Contacts of the helix formed by residues 884 - 891 (chain B) in PDB entry 2O8C
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 884 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790B ASP* 3.4 29.4 - - - -
793B ASP* 3.7 7.0 - - - -
794B ALA* 3.4 13.6 - - - -
797B ASP* 2.9 15.1 + - - -
882B PHE* 4.8 0.3 - - - +
883B LYS* 1.3 79.5 + - - +
885B LYS* 1.3 62.5 + - - +
886B ILE* 4.3 2.0 - - - -
887B LEU* 3.1 22.2 - - - +
888B LYS* 3.4 25.0 + - - +
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Residues in contact with LYS 885 (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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786B TYR* 4.0 25.6 - - + +
790B ASP* 3.1 12.7 + - - +
883B LYS 4.0 1.8 + - - -
884B SER* 1.3 70.1 - - - +
886B ILE* 1.3 66.3 + - - +
888B LYS* 3.2 11.6 + - + +
889B GLN* 3.1 48.3 + - + +
899B GLU* 3.0 34.5 + - - -
901B ARG* 5.1 5.8 - - - +
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Residues in contact with ILE 886 (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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777B TRP* 5.5 6.3 - - + -
790B ASP* 3.4 43.4 + - - +
791B ARG* 4.6 8.3 - - + +
794B ALA* 4.1 11.9 - - + -
884B SER* 4.3 0.4 - - - -
885B LYS* 1.3 80.3 - - - +
887B LEU* 1.3 65.4 + - - +
889B GLN* 3.3 32.2 + - - +
890B VAL* 3.4 16.6 + - + +
1056B VAL* 4.3 27.4 - - + -
1060B LEU* 4.6 6.3 - - + -
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Residues in contact with LEU 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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794B ALA* 4.1 10.3 - - + +
797B ASP* 3.8 20.0 - - + -
798B LEU* 3.8 20.2 - - + -
882B PHE* 3.7 31.6 - - + -
884B SER* 3.1 16.7 + - - +
885B LYS 3.3 0.8 - - - -
886B ILE* 1.3 78.8 - - - +
888B LYS* 1.3 65.5 + - - +
889B GLN 3.3 0.5 + - - -
890B VAL* 3.4 9.6 - - + +
891B ILE* 3.0 36.5 + - + +
1057B LEU* 3.9 28.9 - - + -
1060B LEU* 3.9 18.4 - - + -
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Residues in contact with LYS 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B ALA* 4.4 18.8 - - - +
880B ASP* 5.1 5.7 + - - +
882B PHE* 3.2 33.3 + - + -
883B LYS* 4.8 4.8 - - - +
884B SER 3.4 15.4 + - - +
885B LYS* 3.2 12.2 + - + +
887B LEU* 1.3 77.8 - - - +
889B GLN* 1.3 58.4 + - - +
891B ILE* 3.5 6.4 + - - -
892B SER* 2.5 37.9 + - - +
897B ASN* 3.9 26.6 - - - +
901B ARG* 4.6 1.3 - - - +
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Residues in contact with GLN 889 (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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885B LYS* 3.1 43.2 + - + +
886B ILE* 3.4 26.4 - - - +
887B LEU 3.2 0.2 - - - -
888B LYS* 1.3 81.0 - - - +
890B VAL* 1.3 63.8 + - + +
891B ILE 3.3 0.5 + - - -
892B SER 3.6 4.0 - - - +
899B GLU* 3.6 7.6 + - - +
900B GLY* 3.6 19.4 + - - +
901B ARG* 3.1 51.4 - - - +
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Residues in contact with VAL 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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872B ILE* 4.0 8.1 - - - +
886B ILE* 3.6 15.5 - - + +
887B LEU* 3.4 22.4 - - + +
889B GLN* 1.3 78.6 - - + +
891B ILE* 1.3 69.3 + - + +
892B SER 3.7 0.7 - - - -
900B GLY 5.5 1.3 - - - +
902B PHE* 4.1 1.4 - - - -
1053B CYS* 3.4 53.3 - - - +
1054B ILE* 5.6 0.3 - - - +
1056B VAL* 3.7 38.6 - - + -
1057B LEU* 4.4 5.6 - - - +
1060B LEU* 4.9 0.2 - - + -
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Residues in contact with ILE 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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872B ILE* 3.8 32.4 - - + +
875B MET* 3.8 26.8 - - + +
876B GLU* 5.5 0.9 + - - -
879B ALA* 4.7 13.2 - - + +
882B PHE* 3.3 35.9 - - + -
887B LEU* 3.0 31.2 + - + +
888B LYS* 4.2 4.9 - - - +
889B GLN 3.3 0.8 - - - -
890B VAL* 1.3 88.8 - - + +
892B SER* 1.3 59.0 + - - +
1057B LEU* 3.8 37.0 - - + -
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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