Contacts of the strand formed by residues 777 - 782 (chain A) in PDB entry 2ITN
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 LEU 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A LEU* 4.3 9.6 - - + -
763A ALA* 3.4 39.7 - - + +
766A MET* 3.7 27.2 + - + +
767A ALA* 3.7 16.2 - - + +
775A CYS 3.7 4.6 + - - -
776A ARG* 1.3 84.7 + - - +
778A LEU* 1.3 60.1 + - - +
779A GLY* 3.3 31.0 - - - +
788A LEU* 3.7 25.4 - - + -
789A ILE 3.4 10.8 - - - +
790A THR* 4.5 5.4 - - + -
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Residues in contact with LEU 778 (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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705A ARG* 3.5 24.4 - - - +
707A LEU* 4.3 4.4 - - + +
731A TRP* 3.6 32.5 - - + -
740A ILE* 4.6 2.5 - - + -
742A VAL* 3.8 17.7 - - + -
776A ARG* 4.0 30.1 - - + +
777A LEU* 1.3 75.4 - - - +
779A GLY* 1.3 55.1 + - - +
789A ILE* 2.7 22.4 + - + +
790A THR* 3.4 9.6 - - - +
791A GLN* 3.4 33.9 - - + +
1013A ALA* 4.2 16.8 - - + -
1016A TYR* 4.3 6.7 - - + -
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Residues in contact with GLY 779 (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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704A LEU* 5.4 0.4 - - - -
705A ARG* 3.1 16.6 - - - -
707A LEU* 3.9 12.8 - - - +
777A LEU* 3.3 17.1 - - - +
778A LEU* 1.3 82.5 - - - +
780A ILE* 1.3 64.5 - - - +
789A ILE* 3.1 25.6 + - - +
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Residues in contact with ILE 780 (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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704A LEU* 4.1 19.7 - - + -
705A ARG 2.8 12.9 + - - +
706A ILE* 3.3 36.4 - - + +
707A LEU* 2.7 32.7 + - - -
759A ILE* 6.3 0.2 - - + -
760A LEU* 4.3 16.4 - - + -
763A ALA* 3.8 26.7 - - + -
777A LEU* 4.7 0.7 - - + -
779A GLY* 1.3 79.9 - - - +
781A CYS* 1.3 56.9 + - - +
782A LEU* 3.8 22.4 - - + -
786A VAL* 4.4 9.2 - - + -
787A GLN 3.4 11.7 - - - +
788A LEU* 4.1 9.4 - - + -
789A ILE* 4.4 2.9 - - - -
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Residues in contact with CYS 781 (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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707A LEU 3.0 22.0 - - - +
709A GLU* 3.7 16.4 - - - -
712A PHE* 3.7 31.6 - - + -
780A ILE* 1.3 75.0 - - - +
782A LEU* 1.3 62.1 + - - +
783A THR* 3.4 16.4 + - - -
786A VAL* 3.4 4.7 - - - +
787A GLN* 2.9 52.2 + - + +
789A ILE* 3.9 7.1 - - + +
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Residues in contact with LEU 782 (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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706A ILE* 4.5 24.4 - - + +
707A LEU 4.7 1.0 + - - -
760A LEU* 5.0 4.5 - - + -
780A ILE* 3.8 27.8 + - + -
781A CYS* 1.3 73.6 - - - +
783A THR* 1.3 65.4 + - - +
786A VAL* 3.8 25.6 - - + +
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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