Contacts of the strand formed by residues 763 - 767 (chain C) in PDB entry 4AY6
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 ASN 763 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707C LYS* 6.0 0.2 - - - +
708C LYS 5.0 1.4 - - - +
743C ILE* 3.4 23.7 - - + +
744C VAL 3.3 13.7 - - - +
745C LYS* 4.2 12.3 - - + -
746C MET* 3.7 19.1 - - - +
762C LEU* 1.3 111.4 + - - +
764C MET* 1.3 63.1 + - - +
765C PRO* 3.6 14.7 - - - +
988C TRP* 5.7 0.9 + - - -
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Residues in contact with MET 764 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C LYS* 4.2 23.6 - - + +
709C ALA* 4.7 0.7 - - - -
710C VAL* 3.4 28.7 - - + +
719C ILE* 4.4 16.2 - - + +
721C ASP* 3.8 32.1 - - + -
743C ILE* 4.8 0.2 - - - -
744C VAL* 2.8 46.9 + - + +
746C MET* 4.4 16.9 - - + +
763C ASN* 1.3 74.2 - - - +
765C PRO* 1.3 77.3 - - + +
766C VAL* 3.4 11.1 - - - +
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Residues in contact with PRO 765 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C LYS 3.5 19.1 - - - +
709C ALA* 3.4 6.2 - - + -
710C VAL* 3.0 24.8 + - - +
731C LEU* 6.1 0.2 - - + -
735C LEU* 3.6 33.4 - - + -
741C VAL* 4.1 4.9 - - + -
742C LYS 3.6 7.4 - - - +
743C ILE* 3.8 21.5 - - + -
763C ASN* 3.6 14.6 - - - +
764C MET* 1.3 86.5 - - - +
766C VAL* 1.3 60.3 + - - +
767C ILE* 4.3 0.7 - - - -
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Residues in contact with VAL 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C VAL* 3.3 23.8 - - + +
711C ILE 4.8 0.2 - - - -
712C ASP* 3.8 29.6 - - + +
719C ILE* 4.7 15.5 - - + -
741C VAL* 3.8 3.5 - - - +
742C LYS* 2.8 42.5 + - + +
744C VAL* 3.8 21.8 - - + -
764C MET* 3.4 15.5 - - + +
765C PRO* 1.3 80.0 - - - +
767C ILE* 1.3 65.2 + - - +
768C PRO* 3.6 4.2 - - + +
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Residues in contact with ILE 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C ALA* 5.5 2.0 - - + -
710C VAL 2.8 14.2 + - - +
711C ILE* 3.5 12.7 - - + +
712C ASP* 2.9 26.2 + - - +
726C LEU* 3.7 30.5 - - + -
734C PHE* 4.5 4.7 - - + -
735C LEU* 3.9 17.7 - - + -
738C LEU* 3.8 29.6 - - + -
741C VAL* 5.0 4.7 - - + -
765C PRO 4.3 0.2 - - - -
766C VAL* 1.3 73.2 - - - +
768C PRO* 1.3 82.9 - - + +
770C ASN* 6.0 0.2 - - + -
772C ILE* 4.4 16.8 - - + -
773C ALA* 4.3 13.2 - - + -
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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