Contacts of the helix formed by residues 753 - 764 (chain A) in PDB entry 4GT5
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 PRO 753 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A LEU* 4.0 21.1 - - + -
721A PHE* 4.0 13.5 - - + -
748A ARG* 4.5 0.2 - - - -
751A ALA 3.4 10.5 - - - +
752A CYS* 1.3 89.0 - - + +
754A PRO* 1.3 73.5 - - + +
755A GLU* 3.2 20.4 - - + +
756A VAL* 3.0 32.2 + - + -
757A TYR 3.1 9.5 + - - -
789A PRO* 4.5 4.0 - - + -
791A TYR* 3.8 25.5 - - + -
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Residues in contact with PRO 754 (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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748A ARG* 4.3 13.7 - - - +
752A CYS 3.9 1.1 - - - +
753A PRO* 1.3 84.6 - - + +
755A GLU* 1.3 69.1 + - - +
757A TYR* 3.3 9.8 + - + +
758A ALA* 2.9 29.5 + - - +
791A TYR* 4.0 18.2 - - + -
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Residues in contact with GLU 755 (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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753A PRO* 3.4 9.9 - - + +
754A PRO* 1.3 94.4 - - - +
756A VAL* 1.3 60.1 + - - +
758A ALA* 3.8 7.9 + - - +
759A ILE* 3.3 25.8 + - - +
784A LEU* 4.3 18.3 - - + +
789A PRO* 3.5 39.9 - - + +
790A VAL 5.3 2.1 - - - +
791A TYR* 5.5 0.2 - - - +
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Residues in contact with VAL 756 (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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624A LEU* 5.3 0.2 - - + -
628A LEU* 4.0 25.8 - - + -
717A LEU* 4.0 11.2 - - + -
721A PHE* 3.6 29.2 - - + -
752A CYS* 3.7 12.3 - - - -
753A PRO* 3.0 30.6 + - + +
755A GLU* 1.3 76.7 - - + +
757A TYR* 1.3 60.7 + - - +
758A ALA 3.1 1.3 - - - -
759A ILE* 3.0 12.2 + - + +
760A MET* 3.0 31.7 + - + +
781A LEU* 5.3 1.1 - - + -
784A LEU* 4.1 11.4 - - + -
789A PRO* 5.6 0.4 - - + -
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Residues in contact with TYR 757 (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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745A GLU* 4.0 12.6 + - - +
746A LEU 2.5 31.2 + - - -
747A GLU* 3.8 3.4 - - - -
748A ARG* 3.5 58.5 + - + -
749A PRO* 4.4 0.2 - - + -
752A CYS* 3.6 4.2 - - - -
753A PRO 3.1 6.5 + - - +
754A PRO* 3.7 8.7 - - + +
756A VAL* 1.3 80.3 - - - +
758A ALA* 1.3 54.7 + - - +
760A MET* 3.4 19.4 + - + +
761A ARG* 2.9 54.2 + - + +
764A TRP* 4.1 12.3 - + - -
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Residues in contact with ALA 758 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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754A PRO 2.9 16.5 + - - +
755A GLU* 3.8 10.8 - - - +
756A VAL 3.1 0.2 - - - -
757A TYR* 1.3 77.8 - - - +
759A ILE* 1.3 57.4 + - + +
761A ARG* 3.4 10.9 + - - +
762A GLY* 2.9 23.6 + - - -
772A HIS* 5.6 1.4 - - - -
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Residues in contact with ILE 759 (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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717A LEU* 4.0 11.7 - - + -
755A GLU 3.3 19.7 - - - +
756A VAL* 3.0 10.3 + - - +
758A ALA* 1.3 74.9 - - + +
760A MET* 1.3 66.3 + - - +
762A GLY* 2.9 12.7 + - - -
763A CYS* 2.9 15.9 + - - -
772A HIS* 5.4 1.9 + - - -
777A VAL* 3.8 33.7 - - + -
780A ARG* 4.3 18.8 - - + -
781A LEU* 4.0 18.6 - - + +
784A LEU* 3.7 23.8 - - + -
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Residues in contact with MET 760 (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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714A GLY* 4.2 9.0 - - - +
717A LEU* 3.6 28.0 - - + +
718A TRP* 3.6 41.5 - - - +
721A PHE* 4.1 7.9 - - + -
749A PRO* 4.4 2.2 - - + -
752A CYS* 3.6 26.5 - - + -
756A VAL* 3.0 24.9 + - + +
757A TYR* 3.5 26.2 - - + +
759A ILE* 1.3 76.7 - - - +
761A ARG* 1.3 58.7 + - - +
763A CYS* 3.2 3.3 + - - +
764A TRP* 3.1 52.0 + - + -
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Residues in contact with ARG 761 (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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745A GLU* 2.4 50.3 + - - +
757A TYR* 2.9 51.0 + - + +
758A ALA* 3.7 8.7 - - - +
759A ILE 3.2 0.2 - - - -
760A MET* 1.3 74.5 - - - +
762A GLY* 1.3 65.0 + - - +
764A TRP* 3.2 18.5 + - + +
765A GLN* 3.7 21.6 + - - +
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Residues in contact with GLY 762 (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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758A ALA 2.9 14.6 + - - -
759A ILE* 2.9 5.7 + - - -
761A ARG* 1.3 76.6 - - - +
763A CYS* 1.3 61.9 + - - +
764A TRP 3.3 0.3 + - - -
765A GLN* 3.5 23.1 - - - +
771A ARG* 3.7 12.8 - - - -
772A HIS* 3.8 29.7 + - - -
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Residues in contact with CYS 763 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A VAL* 3.5 40.6 - - - +
711A TRP* 3.6 13.7 - - - -
713A PHE* 4.5 9.0 - - - -
714A GLY* 3.7 20.6 - - - -
717A LEU* 6.0 0.4 - - - -
759A ILE* 2.9 18.6 + - - -
760A MET 3.2 8.5 + - - +
762A GLY* 1.3 76.7 - - - +
764A TRP* 1.3 58.1 + - + +
765A GLN 3.4 1.8 - - - -
771A ARG* 3.4 22.2 - - - -
772A HIS 5.4 0.4 - - - +
777A VAL* 4.1 23.6 - - - -
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Residues in contact with TRP 764 (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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711A TRP* 3.2 58.8 + + + +
714A GLY* 3.6 21.0 - - - -
715A VAL* 3.6 13.0 - - + +
718A TRP* 4.1 11.2 - + + -
745A GLU* 3.9 41.5 - - + +
746A LEU* 3.6 59.2 - - + -
757A TYR* 4.1 8.7 - + - -
760A MET* 3.1 34.7 + - + +
761A ARG* 3.2 7.5 + - - +
762A GLY 3.1 1.2 - - - -
763A CYS* 1.3 84.3 - - + +
765A GLN* 1.3 62.9 + - - +
766A ARG* 3.4 2.1 + - - -
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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