Contacts of the strand formed by residues 987 - 992 (chain C) in PDB entry 2A69
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 ILE 987 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C ILE 4.1 2.2 - - - +
677C MET* 3.8 26.2 - - + -
971C LYS* 3.2 4.7 - - - -
972C VAL* 3.0 28.4 + - - +
974C LEU* 4.3 22.8 - - + +
983C ILE* 3.3 32.5 - - + +
985C GLY 2.8 25.8 - - - +
986C PRO* 1.3 70.1 - - + +
988C VAL* 1.3 77.6 + - - +
989C VAL* 3.8 4.7 + - - +
946D GLY* 3.4 24.5 - - - +
948D THR* 3.1 18.6 - - + -
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Residues in contact with VAL 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 3.1 32.1 + - + +
885C ILE* 5.2 1.1 - - + -
888C THR* 3.5 24.0 - - + -
889C HIS* 3.7 20.0 - - + +
970C GLY 3.3 18.4 - - - +
971C LYS* 3.3 10.5 - - + +
987C ILE* 1.3 81.7 - - - +
989C VAL* 1.3 71.6 + - - +
948D THR* 2.9 22.0 - - - +
949D ILE 3.1 21.3 - - - +
950D GLY* 4.3 2.7 - - - -
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Residues in contact with VAL 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673C LEU* 4.8 8.3 - - + -
674C VAL 3.0 10.3 - - - +
675C ALA* 3.4 26.9 - - + +
861C LEU* 4.8 9.0 - - + -
867C VAL* 4.4 5.2 - - + -
888C THR* 3.6 10.9 - - - +
892C LEU* 3.5 25.6 - - + +
970C GLY 3.7 3.1 + - - +
972C VAL* 3.7 33.9 - - + -
974C LEU* 3.9 21.5 - - + -
988C VAL* 1.3 88.1 - - - +
990C GLY* 1.3 60.5 + - - +
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Residues in contact with GLY 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672C VAL 3.4 0.2 - - - +
673C LEU* 4.1 8.4 - - - +
674C VAL* 2.8 47.6 + - - +
888C THR* 3.5 15.4 - - - +
892C LEU* 3.9 10.8 - - - -
895C TYR* 6.1 0.4 - - - -
989C VAL* 1.3 77.0 - - - +
991C GLN* 1.3 61.9 + - - -
992C MET 3.2 0.6 + - - -
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Residues in contact with GLN 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C VAL* 2.9 51.8 - - + +
671C ASN* 5.0 7.1 - - + +
672C VAL 3.8 7.6 - - - +
673C LEU* 5.1 6.7 - - + +
887C GLU* 4.1 5.2 - - - +
888C THR* 4.2 2.0 + - - -
891C GLY* 2.8 27.2 - - - +
894C GLY* 2.9 8.3 + - - -
895C TYR* 2.6 61.6 + - + +
900C ARG* 4.5 9.7 - - - +
990C GLY* 1.3 68.0 - - - -
992C MET* 1.3 60.2 + - - +
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Residues in contact with MET 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671C ASN* 4.3 1.3 - - - -
672C VAL 3.2 24.7 + - - +
674C VAL* 3.5 17.0 - - + -
676C ILE* 5.2 7.4 - - + -
841C ASN* 3.7 24.7 - - + +
871C LEU* 3.5 33.4 - - + -
884C GLN* 4.4 17.9 - - + +
887C GLU* 3.5 15.9 - - + +
888C THR* 3.1 25.8 - - - +
990C GLY 3.2 5.7 + - - -
991C GLN* 1.3 72.8 - - - +
993C PHE* 1.3 73.8 + - - +
994C ILE* 3.5 19.2 + - + +
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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