Contacts of the strand formed by residues 758 - 762 (chain A) in PDB entry 6S1M
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 758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A THR* 4.4 13.5 - - - -
601A LEU 3.5 6.1 - - - -
602A ASP* 3.7 15.5 - - - -
728A ILE* 4.1 4.0 - - - +
754A GLY* 3.3 20.8 - - - -
755A ASP* 3.4 15.1 + - - +
757A ASP* 1.3 89.8 + - - +
759A VAL* 1.3 69.4 + - - +
760A MET* 5.0 10.4 - - - +
25P DOC 5.0 6.1 + - - -
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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
----------------------------------------------------------
587A ILE* 5.2 4.7 - - + -
599A ALA 3.6 2.1 - - - +
600A THR* 3.4 3.2 - - - -
601A LEU* 2.9 43.0 + - + +
603A PHE* 6.3 0.9 - - + -
728A ILE* 4.6 13.7 - - + +
731A THR* 3.7 33.7 - - + -
732A LYS* 5.0 5.2 - - + +
735A VAL* 5.1 7.9 - - + -
751A VAL* 4.3 19.3 - - + -
753A TYR 3.8 6.3 - - - +
754A GLY* 5.0 2.2 - - - -
758A SER* 1.3 80.6 - - - +
760A MET* 1.3 63.4 + - - +
761A CYS* 4.2 16.8 - - + +
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Residues in contact with MET 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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598A ILE* 3.6 13.2 - - + -
599A ALA 3.6 5.8 - - - -
600A THR* 4.1 25.1 - - + +
751A VAL* 4.6 0.2 - - - -
752A VAL* 3.3 31.0 + - + +
753A TYR* 2.9 35.0 + - + +
754A GLY* 5.8 0.4 - - - -
758A SER* 5.0 10.1 - - - +
759A VAL* 1.3 76.3 - - - +
761A CYS* 1.3 60.9 + - - +
798A TYR* 4.5 9.6 - - + -
801A TYR* 2.8 32.1 - - - -
809A TYR* 3.4 37.7 - - + +
25P DOC 5.7 0.2 - - - +
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Residues in contact with CYS 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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598A ILE* 3.4 1.7 - - - +
599A ALA* 2.9 35.6 + - - +
601A LEU* 5.5 4.3 - - + -
735A VAL* 3.7 29.4 - - + -
736A GLU* 6.0 0.2 - - - -
749A ALA* 3.7 27.6 - - - -
750A LYS 4.6 3.8 - - - -
751A VAL* 4.4 15.9 - - + +
759A VAL* 3.7 6.8 - - + -
760A MET* 1.3 72.5 - - - +
762A ARG* 1.3 65.6 + - - +
763A PHE* 3.9 22.4 + - + -
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Residues in contact with ARG 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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590A LEU* 6.0 2.2 - - - +
594A TYR* 3.4 40.6 + - - -
596A VAL* 3.8 21.6 - - + +
597A PRO 4.1 7.2 - - - +
598A ILE* 3.7 23.6 - - + -
748A SER 5.8 1.8 + - - -
749A ALA* 3.4 3.8 - - - +
750A LYS* 3.3 51.0 + - - +
752A VAL* 3.9 9.0 - - + +
760A MET 3.8 0.8 + - - -
761A CYS* 1.3 73.0 - - - +
763A PHE* 1.3 64.9 + - - +
764A GLY* 4.7 8.1 - - - +
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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