Contacts of the strand formed by residues 862 - 868 (chain A) in PDB entry 3KCK
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 SER 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854A GLN* 5.8 0.7 - - - -
856A GLY 3.4 5.4 - - - -
857A LYS* 3.4 40.0 + - - +
861A GLY* 1.3 74.6 - - - -
863A VAL* 1.3 65.2 + - - +
864A GLU* 4.3 7.8 + - - +
881A VAL 3.6 1.6 - - - +
882A LYS* 3.4 5.1 - - - +
883A LYS* 3.0 52.8 + - - +
885A GLN* 4.4 6.3 - - - +
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Residues in contact with VAL 863 (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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1A 3KC 3.2 64.2 - - + +
854A GLN* 4.0 2.3 - - - +
855A LEU* 2.7 46.5 + - + -
856A GLY 2.8 20.0 + - - +
857A LYS 6.4 0.2 - - - -
861A GLY 5.6 0.2 - - - -
862A SER* 1.3 77.4 - - - +
864A GLU* 1.3 58.2 + - - +
880A ALA* 4.5 6.1 - - + -
881A VAL 3.3 17.9 - - - +
882A LYS* 4.5 6.1 - - + -
929A MET* 4.7 0.2 - - + -
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Residues in contact with GLU 864 (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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851A PHE* 3.5 33.3 - - + +
853A GLN 3.4 11.4 - - - +
854A GLN* 4.9 7.1 - - + +
855A LEU* 3.6 5.6 - - - +
862A SER* 4.6 10.0 + - - +
863A VAL* 1.3 78.8 - - - +
865A MET* 1.3 61.1 + - - +
866A CYS* 3.7 14.8 + - - -
880A ALA* 3.4 2.8 - - - -
881A VAL* 2.8 42.4 + - + +
883A LYS* 3.5 32.4 - - - +
926A LYS* 5.7 0.9 - - - -
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Residues in contact with MET 865 (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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852A LEU* 3.0 55.1 + - + +
853A GLN* 2.7 41.7 + - + +
855A LEU* 3.5 20.3 - - + +
864A GLU* 1.3 70.7 - - - +
866A CYS* 1.3 60.9 + - - +
878A VAL* 3.5 27.6 - - + -
879A VAL 3.5 5.4 - - - +
931A TYR* 4.2 26.9 - - + -
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Residues in contact with CYS 866 (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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849A LEU* 4.0 21.1 - - + -
850A LYS 3.3 16.6 - - - +
851A PHE* 4.0 11.2 - - - -
852A LEU* 3.7 6.7 - - - -
864A GLU* 3.7 17.7 + - - -
865A MET* 1.3 81.5 - - - +
867A ARG* 1.3 58.2 + - - +
868A TYR 4.0 0.2 - - - -
878A VAL* 3.2 5.0 - - - +
879A VAL* 2.7 39.5 + - + +
881A VAL* 3.8 32.8 - - + -
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Residues in contact with ARG 867 (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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848A HIS 3.1 4.2 - - - +
849A LEU* 3.6 0.4 - - - -
850A LYS* 2.9 43.0 + - + +
852A LEU* 3.6 24.3 - - + +
866A CYS* 1.3 74.4 - - - +
868A TYR* 1.3 60.1 + - - +
869A ASP* 3.2 9.9 + - + -
874A ASN* 3.7 44.2 + - - +
875A THR 4.5 1.8 - - - -
876A GLY* 2.9 52.4 + - - +
877A GLU 3.4 3.1 - - - +
878A VAL* 3.6 22.8 - - + +
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Residues in contact with TYR 868 (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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843A GLN 3.5 9.9 + - - -
844A PHE* 3.5 37.9 - + + -
845A GLU* 2.9 59.1 + - - +
848A HIS* 3.6 18.6 + - + -
849A LEU* 3.6 25.8 - - + -
866A CYS 3.9 1.2 + - - -
867A ARG* 1.3 70.5 - - - +
869A ASP* 1.3 57.1 + - - +
870A PRO* 3.2 29.6 - - + +
876A GLY* 3.1 20.0 - - - -
877A GLU* 2.6 22.2 + - + +
879A VAL* 4.4 8.3 - - + +
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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