Contacts of the strand formed by residues 988 - 991 (chain C) in PDB entry 4OQB
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 GLU 988 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890C MET* 3.6 18.4 - - - +
891C PHE* 3.3 22.6 - - - -
896C TYR* 4.0 16.5 - - + -
897C PHE 3.4 7.0 - - - +
898C ALA* 6.0 0.2 - - + -
903C LYS* 3.2 33.7 + - - +
907C TYR* 5.3 4.2 + - - -
949C LYS* 3.4 9.7 - - - +
950C GLY* 2.8 37.0 + - - +
984C LEU* 4.0 15.5 - - + +
986C TYR 4.3 2.5 - - - +
987C ASN* 1.3 72.9 - - - +
989C TYR* 1.3 64.1 + - - +
990C ILE* 3.5 9.3 - - + +
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Residues in contact with TYR 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858C ARG* 3.0 28.6 + - - -
860C LEU* 3.3 47.8 - - + -
895C ILE 3.6 1.4 - - - +
896C TYR* 3.5 2.4 - - - -
897C PHE* 2.7 54.1 + - + +
898C ALA* 4.2 0.7 - - - -
899C ASP* 3.3 33.4 + - + +
926C LEU* 3.7 16.8 - - + -
929C MET* 3.6 23.3 - - + -
948C VAL 3.8 2.0 - - - -
949C LYS* 3.7 25.4 - - + -
956C PRO* 5.7 0.3 - - - +
970C PRO* 5.6 0.5 - - - +
987C ASN* 3.4 17.6 + - + -
988C GLU* 1.3 75.2 - - - +
990C ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891C PHE* 3.5 27.8 - - + -
894C GLY* 4.6 1.8 - - - -
895C ILE 3.4 9.2 - - - +
896C TYR* 3.5 39.9 - - + -
926C LEU* 5.1 1.0 - - - +
947C SER* 3.4 9.2 - - - -
948C VAL* 3.0 51.3 + - + +
950C GLY 4.1 0.7 - - - +
988C GLU* 3.5 19.5 - - + +
989C TYR* 1.3 76.3 - - - +
991C VAL* 1.3 67.1 + - - +
992C TYR* 3.4 37.8 - - + +
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Residues in contact with VAL 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894C GLY* 3.6 3.1 - - - -
895C ILE* 3.0 55.8 + - + +
897C PHE* 4.1 4.0 - - + -
924C VAL* 3.4 35.4 - - + -
925C ALA 4.2 4.9 - - - +
926C LEU* 4.5 4.7 - - + -
946C HIS 4.9 0.2 - - - -
947C SER* 4.4 7.2 - - - -
990C ILE* 1.3 78.7 - - - +
992C TYR* 1.3 62.6 + - - +
993C ASP 3.4 11.0 + - - +
996C GLN* 3.3 32.3 - - + +
997C VAL* 5.0 3.6 - - + -
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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