Contacts of the strand formed by residues 756 - 761 (chain C) in PDB entry 3JW0
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 CYS 756 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 6.0 4.7 - - - -
754C MET* 2.7 35.2 + - - +
755C PHE* 1.3 76.3 - - - +
757C ILE* 1.3 69.5 + - - +
758C ASP* 5.1 0.7 - - - -
767C GLN* 3.3 37.0 - - + -
768C VAL 3.0 20.9 - - - +
769C ASP* 3.8 9.9 - - - +
770C LEU* 3.9 10.5 - - - +
775C SER* 4.2 6.3 - - - -
787C TYR* 4.4 6.4 + - - -
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Residues in contact with ILE 757 (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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2A ALA* 5.8 0.7 - - - -
58A THR 5.0 2.0 - - - +
59A ASP* 4.8 11.7 - - - +
62A PHE* 6.4 2.0 - - + -
736C TYR* 5.2 7.2 - - - +
756C CYS* 1.3 79.8 - - - +
758C ASP* 1.3 88.3 + - - +
759C GLU* 4.1 0.9 - - - +
767C GLN* 3.4 4.7 - - - +
768C VAL* 2.7 35.5 + - + +
770C LEU* 3.3 28.3 - - + -
787C TYR* 6.1 0.2 - - - +
791C VAL* 5.4 7.0 - - + -
794C TRP* 3.1 61.9 - - + +
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Residues in contact with ASP 758 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 2.6 34.8 - - - +
3A SER 4.5 0.2 + - - -
31A PHE* 3.9 17.1 - - - -
58A THR* 3.5 42.0 + - + +
59A ASP* 5.1 1.9 - - - +
756C CYS* 5.1 0.5 - - - -
757C ILE* 1.3 96.5 - - - +
759C GLU* 1.3 72.4 + - - +
765C THR* 4.3 6.1 - - - +
766C TYR 3.9 3.1 - - - -
767C GLN* 3.5 25.5 + - - +
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Residues in contact with GLU 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 5.2 0.2 - - - -
757C ILE* 4.1 0.9 - - - +
758C ASP* 1.3 88.1 - - - +
760C GLU* 1.3 62.3 + - - +
765C THR* 3.1 7.6 + - - -
766C TYR* 2.7 67.8 + - + +
768C VAL* 3.5 25.1 - - + -
794C TRP* 3.0 39.1 - - + -
799C ARG* 4.3 9.6 + - - -
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Residues in contact with GLU 760 (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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31A PHE* 5.9 2.3 - - - +
55A HIS* 5.1 8.5 + - - -
58A THR* 3.2 41.1 + - + +
759C GLU* 1.3 77.3 + - - +
761C ASN* 1.3 67.5 + - - +
763C GLY* 5.7 5.1 - - - +
764C GLN 3.3 7.6 - - - +
765C THR* 4.4 10.4 - - - -
766C TYR* 4.4 2.3 - - - -
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Residues in contact with ASN 761 (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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760C GLU* 1.3 77.2 - - - +
762C PHE* 1.3 97.9 + - + +
763C GLY 3.2 0.8 - - - +
764C GLN* 3.0 28.5 + - - +
766C TYR* 3.5 24.1 - - + +
582D ASP* 4.5 2.1 + - - +
586D LYS* 4.3 14.0 + - - -
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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