Contacts of the helix formed by residues 776 - 789 (chain A) in PDB entry 4G0U
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 GLY 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773A TYR* 3.6 5.2 - - - -
775A HIS* 1.3 70.8 - - - +
777A GLU* 1.3 68.3 + - - -
778A GLN* 3.1 18.6 - - - -
779A ALA* 3.1 21.1 + - - +
8C C 2.9 21.4 + - - -
9D T 3.9 17.4 + - - -
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Residues in contact with GLU 777 (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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764A ALA* 4.0 8.9 - - + +
765A GLY* 4.7 7.4 - - - +
768A ALA* 3.9 21.3 - - + +
773A TYR* 4.6 2.2 - - - +
775A HIS 4.1 7.4 - - - +
776A GLY* 1.3 69.3 - - - -
778A GLN* 1.3 65.9 + - - +
779A ALA 3.1 0.4 - - - -
780A LEU* 3.2 12.8 + - + +
781A MET* 3.1 36.6 + - + +
759B LYS* 3.1 25.3 + - - +
761B ALA* 5.4 2.8 - - - +
762B GLN* 3.0 28.5 + - - -
820B ARG* 4.2 22.6 - - - +
9D T 5.5 0.3 + - - -
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Residues in contact with GLN 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A GLY* 3.4 23.6 + - - -
777A GLU* 1.3 73.4 + - - +
779A ALA* 1.3 69.3 + - - +
781A MET* 3.1 27.4 + - + +
782A MET* 3.2 24.1 + - - +
820B ARG* 5.1 3.3 - - - -
8C C 4.0 17.2 + - - +
9D T 3.3 30.3 + - + +
101F ASW 3.7 27.2 - - + -
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Residues in contact with ALA 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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773A TYR* 3.6 13.0 - - - +
776A GLY* 3.1 13.0 + - - +
778A GLN* 1.3 84.5 - - - +
780A LEU* 1.3 65.9 + - - +
782A MET* 3.2 9.3 + - - +
783A THR* 3.0 26.4 + - - -
6C A 4.5 5.0 - - + +
7C G 4.2 35.4 - - + +
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Residues in contact with LEU 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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741A GLY* 4.2 11.9 - - - +
745A VAL* 4.0 24.0 - - + -
764A ALA* 3.5 31.9 - - + +
767A VAL* 3.7 17.5 - - + -
768A ALA* 3.8 7.2 - - + +
773A TYR* 3.5 50.4 + - + +
776A GLY 3.9 0.6 + - - -
777A GLU* 3.2 12.8 + - + +
779A ALA* 1.3 76.9 - - - +
781A MET* 1.3 57.8 + - - +
783A THR* 3.2 7.1 + - - +
784A ILE* 2.7 37.7 + - + +
7C G 5.3 0.7 - - - +
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Residues in contact with MET 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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760A VAL* 4.0 8.8 - - + +
761A ALA* 3.9 31.9 - - + +
764A ALA* 3.5 15.3 - - + -
765A GLY 5.6 0.2 - - - +
777A GLU* 3.1 31.0 + - + +
778A GLN* 3.4 18.4 - - - +
779A ALA 3.1 1.0 - - - -
780A LEU* 1.3 76.3 - - - +
782A MET* 1.3 64.1 + - + +
784A ILE* 3.4 3.3 + - - +
785A VAL* 3.1 28.6 + - - +
819A PRO* 3.7 38.4 - - + -
820A ARG* 6.2 0.4 - - - -
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Residues in contact with MET 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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778A GLN* 3.2 18.5 + - - +
779A ALA* 3.2 9.1 + - - +
781A MET* 1.3 77.0 - - + +
783A THR* 1.3 54.3 + - - +
785A VAL* 3.2 10.0 + - + +
786A ASN* 2.8 35.0 + - - +
819A PRO* 6.1 2.9 - - + -
5C G 5.9 5.4 - - + -
6C A 4.7 13.5 - - + +
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Residues in contact with THR 783 (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 GLY* 4.5 3.2 - - - -
742A GLN* 3.7 42.2 - - + +
745A VAL* 4.3 11.2 - - + -
779A ALA 3.0 13.9 + - - -
780A LEU* 3.4 13.1 - - + +
782A MET* 1.3 74.0 - - - +
784A ILE* 1.3 65.6 + - - +
786A ASN* 3.3 3.6 + - - +
787A LEU* 3.0 24.2 + - + +
6C A 3.0 36.6 + - - +
7C G 4.9 2.1 + - - -
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Residues in contact with ILE 784 (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 VAL* 3.9 26.2 - - + -
760A VAL* 3.9 31.6 - - + +
763A LEU* 3.9 16.2 - - + -
764A ALA* 3.8 32.1 - - + +
767A VAL* 4.7 1.3 - - + -
780A LEU* 2.7 25.0 + - + +
781A MET 3.6 4.7 - - - +
782A MET 3.3 0.2 - - - -
783A THR* 1.3 72.3 - - - +
785A VAL* 1.3 63.7 + - - +
787A LEU* 3.1 15.1 + - - +
788A ALA* 3.2 12.5 + - - +
800A LEU* 3.8 20.2 - - + +
806A PHE* 5.3 1.3 - - + -
824A THR* 4.2 10.3 - - + -
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Residues in contact with VAL 785 (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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760A VAL* 4.5 7.6 - - + -
781A MET 3.1 15.8 + - - +
782A MET* 3.2 11.0 + - - +
784A ILE* 1.3 76.8 - - - +
786A ASN* 1.3 61.5 + - - +
788A ALA* 3.1 11.8 + - - +
789A GLN* 3.3 35.4 + - - +
806A PHE* 4.0 23.3 - - + +
816A ALA* 4.4 11.9 - - + -
817A ALA 5.8 0.7 - - - +
819A PRO* 5.3 5.8 - - + -
822A ILE* 3.8 26.9 - - + -
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Residues in contact with ASN 786 (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 GLN* 4.3 16.2 + - - +
782A MET 2.8 20.2 + - - +
783A THR* 3.5 10.1 - - - +
785A VAL* 1.3 75.2 - - - +
787A LEU* 1.3 57.5 + - - +
789A GLN* 3.8 18.4 + - - +
794A SER* 5.7 0.2 - - - -
795A ASN* 3.0 24.9 + - - +
5C G 3.1 42.2 + - - +
6C A 4.4 11.7 + - - +
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Residues in contact with LEU 787 (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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738A PHE* 4.4 13.5 - - + -
742A GLN* 4.0 38.1 - - + +
745A VAL* 3.9 32.3 - - + -
746A LEU* 5.2 6.7 - - + -
783A THR* 3.0 26.1 + - + +
784A ILE* 3.1 6.2 + - - +
786A ASN* 1.3 77.8 - - - +
788A ALA* 1.3 60.8 + - - +
789A GLN 3.4 0.4 - - - -
795A ASN* 3.8 9.2 + - - +
798A ASN* 3.6 5.2 - - - +
799A LEU* 3.6 31.1 + - + +
800A LEU* 3.7 17.9 + - + +
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Residues in contact with ALA 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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784A ILE 3.2 12.3 + - - +
785A VAL 3.1 3.3 + - - +
787A LEU* 1.3 78.4 - - - +
789A GLN* 1.3 64.1 + - - +
790A ASN 3.4 0.2 + - - -
798A ASN* 3.6 4.0 + - - -
800A LEU* 3.3 29.2 - - + +
801A GLN 4.0 8.5 - - - +
802A PRO* 3.2 26.5 - - - +
806A PHE* 3.9 26.2 - - + -
824A THR* 4.3 1.3 - - - +
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Residues in contact with GLN 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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785A VAL* 3.3 26.3 + - - +
786A ASN* 3.8 20.5 + - - +
787A LEU 3.4 1.4 - - - -
788A ALA* 1.3 79.7 - - - +
790A ASN* 1.3 59.2 + - - +
791A PHE* 3.6 27.4 - - + -
794A SER* 3.3 19.9 + - - +
795A ASN* 2.7 33.2 + - - +
798A ASN* 3.5 3.1 - - - +
802A PRO* 5.0 2.2 - - - -
806A PHE* 2.7 33.9 + - + +
812A GLY 5.5 0.2 - - - +
813A GLY* 3.8 15.6 + - - -
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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