Contacts of the helix formed by residues 893 - 906 (chain A) in PDB entry 4YOC
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 893 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A THR* 3.8 17.3 - - - +
793A HIS* 3.6 17.3 - - + -
795A HIS* 4.1 9.4 - - - -
891A LYS 3.3 3.4 + - - +
892A PHE* 1.3 81.5 - - - +
894A VAL* 1.3 67.7 + - - +
895A SER* 3.5 15.5 - - - -
896A CYS* 3.6 9.5 - - + +
897A ALA* 3.2 21.3 + - - +
1702A ZN 2.3 37.0 - - - -
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Residues in contact with VAL 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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795A HIS* 4.3 16.1 + - + +
818A ASP* 5.5 0.2 - - - +
880A PRO* 4.2 18.6 - - + +
882A THR* 3.8 22.4 - - - +
892A PHE* 3.9 23.6 - - + -
893A CYS* 1.3 72.1 - - - +
895A SER* 1.3 61.1 + - - +
897A ALA* 3.1 4.9 + - - +
898A ARG* 2.9 45.2 + - - +
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Residues in contact with SER 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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795A HIS* 3.6 30.7 - - - -
818A ASP* 3.3 19.5 - - - +
819A GLU 3.0 24.1 + - - -
820A CYS* 3.5 12.5 - - - -
893A CYS* 3.4 8.4 - - - -
894A VAL* 1.3 80.8 - - - +
896A CYS* 1.3 56.9 + - - +
898A ARG* 3.4 1.2 + - - +
899A LEU* 2.9 35.1 + - - +
1702A ZN 4.3 0.2 - - - -
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Residues in contact with CYS 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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793A HIS* 3.1 14.1 - - - -
820A CYS* 3.5 7.0 - - - -
893A CYS* 3.5 13.9 + - + +
894A VAL 3.2 0.4 - - - -
895A SER* 1.3 78.6 - - - +
897A ALA* 1.3 58.8 + - - +
899A LEU* 3.4 7.4 + - - +
900A ALA* 2.9 29.3 + - - +
1702A ZN 2.4 35.1 - - - -
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Residues in contact with ALA 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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882A THR* 4.9 11.0 - - - +
892A PHE* 4.2 21.3 - - + -
893A CYS 3.2 10.7 + - - +
894A VAL* 3.1 10.4 + - - +
896A CYS* 1.3 79.8 - - - +
898A ARG* 1.3 56.6 + - - +
900A ALA* 3.3 7.7 + - - +
901A GLU* 2.9 37.0 + - + +
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Residues in contact with ARG 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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818A ASP* 2.4 46.7 + - - +
868A TRP* 3.5 26.4 - - - -
880A PRO* 3.4 26.0 - - - +
882A THR* 4.4 9.8 - - + +
894A VAL* 2.9 38.3 + - + +
895A SER 3.9 3.1 - - - +
897A ALA* 1.3 74.7 - - - +
899A LEU* 1.3 60.5 + - - +
901A GLU* 3.7 14.5 - - - +
902A MET* 2.9 57.3 + - + +
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Residues in contact with LEU 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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818A ASP* 3.9 21.1 - - + +
819A GLU 5.0 0.4 - - - +
820A CYS* 5.3 9.4 - - - -
895A SER* 2.9 39.5 + - - +
896A CYS* 3.6 6.5 - - - +
898A ARG* 1.3 75.0 - - - +
900A ALA* 1.3 58.0 + - - +
902A MET* 3.8 8.9 - - - +
903A ARG* 2.9 37.6 + - + +
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Residues in contact with ALA 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 CYS 2.9 15.0 + - - +
897A ALA* 3.3 12.8 - - - +
898A ARG 3.2 0.2 - - - -
899A LEU* 1.3 75.9 - - - +
901A GLU* 1.3 64.4 + - + +
903A ARG* 4.3 2.3 - - - +
904A GLN* 2.9 32.8 + - - +
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Residues in contact with GLU 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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882A THR* 3.3 30.8 - - - +
897A ALA* 2.9 24.4 + - - +
898A ARG* 3.7 13.2 - - - +
900A ALA* 1.3 75.5 - - + +
902A MET* 1.3 58.5 + - + +
904A GLN* 3.7 4.4 - - - +
905A LYS* 2.9 31.6 + - - +
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Residues in contact with MET 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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818A ASP* 4.4 6.1 - - - +
868A TRP* 5.6 3.8 - - + -
870A ASP* 6.0 1.6 - - - +
898A ARG* 2.9 53.6 + - - +
899A LEU* 3.8 8.1 - - - +
901A GLU* 1.3 77.2 - - + +
903A ARG* 1.3 60.4 + - + +
905A LYS* 2.9 29.5 + - - +
906A GLU* 2.9 27.0 + - - +
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Residues in contact with ARG 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 LEU* 2.9 24.2 + - + +
900A ALA* 4.3 2.7 - - - +
902A MET* 1.3 74.2 - - + +
904A GLN* 1.3 60.7 + - - +
906A GLU* 2.8 54.1 + - - +
907A ILE* 3.6 35.1 - - - +
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Residues in contact with GLN 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 ALA* 2.9 22.5 + - - +
901A GLU* 3.8 4.7 - - - +
903A ARG* 1.3 76.2 - - - +
905A LYS* 1.3 64.6 + - - +
906A GLU 3.3 0.4 - - - -
907A ILE* 3.4 37.3 - - - +
909A ARG* 3.7 23.3 + - - +
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Residues in contact with LYS 905 (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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901A GLU 2.9 17.3 + - - +
902A MET* 2.9 12.9 + - - +
904A GLN* 1.3 80.6 - - - +
906A GLU* 1.3 60.6 + - - +
907A ILE 3.5 3.7 + - - +
909A ARG* 4.9 6.7 + - - +
928A LYS* 4.4 1.0 - - - -
929A ASN* 3.4 40.9 + - - -
930A GLY* 3.7 25.6 + - - +
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Residues in contact with GLU 906 (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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902A MET* 2.9 35.3 - - - +
903A ARG* 2.8 53.9 + - - +
904A GLN 3.3 0.2 - - - -
905A LYS* 1.3 81.0 - - + +
907A ILE* 1.3 60.5 + - - +
908A PRO* 3.3 10.7 - - - +
928A LYS* 5.3 2.0 - - - +
929A ASN* 4.4 24.2 + - - +
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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