Contacts of the strand formed by residues 809 - 812 (chain B) in PDB entry 4BIC
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 VAL 809 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B SER* 3.1 5.4 - - - -
762B LEU* 2.9 49.4 + - + -
787B ILE* 4.5 18.2 - - + -
804B ILE* 5.3 4.0 - - + -
805B LYS 3.4 22.2 - - - +
806B GLY* 3.2 4.0 - - - +
807B ASP 3.2 1.8 + - - -
808B ASN* 1.3 82.8 - - + +
810B LEU* 1.3 62.2 + - - +
811B ILE* 4.6 1.8 - - + -
818B LEU* 3.6 34.3 - - + -
819B LYS 3.9 2.7 - - - -
820B ILE* 4.5 19.7 - - + -
870B THR* 5.4 0.4 - - + -
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Residues in contact with LEU 810 (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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2A IE4 3.4 67.1 - - + +
738B VAL* 3.8 10.8 - - + -
757B VAL* 4.0 20.1 - - + +
760B GLY* 3.4 4.5 - - - +
761B SER* 3.9 26.5 - - - +
807B ASP 5.0 0.2 - - - +
809B VAL* 1.3 73.7 - - - +
811B ILE* 1.3 62.6 + - - +
812B ASN 4.3 0.2 + - - -
817B VAL 4.1 0.3 - - - +
818B LEU* 3.4 2.1 - - - +
819B LYS* 2.7 42.3 + - - +
821B SER* 3.8 24.5 - - - +
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Residues in contact with ILE 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B VAL* 3.6 5.1 - - - +
759B GLY* 3.4 2.9 - - - -
760B GLY 2.8 30.8 + - - -
762B LEU* 3.7 40.6 - - + -
765B LEU* 3.8 7.9 - - + -
770B TRP* 3.7 22.2 - - + -
783B TYR* 3.7 38.4 - - + +
809B VAL* 4.6 2.0 - - + -
810B LEU* 1.3 78.3 - - - +
812B ASN* 1.4 72.2 + - - +
813B THR* 3.3 12.9 + - + +
816B GLY 4.8 0.2 - - - +
817B VAL 3.8 4.7 - - - +
818B LEU* 3.9 20.6 - - + -
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Residues in contact with ASN 812 (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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757B VAL* 3.6 12.7 - - + +
758B PRO* 3.2 31.6 - - - +
811B ILE* 1.4 69.0 - - - +
813B THR* 1.3 55.6 + - - +
814B TYR* 2.8 36.6 + - - +
815B SER* 3.1 25.6 + - - +
816B GLY* 2.8 36.2 + - - -
817B VAL* 2.9 22.8 + - + +
819B LYS* 6.2 3.9 - - + +
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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
------------------------------------------------------------
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