Contacts of the strand formed by residues 883 - 889 (chain B) 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 GLN 883 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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880B PRO* 4.8 13.7 + - + +
881B VAL 5.5 0.2 - - - -
882B GLU* 1.3 81.2 - - - +
884B VAL* 1.3 65.1 + - - +
885B LEU* 3.6 13.9 + - + -
922B LYS* 2.9 40.6 + - - +
946B ALA 3.5 0.3 - - - +
947B ARG* 3.7 1.4 - - - -
948B VAL* 2.9 35.4 + - - +
950B THR* 2.9 26.6 + - - +
953B TYR* 4.5 6.5 - - - -
988B PHE* 3.3 34.3 - - - -
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Residues in contact with VAL 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882B GLU* 6.4 0.4 - - + -
883B GLN* 1.3 73.2 - - - +
885B LEU* 1.3 70.9 + - - +
886B TYR* 5.1 10.3 - - + +
922B LYS* 4.8 9.6 + - - +
945B VAL* 3.5 29.2 - - + -
946B ALA 3.3 8.1 - - - +
947B ARG* 4.6 14.8 - - + -
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Residues in contact with LEU 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883B GLN* 4.1 17.0 - - + +
884B VAL* 1.3 83.9 - - - +
886B TYR* 1.3 67.6 + - - +
920B PHE* 3.6 28.9 - - + -
921B ALA 3.4 4.9 - - - +
922B LYS* 3.6 38.6 - - + +
945B VAL* 3.6 4.0 - - - +
946B ALA* 2.9 33.8 + - - +
948B VAL* 3.8 25.1 - - + -
950B THR* 4.1 11.2 - - + -
988B PHE* 3.8 25.4 - - + -
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Residues in contact with TYR 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 3AB 3.9 0.3 - - - +
833B VAL 4.9 0.7 + - - -
836B ALA* 3.4 15.9 + - - +
837B PHE* 3.4 39.5 + + + -
840B THR* 3.8 13.6 - - + +
884B VAL* 5.1 8.0 - - + +
885B LEU* 1.3 77.9 - - - +
887B HIS* 1.3 60.4 + - - +
920B PHE* 3.4 7.5 - - - -
921B ALA 2.8 40.3 + - - +
922B LYS 3.6 15.3 - - - -
924B ALA* 3.5 21.3 - - + +
927B SER* 3.3 24.5 + - - +
943B VAL* 4.0 10.8 - - + -
944B PHE 3.4 11.7 - - - +
945B VAL* 3.7 30.9 - - + +
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Residues in contact with HIS 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 3AB 3.5 16.6 + - - -
886B TYR* 1.3 75.6 - - - +
888B GLY* 1.3 67.7 + - - +
889B THR* 3.8 14.2 + - - -
897B ILE* 4.5 2.0 - - + -
902B PHE* 3.5 26.7 - + + -
907B CYS* 3.7 24.1 - - + +
908B GLY 5.1 3.3 + - - -
918B VAL* 3.9 18.6 - - + +
919B TYR* 2.7 28.5 + - + -
920B PHE* 3.8 17.5 - + + -
943B VAL* 3.6 2.6 - - - -
944B PHE* 2.9 40.3 + + + +
946B ALA* 5.9 0.4 - - + +
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Residues in contact with GLY 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B 3AB 2.7 34.8 + - - -
887B HIS* 1.3 81.0 + - - +
889B THR* 1.3 59.5 + - - -
927B SER* 3.6 22.7 - - - -
932B TYR 3.1 11.4 - - - +
933B SER* 4.0 0.9 - - - -
942B ALA 3.5 9.4 - - - -
943B VAL* 4.3 2.0 - - - -
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Residues in contact with THR 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887B HIS* 4.0 14.7 + - - -
888B GLY* 1.3 75.0 - - - -
890B THR* 1.3 76.6 + - - +
893B ALA* 3.3 18.8 - - + +
894B VAL* 4.0 10.3 - - + -
897B ILE* 3.9 8.8 - - + +
906B PHE 4.9 0.2 + - - -
907B CYS* 4.9 5.0 - - - -
908B GLY 5.2 2.8 + - - -
932B TYR 3.2 10.4 + - - -
933B SER* 3.4 16.3 - - - +
934B PRO* 3.9 1.4 - - - +
942B ALA* 3.2 18.3 + - + +
944B PHE* 3.8 30.1 - - + -
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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