Contacts of the strand formed by residues 936 - 939 (chain B) in PDB entry 4CEJ
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 THR 936 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786B GLU 3.6 3.7 + - - +
787B ARG* 2.4 43.7 + - - +
788B ILE* 2.9 24.0 + - - +
928B THR* 4.5 6.3 - - - +
929B PHE 3.4 10.1 - - - +
930B GLN* 5.2 8.5 - - + -
931B LEU* 4.8 0.4 - - - -
934B GLY 4.5 6.5 - - - +
935B CYS* 1.3 78.3 - - - +
937B MET* 1.3 60.4 + - - +
938B GLU 3.9 0.2 - - - -
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Residues in contact with MET 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ILE* 3.3 31.0 - - + +
795B MET* 3.9 28.0 - - - +
928B THR* 3.6 3.1 - - - -
929B PHE* 2.9 67.2 + - + +
931B LEU* 4.6 13.4 - - + +
935B CYS 4.2 0.8 + - - -
936B THR* 1.3 72.3 - - - +
938B GLU* 1.3 57.0 + - - +
939B LEU* 3.9 13.2 - - + -
1096B PHE* 3.2 30.7 - - + +
1097B GLN* 4.9 0.9 - - - -
1100B GLY* 3.6 23.3 - - - +
1103B ILE* 5.4 0.7 - - - -
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Residues in contact with GLU 938 (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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787B ARG* 2.9 41.6 + - - +
788B ILE 2.9 11.3 + - - +
789B GLN* 2.9 40.4 + - + +
790B GLY 2.9 23.4 + - - -
920B GLY 5.0 5.5 + - - -
926B PRO* 3.2 31.5 - - + +
927B LEU 3.6 10.3 - - - +
928B THR* 4.3 5.6 - - - +
936B THR 3.9 2.0 - - - -
937B MET* 1.3 74.5 - - - +
939B LEU* 1.3 61.7 + - - +
940B VAL* 4.1 4.0 + - + +
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Residues in contact with LEU 939 (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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790B GLY* 3.3 30.3 - - - +
791B SER* 4.1 9.0 - - - +
792B VAL* 5.1 4.3 - - + +
795B MET* 4.0 24.0 - - + -
918B PHE* 3.4 19.5 - - + -
926B PRO* 3.9 11.6 - - - +
927B LEU* 3.2 36.2 + - + +
929B PHE* 4.2 6.1 - - + -
937B MET* 3.9 20.9 - - + -
938B GLU* 1.3 77.5 - - - +
940B VAL* 1.3 59.7 + - - +
984B THR* 6.2 0.7 - - + -
1096B PHE* 4.0 34.8 - - + -
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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