALA* 3.2 4.7 - - - +
832A VAL 2.9 30.5 + - - +
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Residues in contact with VAL 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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606A VAL* 4.2 10.5 - - + -
759A LEU* 3.7 25.8 - - + -
760A VAL* 1.3 73.6 - - - +
762A PRO* 1.4 71.8 - - + +
763A LYS* 3.6 4.9 + - + -
769A MET* 4.2 2.2 - - - -
770A ASP* 2.8 46.3 + - + +
772A TYR* 4.1 17.3 - - + +
831A ALA* 3.5 22.7 - - + -
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Residues in contact with PRO 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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760A VAL 3.9 1.6 - - - +
761A VAL* 1.4 90.9 - - + +
763A LYS* 1.3 64.9 + - - +
764A GLY* 4.6 4.7 - - - +
767A GLN 6.4 0.2 - - - -
768A GLU 3.5 7.9 - - - +
769A MET* 3.6 27.1 - - + -
825A ALA 4.1 7.0 - - - +
826A ASN* 5.0 2.7 - - - -
829A GLY* 4.2 7.6 - - - -
830A ARG 3.4 44.6 - - - +
831A ALA* 3.8 2.2 - - - +
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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