Contacts of the helix formed by residues 888 - 904 (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 THR 888 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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886A HIS* 3.1 11.7 + - + +
887A SER* 1.3 82.5 - - - +
889A GLU* 1.3 65.5 + - - +
890A GLU* 3.2 5.3 + - - +
891A HIS* 3.3 28.2 + - - -
892A LEU* 3.1 20.1 + - - +
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Residues in contact with GLU 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 SER 3.8 0.6 + - - -
888A THR* 1.3 73.8 - - - +
890A GLU* 1.3 59.9 + - + +
892A LEU* 3.9 8.0 - - - +
893A ARG* 3.0 29.3 + - - +
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Residues in contact with GLU 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A THR* 3.2 6.2 + - - +
889A GLU* 1.3 79.2 - - + +
891A HIS* 1.3 75.2 + - - +
893A ARG* 3.4 9.6 + - + +
894A ASP* 3.1 43.6 + - - +
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Residues in contact with HIS 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A LEU* 3.9 24.0 - - + +
886A HIS* 4.1 18.6 + + - +
888A THR* 3.3 23.1 + - - +
890A GLU* 1.3 89.9 + - - +
892A LEU* 1.3 59.9 + - - +
894A ASP* 3.3 12.5 + - + +
895A PHE* 2.9 30.0 + - - +
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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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884A LEU* 3.5 16.3 - - + +
887A SER* 3.4 42.0 - - - +
888A THR 3.1 10.6 + - - +
889A GLU* 3.9 8.3 - - - +
891A HIS* 1.3 73.8 - - - +
893A ARG* 1.3 58.9 + - - +
895A PHE* 3.3 4.3 + - + +
896A GLU* 2.8 47.2 + - - +
922A ARG* 5.5 1.3 - - - +
923A ARG* 4.2 21.5 - - - +
924A ASN* 4.1 9.0 - - - +
925A LEU* 4.8 11.4 - - + -
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Residues in contact with ARG 893 (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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889A GLU 3.0 19.3 + - - +
890A GLU* 3.5 10.1 - - + +
892A LEU* 1.3 77.8 - - - +
894A ASP* 1.3 59.1 + - - +
896A GLU* 3.7 6.0 + - + +
897A ARG* 3.2 52.8 + - - +
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Residues in contact with ASP 894 (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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890A GLU* 3.1 34.4 + - - +
891A HIS* 3.7 15.4 - - + +
892A LEU 3.3 0.4 - - - -
893A ARG* 1.3 74.7 - - - +
895A PHE* 1.3 60.1 + - - +
897A ARG* 3.2 23.8 + - - +
898A GLU* 2.9 27.4 + - - +
996A GLY* 5.1 12.8 - - - +
999A LYS* 4.8 11.9 + - - -
1008A PTR 5.5 0.3 + - - -
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Residues in contact with PHE 895 (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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882A LYS* 3.4 52.5 - - + -
883A LYS* 4.3 6.3 - - - -
884A LEU* 3.9 27.1 - - + -
891A HIS 2.9 16.9 + - - +
892A LEU* 3.5 7.9 - - + +
894A ASP* 1.3 73.5 - - - +
896A GLU* 1.3 60.5 + - - +
898A GLU* 3.2 15.7 + - - +
899A ILE* 2.8 50.1 + - + +
924A ASN* 6.2 0.7 - - - -
925A LEU* 3.6 35.0 - - + -
927A LEU* 3.7 24.2 - - + -
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Residues in contact with GLU 896 (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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892A LEU* 2.8 26.0 + - - +
893A ARG* 3.9 7.0 - - + +
895A PHE* 1.3 76.6 - - - +
897A ARG* 1.3 63.1 + - - +
899A ILE* 3.4 11.1 + - + +
900A GLU* 3.1 29.7 + - + +
918A TYR* 5.2 3.5 + - - -
923A ARG* 3.3 35.2 + - - -
925A LEU* 3.7 24.1 - - - +
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Residues in contact with ARG 897 (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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893A ARG* 3.2 45.6 + - - +
894A ASP* 3.6 23.6 + - - +
895A PHE 3.1 0.6 - - - -
896A GLU* 1.3 75.8 - - - +
898A GLU* 1.3 66.7 + - - +
900A GLU* 3.2 8.3 + - + +
901A ILE* 2.9 38.5 + - + +
998A THR 6.1 0.4 - - - +
999A LYS* 5.1 3.0 - - - +
1000A VAL* 6.0 5.2 - - - -
1008A PTR 2.6 39.2 + - - -
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Residues in contact with GLU 898 (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 2.2 45.2 + - - +
882A LYS* 2.9 31.3 + - - +
894A ASP 2.9 13.9 + - - +
895A PHE* 3.4 14.8 - - + +
897A ARG* 1.3 75.8 - - - +
899A ILE* 1.4 64.4 + - - +
901A ILE* 3.7 10.9 - - - +
902A LEU* 3.0 23.7 + - + +
927A LEU* 4.3 8.4 - - + +
994A ASP 4.8 0.2 - - - -
995A PHE* 3.8 11.9 - - + +
996A GLY* 3.3 28.3 + - - +
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Residues in contact with ILE 899 (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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895A PHE* 2.8 41.9 + - + +
896A GLU* 3.6 8.3 - - + +
898A GLU* 1.4 73.2 - - - +
900A GLU* 1.3 65.0 + - - +
902A LEU* 3.9 3.7 - - - +
903A LYS* 3.0 33.2 + - - +
913A TYR* 3.9 12.8 - - + -
916A VAL* 3.7 32.1 - - + -
925A LEU* 3.6 33.2 - - + -
927A LEU* 4.2 23.8 - - + -
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Residues in contact with GLU 900 (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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896A GLU* 3.1 22.1 + - + +
897A ARG* 3.8 9.9 - - + +
899A ILE* 1.3 77.6 - - - +
901A ILE* 1.3 62.1 + - + +
903A LYS* 3.4 36.9 + - - +
904A SER* 3.1 23.2 + - - -
972A TYR* 5.2 0.4 - - - -
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Residues in contact with ILE 901 (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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897A ARG* 2.9 39.0 + - + +
898A GLU* 3.3 8.0 + - - +
900A GLU* 1.3 69.9 - - + +
902A LEU* 1.3 65.8 + - - +
904A SER* 2.8 23.8 + - - -
905A LEU* 3.4 20.0 - - + +
972A TYR* 3.7 39.7 - - + +
995A PHE* 4.2 18.2 - - + +
998A THR* 3.9 35.2 - - + +
1000A VAL* 4.8 11.7 - - + -
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Residues in contact with LEU 902 (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 4.1 11.7 - - - +
898A GLU 3.0 13.4 + - - +
899A ILE* 3.9 4.5 - - - +
901A ILE* 1.3 80.1 - - + +
903A LYS* 1.3 61.6 + - - +
905A LEU* 3.2 24.5 + - + +
910A ILE* 4.4 5.2 - - + -
911A VAL* 3.4 28.7 - - + +
913A TYR* 3.9 21.3 + - + +
927A LEU* 4.3 10.1 - - + -
929A MET* 3.9 34.5 - - + -
995A PHE* 3.5 35.4 - - + -
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Residues in contact with LYS 903 (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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899A ILE* 3.0 25.1 + - - +
900A GLU* 3.4 38.1 + - - +
902A LEU* 1.3 77.8 - - - +
904A SER* 1.3 59.4 + - - +
905A LEU 3.5 0.7 + - - -
906A GLN* 3.8 12.3 + - - +
913A TYR* 3.4 52.6 + - + +
916A VAL* 4.9 2.6 - - - +
918A TYR* 5.2 5.7 + - - -
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Residues in contact with SER 904 (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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900A GLU 3.1 12.4 + - - -
901A ILE 2.8 13.4 + - - -
903A LYS* 1.3 76.2 - - - +
905A LEU* 1.3 57.7 + - - +
906A GLN* 3.4 15.2 - - - +
966A TYR* 3.8 0.2 + - - -
970A LYS* 3.6 23.3 + - - +
972A TYR* 2.6 32.2 + - - -
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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