Contacts of the helix formed by residues 760 - 769 (chain A) in PDB entry 1QU2
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 760 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ASP* 3.6 39.0 - - - +
620A LEU* 4.3 17.5 - - + -
645A TYR* 4.1 23.8 - - + -
648A ILE* 4.0 36.6 - - + -
652A LEU* 5.8 0.9 - - + -
756A LEU* 2.9 32.3 + - + +
757A ALA 3.8 2.7 - - - -
759A ILE* 1.3 78.3 - - + +
761A VAL* 1.3 58.2 + - - +
762A HIS 3.3 3.1 - - - -
763A THR* 4.3 10.1 - - + -
764A ALA* 2.9 31.3 + - + +
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Residues in contact with VAL 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.4 20.1 - - + -
79A ARG* 3.3 33.2 - - - +
143A GLY 4.2 4.7 - - - +
616A ASP* 3.6 1.5 + - - +
619A ARG* 3.6 32.8 - - - +
757A ALA 3.3 19.3 - - - +
758A PRO 3.8 0.7 - - - +
759A ILE 3.0 2.4 + - - -
760A LEU* 1.3 75.0 - - - +
762A HIS* 1.3 92.1 + - + +
765A GLU 3.5 7.8 + - - -
780A HIS* 2.8 23.7 + - + -
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Residues in contact with HIS 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 5.6 2.2 - - + -
24A GLU* 3.3 43.5 + - + +
27A ILE* 3.8 18.4 - - + +
28A GLN* 2.9 33.7 + - + +
31A TRP* 4.0 16.2 - + - -
142A LEU 4.2 0.4 - - - -
143A GLY* 3.8 9.4 - - - -
615A ALA* 3.7 20.4 - - + -
616A ASP* 2.5 26.7 + - - +
761A VAL* 1.3 91.2 - - + +
763A THR* 1.3 63.1 + - - +
765A GLU* 3.2 4.9 + - - +
766A GLU* 2.9 28.2 + - - +
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Residues in contact with THR 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.4 4.7 - - + -
20A LEU* 4.4 3.3 - - - +
616A ASP* 2.6 26.5 + - - +
645A TYR* 2.6 39.8 + - + +
648A ILE* 6.2 0.2 - - + -
649A ARG* 3.9 18.5 + - + +
652A LEU* 4.9 10.1 - - + -
760A LEU* 4.3 10.5 - - + -
762A HIS* 1.3 74.1 - - - +
764A ALA* 1.3 58.2 + - - +
766A GLU* 3.6 7.5 - - - +
767A VAL* 2.8 41.7 + - + +
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Residues in contact with ALA 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A LEU* 6.3 1.1 - - - -
753A THR* 3.9 17.6 - - - +
756A LEU* 4.7 2.5 - - + -
757A ALA* 3.7 29.4 - - + +
760A LEU* 2.9 22.3 + - + +
761A VAL 4.1 3.1 - - - +
763A THR* 1.3 76.8 - - - +
765A GLU* 1.3 57.7 + - - +
767A VAL* 3.4 5.9 + - - +
768A TRP* 2.9 23.6 + - - +
779A VAL* 3.1 14.9 - - + +
780A HIS* 4.7 0.2 - - + -
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Residues in contact with GLU 765 (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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27A ILE* 4.2 11.9 - - + -
30A LYS* 6.6 0.2 - - + -
31A TRP* 2.9 31.2 + - + +
761A VAL 3.5 12.2 + - - +
762A HIS 3.2 8.8 + - - +
764A ALA* 1.3 76.7 - - - +
766A GLU* 1.3 59.6 + - - +
768A TRP* 3.1 7.6 + - - +
769A SER* 2.8 40.1 + - - +
778A SER* 2.7 48.9 + - - -
779A VAL* 3.1 13.6 + - + +
780A HIS* 3.5 3.7 - - - +
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Residues in contact with GLU 766 (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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14A PHE* 3.4 12.6 - - + -
15A PRO* 3.7 14.0 - - - +
18A GLY 5.0 2.4 - - - +
20A LEU* 5.2 2.4 - - - +
23A LYS* 3.8 34.0 + - - +
27A ILE* 4.7 10.2 - - + +
649A ARG* 2.9 43.2 + - - -
762A HIS 2.9 15.6 + - - +
763A THR* 3.2 8.8 + - - +
765A GLU* 1.3 77.8 - - - +
767A VAL* 1.3 60.1 + - - +
769A SER* 3.3 9.8 + - - -
770A HIS* 2.8 35.8 + - + +
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Residues in contact with VAL 767 (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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14A PHE* 3.7 26.7 - - + -
652A LEU* 3.9 26.9 - - + -
656A LEU* 4.1 11.6 - - + +
749A LEU* 3.7 15.9 - - + -
753A THR* 3.4 31.2 - - + -
763A THR* 2.8 21.4 + - + +
764A ALA* 3.7 5.2 - - - +
766A GLU* 1.3 72.8 - - - +
768A TRP* 1.3 66.4 + - - +
770A HIS* 2.9 12.6 + - - +
771A THR* 2.9 20.3 + - - +
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Residues in contact with TRP 768 (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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750A VAL* 3.9 18.8 - - + -
753A THR* 3.5 20.2 - - + -
754A LYS* 3.7 33.2 - - + -
764A ALA 2.9 13.0 + - - +
765A GLU* 3.3 10.1 - - - +
767A VAL* 1.3 75.6 - - - +
769A SER* 1.3 63.9 + - - +
771A THR* 3.0 27.1 + - - +
774A VAL* 3.7 37.0 - - + +
776A GLU* 3.0 49.3 + - + -
777A GLU* 4.9 0.2 - - - -
778A SER* 3.6 14.1 - - - -
779A VAL* 3.4 41.4 - - + +
782A ALA* 4.3 3.1 - - + -
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Residues in contact with SER 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A GLU* 2.8 24.0 + - - +
766A GLU* 3.4 14.7 - - - -
767A VAL 3.1 0.2 - - - -
768A TRP* 1.3 77.3 - - - +
770A HIS* 1.3 65.7 + - - +
771A THR 3.5 1.6 - - - +
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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