Contacts of the strand formed by residues 787 - 791 (chain A) in PDB entry 2ITQ
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 GLN 787 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709A GLU* 3.7 11.4 + - - -
712A PHE* 3.5 28.5 - - - -
714A LYS* 3.0 27.2 + - - -
744A ILE* 3.4 24.2 - - + +
745A LYS 3.1 8.1 - - - +
746A GLU* 3.1 20.6 - - + +
759A ILE* 4.7 0.2 - - - -
780A ILE* 3.3 8.2 - - - +
781A CYS* 2.7 52.0 + - + -
783A THR* 3.8 6.3 + - - +
785A THR 3.6 12.6 - - - +
786A VAL* 1.3 77.0 - - - +
788A LEU* 1.3 60.0 - - - +
789A ILE* 3.5 3.1 - - + +
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Residues in contact with LEU 788 (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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743A ALA 3.6 1.2 - - - +
744A ILE* 3.3 5.5 - - - -
745A LYS* 2.7 63.7 + - + +
759A ILE* 3.7 27.1 - - + +
762A GLU* 4.4 6.7 - - + +
763A ALA* 3.7 35.9 - - + +
766A MET* 3.2 29.6 - - + -
777A LEU* 4.1 11.0 - - + -
779A GLY 4.2 2.0 - - - -
780A ILE* 4.3 4.3 - - + -
787A GLN* 1.3 70.9 - - - +
789A ILE* 1.3 62.1 + - - +
790A THR* 4.0 11.4 - - + +
2019A ITQ 4.5 1.8 - - + -
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Residues in contact with ILE 789 (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* 4.0 19.5 - - + -
712A PHE* 4.2 13.2 - - + -
731A TRP* 5.2 4.0 - - + -
742A VAL* 3.6 37.5 - - + -
743A ALA 3.6 2.5 - - - +
744A ILE* 4.1 16.6 - - + -
777A LEU* 3.4 3.6 - - - +
778A LEU* 2.6 42.1 + - + +
779A GLY 2.9 23.3 + - - +
780A ILE 3.9 1.8 - - - -
781A CYS* 3.7 23.3 - - + +
787A GLN* 3.5 19.3 - - + +
788A LEU* 1.3 75.3 - - - +
790A THR* 1.3 57.0 + - - +
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Residues in contact with THR 790 (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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742A VAL* 3.3 9.4 - - - +
743A ALA* 2.8 33.1 + - - +
745A LYS* 5.9 2.0 - - + -
766A MET* 4.3 15.3 - - - -
775A CYS* 4.4 4.9 - - - -
776A ARG 3.3 14.4 - - - +
777A LEU* 4.5 2.0 - - + -
778A LEU* 3.3 6.7 - - - -
788A LEU* 4.1 27.1 - - + +
789A ILE* 1.3 79.8 - - - +
791A GLN* 1.3 60.0 + - - +
2019A ITQ 3.0 38.8 + - + -
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Residues in contact with GLN 791 (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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741A PRO 4.1 2.9 - - - +
743A ALA 4.1 0.2 - - - -
775A CYS* 4.4 1.4 - - - -
776A ARG* 3.1 29.1 + - + +
778A LEU* 3.4 8.4 - - + +
790A THR* 1.3 74.3 + - - +
792A LEU* 1.4 71.2 + - - +
793A MET* 3.4 15.1 + - - +
846A LYS* 3.7 6.9 - - - +
852A LYS* 2.9 24.8 + - - +
1012A ASP* 2.8 33.4 + - - +
1013A ALA* 3.7 18.1 - - + +
1014A ASP* 3.2 21.2 + - - +
2019A ITQ 2.9 21.8 + - - -
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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