Contacts of the strand formed by residues 762 - 767 (chain A) in PDB entry 5KZW
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 GLU 762 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A VAL* 4.0 2.8 - - - +
760A LYS* 3.5 21.8 - - + +
761A ALA* 1.3 82.0 - - - +
763A VAL* 1.3 64.8 + - - +
764A THR* 5.6 0.3 + - - -
806A THR* 3.7 24.5 - - + +
807A LEU 3.2 16.6 - - - +
808A PRO* 4.5 1.8 - - + -
809A ALA* 3.7 7.1 + - - +
1018A EDO 4.2 14.1 + - - +
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Residues in contact with VAL 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A THR* 3.8 33.4 - - + +
754A PRO 3.5 21.5 - - - +
755A VAL* 4.0 10.8 - - + -
756A LEU 5.7 0.2 - - - +
762A GLU* 1.3 78.1 - - - +
764A THR* 1.3 70.3 + - - +
805A VAL 3.8 0.5 - - - +
806A THR* 3.4 2.3 - - - -
807A LEU* 2.7 43.6 + - + +
809A ALA* 4.0 5.2 - - + -
815A ASN* 4.0 19.1 - - - +
1018A EDO 3.8 13.0 - - - +
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Residues in contact with THR 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A THR* 4.7 0.3 - - - +
762A GLU* 5.6 0.7 + - - +
763A VAL* 1.3 79.6 - - - +
765A GLY* 1.3 60.3 + - - +
804A TRP* 4.0 34.8 - - + -
805A VAL 3.3 12.1 - - - +
806A THR* 2.6 28.6 + - - +
1018A EDO 3.1 29.5 + - - -
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Residues in contact with GLY 765 (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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743A GLN* 3.5 21.3 - - - -
753A THR* 3.9 11.0 - - - +
763A VAL 4.1 0.6 - - - -
764A THR* 1.3 74.1 - - - +
766A TYR* 1.3 62.7 + - - -
767A PHE* 3.6 7.4 - - - -
804A TRP* 3.3 8.9 - - - -
805A VAL 2.9 33.7 + - - +
807A LEU* 5.1 0.4 - - - +
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Residues in contact with TYR 766 (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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727A LEU* 3.7 7.8 - - + +
734A ASP* 2.5 35.2 + - - -
736A SER* 3.5 23.3 + - - -
737A THR* 3.9 22.9 - - + -
740A VAL* 4.1 9.2 - - + -
743A GLN* 2.8 33.3 + - - +
751A LEU* 3.8 2.6 - - - +
765A GLY* 1.3 71.7 - - - -
767A PHE* 1.3 59.8 + - - +
768A PRO* 3.7 27.4 - - + +
802A GLY* 3.2 16.7 + - - -
803A GLN* 3.4 30.5 - - - -
804A TRP* 3.3 42.3 - + + -
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Residues in contact with PHE 767 (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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751A LEU* 3.8 20.0 - - + -
753A THR* 4.5 6.3 - - - -
765A GLY 3.6 17.3 - - - -
766A TYR* 1.3 77.9 - - - +
768A PRO* 1.4 63.9 - - - +
772A TRP* 3.7 25.4 - + + -
798A ILE* 3.5 32.5 - - + -
800A SER* 2.6 39.1 + - - +
803A GLN 2.9 23.4 + - - +
805A VAL* 3.8 18.2 - - + -
807A LEU* 3.8 23.3 - - + -
817A HIS* 3.8 26.5 - + - -
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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