Contacts of the strand formed by residues 882 - 889 (chain A) in PDB entry 3HKV
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 882 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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865A TYR* 2.7 29.4 + - - +
869A ARG* 3.3 22.1 + - - -
873A LEU* 6.3 1.1 - - + -
880A PRO* 3.5 15.4 - - - +
881A VAL* 1.3 81.4 - - + +
883A GLN* 1.3 73.1 + - - +
884A VAL* 6.4 0.2 - - + -
947A ARG* 2.7 38.3 + - + -
948A VAL 3.3 6.7 - - - +
949A LEU* 3.9 7.9 - - + +
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Residues in contact with GLN 883 (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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880A PRO* 4.6 14.9 + - + -
882A GLU* 1.3 81.0 - - - +
884A VAL* 1.3 64.7 + - - +
885A LEU* 3.6 16.4 + - + +
922A LYS* 3.2 36.0 + - - +
946A ALA 3.5 0.5 - - - +
947A ARG* 3.6 2.2 - - - -
948A VAL* 2.8 33.8 + - - +
950A THR* 3.1 24.3 + - - +
953A TYR* 4.6 6.1 - - - -
988A PHE* 3.2 34.4 - - - -
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Residues in contact with VAL 884 (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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836A ALA* 6.3 2.5 - - + -
882A GLU* 6.4 0.2 - - + -
883A GLN* 1.3 73.6 - - - +
885A LEU* 1.3 70.0 + - - +
886A TYR* 5.2 10.1 - - + +
922A LYS* 4.7 8.0 + - - +
945A VAL* 3.5 30.3 - - + -
946A ALA 3.3 6.1 - - - +
947A ARG* 4.6 16.2 - - + -
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Residues in contact with LEU 885 (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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883A GLN* 4.0 26.5 - - + +
884A VAL* 1.3 83.1 - - - +
886A TYR* 1.3 68.1 + - - +
920A PHE* 3.6 28.7 - - + -
921A ALA 3.5 4.7 - - - +
922A LYS* 3.6 28.3 - - + +
945A VAL* 3.6 3.3 - - - +
946A ALA* 2.8 35.5 + - - +
948A VAL* 3.6 29.8 - - + -
950A THR* 4.0 7.9 - - + -
988A PHE* 3.8 23.8 - - + -
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Residues in contact with TYR 886 (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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833A VAL 4.9 0.6 + - - -
836A ALA* 3.3 36.0 + - - +
837A PHE* 3.5 16.2 + + - +
840A THR* 3.7 17.3 - - + -
884A VAL* 5.2 7.3 - - + +
885A LEU* 1.3 78.5 - - - +
887A HIS* 1.3 60.3 + - - +
920A PHE* 3.3 8.6 - - - -
921A ALA* 2.8 40.7 + - + +
922A LYS 3.8 9.2 - - - -
924A ALA* 3.6 25.4 - - + -
927A SER* 3.4 23.3 + - - +
943A VAL* 4.0 12.3 - - + -
944A PHE 3.4 11.7 - - - +
945A VAL* 3.9 28.5 - - + +
1002A ILE* 4.7 1.1 - - + -
1025A 3AB 4.1 0.5 - - - +
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Residues in contact with HIS 887 (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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886A TYR* 1.3 74.7 - - - +
888A GLY* 1.3 72.4 + - - +
889A THR* 3.7 14.0 + - - -
897A ILE* 4.4 3.6 - - + -
902A PHE* 3.6 33.4 - + + -
907A CYS* 3.7 13.9 - - - +
908A GLY 5.4 1.2 + - - -
910A ASN* 3.2 30.1 - - - -
918A VAL* 3.9 13.2 - - + +
919A TYR 2.7 19.4 + - - -
920A PHE* 3.8 9.4 - - + -
943A VAL* 3.6 1.7 - - - -
944A PHE* 2.9 38.4 + + + +
946A ALA* 5.8 0.2 - - + -
1025A 3AB 3.5 13.6 + - - -
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Residues in contact with GLY 888 (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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887A HIS* 1.3 78.5 + - - +
889A THR* 1.3 61.9 + - - -
927A SER* 3.6 23.6 - - - -
932A TYR 3.2 10.7 - - - +
933A SER* 4.1 0.7 - - - -
942A ALA 3.6 9.2 - - - -
943A VAL* 4.2 2.9 - - - -
1025A 3AB 2.7 36.9 + - - -
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Residues in contact with THR 889 (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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887A HIS* 3.7 12.9 + - - -
888A GLY* 1.3 75.5 - - - -
890A THR* 1.3 76.7 + - - +
891A ALA 4.1 0.2 + - - -
893A ALA* 3.5 17.5 - - - +
894A VAL* 3.9 11.9 - - + +
897A ILE* 4.0 7.8 - - + +
908A GLY* 4.4 8.0 + - - -
932A TYR 3.2 10.2 + - - -
933A SER* 3.3 18.4 - - - +
934A PRO* 3.8 1.6 - - - +
942A ALA* 3.0 24.0 + - + +
944A PHE* 3.8 29.6 - - + -
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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