Contacts of the strand formed by residues 886 - 892 (chain A) in PDB entry 1HKC
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A VAL* 3.7 44.0 - - + -
843A ASP* 3.2 27.6 - - - -
846A ARG* 3.9 11.4 - - - -
853A ARG* 5.1 1.6 - - - -
854A LEU* 3.3 10.8 - - + +
856A VAL* 5.3 0.9 - - + -
880A LYS* 5.7 3.1 - - - +
883A SER* 3.2 19.8 + - - +
884A PRO* 3.0 5.6 - - - +
885A LYS* 1.3 83.4 - - - +
887A ASN* 1.3 61.1 + - - +
888A VAL* 3.6 11.0 + - + +
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Residues in contact with ASN 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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853A ARG* 3.1 30.8 - - - +
854A LEU 2.5 9.2 + - - +
855A ASN* 3.1 23.4 + - - +
856A VAL 3.1 21.0 + - - +
886A CYS* 1.3 70.3 - - - +
888A VAL* 1.3 64.7 + - - +
889A SER* 4.0 6.9 + - - -
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Residues in contact with VAL 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A VAL* 4.2 11.7 - - + -
856A VAL* 3.0 18.6 - - + +
858A VAL* 4.0 15.5 - - + -
879A VAL* 3.7 28.0 - - + +
880A LYS* 5.8 1.1 - - - +
883A SER 5.3 0.4 - - - +
886A CYS* 3.7 16.1 + - + +
887A ASN* 1.3 77.1 + - - +
889A SER* 1.3 63.0 + - - +
890A PHE* 3.2 39.1 + - + -
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Residues in contact with SER 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A VAL 2.8 10.1 + - - -
857A THR* 3.0 25.8 + - - +
858A VAL* 2.5 35.0 + - - +
887A ASN* 4.2 8.7 + - - -
888A VAL* 1.3 77.1 + - - +
890A PHE* 1.3 58.6 + - - +
891A LEU* 5.5 3.8 - - - -
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Residues in contact with PHE 890 (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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676A LEU* 4.7 0.7 - - + -
838A MET* 4.0 13.0 - - + -
858A VAL* 3.5 27.1 - - + -
860A VAL* 3.9 14.8 - - + -
865A TYR* 3.6 9.5 + - + +
875A MET* 3.7 30.1 - - + -
876A HIS* 3.2 49.3 - + + +
879A VAL* 3.9 20.0 - - + -
888A VAL* 3.2 32.3 - - + -
889A SER* 1.3 72.9 - - - +
891A LEU* 1.3 68.4 + - - +
892A LEU 4.3 0.4 + - - -
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Residues in contact with LEU 891 (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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665A CYS* 4.1 12.6 - - - -
668A GLU* 6.4 0.9 - - + -
669A GLU* 3.7 25.6 - - + -
857A THR* 3.7 23.1 - - + -
858A VAL 2.8 12.7 + - - +
859A GLY* 3.4 1.0 - - - -
860A VAL* 2.9 26.0 + - - +
889A SER* 5.2 4.0 - - - -
890A PHE* 1.3 81.3 - - - +
892A LEU* 1.3 65.5 + - - +
893A SER* 3.0 5.8 + - - +
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Residues in contact with LEU 892 (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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860A VAL* 3.3 17.4 - - + +
861A ASP* 4.2 13.5 - - - +
865A TYR* 4.1 27.7 + - + -
866A LYS* 3.9 30.7 - - + -
890A PHE 4.3 0.6 + - - -
891A LEU* 1.3 72.7 - - - +
893A SER* 1.3 58.8 + - - +
894A GLU* 3.9 29.5 + - + +
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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