Contacts of the strand formed by residues 809 - 814 (chain A) in PDB entry 4ZZ0
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 ARG 809 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808A ALA* 1.3 73.9 - - - +
810A VAL* 1.3 60.1 + - - +
836A GLN* 3.8 22.7 + - - +
838A ASP* 3.2 40.7 + - - +
885A PHE* 2.8 38.4 + - - +
886A SER* 3.2 25.9 + - - +
887A ILE* 3.6 4.2 - - + +
888A ASP* 2.8 45.4 + - - +
889A ILE 3.0 8.7 + - - -
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Residues in contact with VAL 810 (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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808A ALA 3.9 4.0 - - - +
809A ARG* 1.3 78.1 - - - +
811A ALA* 1.3 76.9 + - - +
812A VAL* 4.2 10.1 - - + -
835A ALA* 3.8 26.2 - - + -
836A GLN 2.8 21.8 + - - +
837A ILE* 3.5 6.4 - - + +
838A ASP* 2.9 26.9 + - - -
839A ILE 3.7 2.3 + - - -
887A ILE* 3.7 5.4 - - - +
889A ILE* 3.2 17.9 - - + +
891A CYS* 4.0 21.5 - - - -
988A LEU* 4.0 15.5 - - + -
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Residues in contact with ALA 811 (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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810A VAL* 1.3 76.8 - - - +
812A VAL* 1.3 61.0 + - - +
813A LEU* 4.1 9.6 + - + -
839A ILE* 3.3 21.3 - - + +
841A ILE* 5.1 0.9 - - + -
882A LEU* 3.4 33.2 - - + -
887A ILE* 3.7 7.9 - - + +
889A ILE 3.0 7.4 + - - +
890A VAL* 3.5 3.4 - - + +
891A CYS 2.9 25.5 + - - -
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Residues in contact with VAL 812 (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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810A VAL* 4.2 7.2 - - + -
811A ALA* 1.3 77.0 - - - +
813A LEU* 1.3 64.4 + - - +
814A ILE* 4.0 6.7 - - + -
821A LEU* 3.8 24.9 - - + -
824A LEU* 4.2 16.6 - - + -
837A ILE* 4.0 35.0 - - + -
839A ILE 3.0 7.3 + - - -
840A VAL* 3.3 9.7 - - + +
841A ILE 2.9 23.4 + - - +
891A CYS* 3.4 7.9 - - + +
893A ALA* 3.7 28.3 - - + -
988A LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 813 (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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811A ALA* 4.3 8.7 - - + -
812A VAL* 1.3 77.5 - - - +
814A ILE* 1.3 64.8 + - - +
841A ILE* 3.2 35.4 - - + +
878A ILE* 4.2 20.4 - - + -
882A LEU* 4.7 3.1 - - + -
890A VAL* 4.0 20.4 - - + -
891A CYS 2.8 7.5 + - - -
892A LEU* 3.6 26.5 - - + -
893A ALA* 2.9 27.4 + - - -
895A PHE* 3.5 37.4 - - + +
899A LEU* 5.3 4.0 - - + -
903A PHE* 5.5 2.0 - - + -
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Residues in contact with ILE 814 (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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812A VAL* 4.0 16.2 - - + -
813A LEU* 1.3 80.1 - - - +
815A SER* 1.3 62.9 + - - +
816A GLY 4.3 5.2 - - - +
818A GLY* 5.1 4.9 - - - -
821A LEU* 4.3 17.9 - - + -
840A VAL* 4.0 16.2 - - + -
841A ILE 2.8 10.5 + - - +
842A SER* 3.3 36.6 - - - +
843A ASN* 3.3 8.5 + - - +
847A VAL* 4.2 7.0 - - + -
849A GLY* 3.6 37.2 - - - -
850A LEU* 3.8 4.9 - - + +
893A ALA 3.5 17.0 - - - +
895A PHE* 3.6 7.1 - - - +
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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