Contacts of the strand formed by residues 886 - 892 (chain B) in PDB entry 1HKB
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 CYS 886 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B VAL* 3.6 33.9 - - + -
843B ASP* 3.1 27.6 - - - -
846B ARG* 4.0 10.5 - - - -
854B LEU* 3.2 13.2 - - + +
856B VAL* 5.3 0.4 - - + -
879B VAL* 6.1 0.3 - - - +
880B LYS* 5.5 5.5 - - - +
883B SER* 3.2 17.1 + - - +
884B PRO* 3.3 4.0 - - - +
885B LYS* 1.3 84.9 - - - +
887B ASN* 1.3 59.6 + - - +
888B VAL* 3.6 21.2 + - + +
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Residues in contact with ASN 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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854B LEU 2.7 10.0 + - - -
855B ASN* 3.4 35.3 + - - +
856B VAL 3.2 20.1 + - - +
880B LYS* 6.1 3.0 - - - +
886B CYS* 1.3 71.0 - - - +
888B VAL* 1.3 67.6 + - - +
889B SER* 4.0 7.7 + - - -
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Residues in contact with VAL 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B MET* 5.6 0.4 - - + -
842B VAL* 3.7 30.5 - - + -
856B VAL* 3.1 14.4 - - + +
858B VAL* 3.7 26.7 - - + -
879B VAL* 4.0 19.1 - - + -
886B CYS* 3.6 14.8 + - + +
887B ASN* 1.3 81.2 + - - +
889B SER* 1.3 66.7 + - - +
890B PHE* 3.8 28.2 - - + -
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Residues in contact with SER 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B VAL 3.0 10.9 + - - -
857B THR* 3.0 20.1 - - - +
858B VAL* 2.5 36.7 + - - +
887B ASN* 4.0 8.7 + - - -
888B VAL* 1.3 76.7 - - - +
890B PHE* 1.3 58.8 + - - +
891B LEU 4.0 0.2 - - - -
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Residues in contact with PHE 890 (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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676B LEU* 4.7 2.0 - - + -
838B MET* 4.5 7.9 - - + -
858B VAL* 3.4 35.0 - - + -
860B VAL* 3.9 12.1 - - + -
865B TYR* 3.6 16.8 - - - +
875B MET* 3.9 26.0 - - + -
876B HIS* 3.3 45.9 - + + +
879B VAL* 4.2 16.2 - - + -
888B VAL* 3.8 26.9 - - + -
889B SER* 1.3 77.4 - - - +
891B LEU* 1.3 61.9 + - - +
892B LEU 4.0 1.2 + - - -
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Residues in contact with LEU 891 (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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665B CYS* 3.7 42.1 - - + +
668B GLU* 5.4 5.2 - - + -
669B GLU* 4.1 17.5 - - + +
857B THR* 4.3 11.7 - - - +
858B VAL 2.8 11.3 + - - +
859B GLY* 3.4 2.4 - - - -
860B VAL* 2.9 26.3 + - - +
889B SER 3.9 1.2 + - - -
890B PHE* 1.3 73.4 - - - +
892B LEU* 1.3 67.4 + - - +
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Residues in contact with LEU 892 (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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665B CYS* 4.4 2.1 - - - -
860B VAL* 3.8 13.9 - - - +
861B ASP* 4.6 0.7 - - - -
865B TYR* 3.7 36.6 - - + -
866B LYS* 3.8 39.9 - - + -
890B PHE 4.0 1.6 + - - -
891B LEU* 1.3 83.1 - - - +
893B SER* 1.3 64.6 + - - +
894B GLU* 3.4 27.0 + - + +
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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