Contacts of the helix formed by residues 776 - 789 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A ARG* 6.2 0.2 - - - -
821A TYR* 5.4 0.2 - - - -
773B TYR* 3.5 6.1 - - - -
775B HIS* 1.3 75.4 - - - +
777B GLU* 1.3 68.8 + - - -
778B GLN* 3.1 18.0 + - - -
779B ALA* 3.1 19.8 + - - +
8E C 3.1 14.6 + - - -
9F T 4.0 19.5 + - - -
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Residues in contact with GLU 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759A LYS* 3.1 23.9 + - - +
761A ALA* 5.7 4.9 - - - -
762A GLN* 2.9 30.0 + - + +
820A ARG* 4.8 16.8 - - - +
764B ALA* 3.9 7.6 - - + +
765B GLY* 4.5 10.8 - - - +
768B ALA* 3.8 21.9 - - + +
773B TYR* 4.6 0.6 - - - +
775B HIS 3.9 7.8 - - - +
776B GLY* 1.3 74.6 - - - -
778B GLN* 1.3 58.6 + - - +
779B ALA 3.3 0.2 - - - -
780B LEU* 3.1 12.6 + - + +
781B MET* 2.8 45.2 + - + +
9F T 5.3 0.2 + - - -
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Residues in contact with GLN 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A ARG* 5.7 1.4 - - - -
776B GLY* 3.3 21.0 - - - -
777B GLU* 1.3 70.1 + - - +
779B ALA* 1.3 73.5 + - - +
781B MET* 3.3 18.7 + - + +
782B MET* 3.0 34.7 + - + +
1301B ASW 3.5 32.0 - - + -
8E C 3.9 18.3 + - - +
9F T 3.6 24.9 + - + +
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Residues in contact with ALA 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B TYR* 3.5 13.5 - - - +
776B GLY 3.1 12.4 + - - +
778B GLN* 1.3 85.0 - - - +
780B LEU* 1.3 65.6 + - - +
782B MET* 3.3 9.3 + - - +
783B THR* 3.0 26.9 + - - -
6E A 4.6 4.8 - - + +
7E G 4.2 35.9 - - + +
8E C 5.1 2.0 - - - +
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Residues in contact with LEU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B GLY* 4.3 11.7 - - - +
745B VAL* 4.0 21.1 - - + -
764B ALA* 3.6 28.7 - - + +
767B VAL* 3.7 20.4 - - + -
768B ALA* 3.9 6.1 - - + +
773B TYR* 3.4 52.2 + - + -
776B GLY 3.6 1.2 + - - -
777B GLU* 3.1 15.8 + - - +
779B ALA* 1.3 80.1 - - - +
781B MET* 1.3 56.0 + - - +
783B THR* 3.3 8.8 + - - +
784B ILE* 2.9 34.9 + - + +
7E G 5.1 0.7 - - - +
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Residues in contact with MET 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760B VAL* 4.1 4.3 - - + +
761B ALA* 4.0 23.6 - - + +
764B ALA* 3.4 23.6 - - + -
777B GLU* 2.8 32.6 + - + +
778B GLN* 3.5 18.4 - - + +
779B ALA 3.2 0.4 - - - -
780B LEU* 1.3 77.0 - - - +
782B MET* 1.3 64.1 + - + +
784B ILE* 3.2 10.2 + - - +
785B VAL* 3.0 27.6 + - - +
819B PRO* 3.6 37.9 - - + -
820B ARG* 6.2 0.4 - - - -
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Residues in contact with MET 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778B GLN* 3.0 27.0 + - + +
779B ALA* 3.9 7.0 - - - +
781B MET* 1.3 75.7 - - + +
783B THR* 1.3 57.2 + - - +
785B VAL* 3.1 10.6 + - - +
786B ASN* 2.9 28.7 + - - +
819B PRO* 6.1 2.9 - - + -
5E G 5.8 5.4 - - + -
6E A 4.9 15.3 - - + +
7E G 5.9 6.7 - - - +
8E C 6.3 1.1 - - - -
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Residues in contact with THR 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B GLY* 4.7 2.7 - - - -
742B GLN* 3.8 39.5 - - + +
745B VAL* 4.6 8.1 - - + -
779B ALA 3.0 14.8 + - - -
780B LEU* 3.3 14.1 - - + +
782B MET* 1.3 75.2 - - - +
784B ILE* 1.3 63.2 + - - +
786B ASN* 3.1 6.4 + - - +
787B LEU* 2.9 27.4 + - + +
6E A 3.1 37.7 + - - +
7E G 4.7 1.9 + - - -
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Residues in contact with ILE 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745B VAL* 3.9 28.0 - - + -
760B VAL* 4.0 23.6 - - + +
763B LEU* 4.1 12.3 - - + -
764B ALA* 3.9 33.2 - - + +
767B VAL* 4.7 1.8 - - + -
780B LEU* 2.9 26.1 + - + +
781B MET* 3.2 8.0 + - - +
783B THR* 1.3 71.6 - - - +
785B VAL* 1.3 63.1 + - - +
787B LEU* 3.2 13.2 + - - +
788B ALA* 3.2 13.2 + - - +
800B LEU* 3.7 20.5 - - + +
806B PHE* 5.3 1.1 - - + -
824B THR* 4.0 18.4 - - + -
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Residues in contact with VAL 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760B VAL* 4.5 7.9 - - + -
781B MET 3.0 19.8 + - - +
782B MET* 3.1 11.2 + - - +
784B ILE* 1.3 74.9 - - - +
786B ASN* 1.3 61.9 + - - +
788B ALA* 3.2 11.8 + - - +
789B GLN* 3.2 36.4 + - - +
806B PHE* 3.8 24.0 - - + +
816B ALA* 4.3 13.7 - - + -
817B ALA 5.6 0.7 - - - +
819B PRO* 5.2 7.0 - - + -
822B ILE* 4.0 23.1 - - + -
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Residues in contact with ASN 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742B GLN* 4.4 13.7 + - - +
782B MET 2.9 11.8 + - - +
783B THR* 3.2 14.4 - - + +
785B VAL* 1.3 78.8 - - - +
787B LEU* 1.3 60.0 + - + +
788B ALA 3.3 0.7 + - - -
789B GLN* 3.5 20.9 + - - +
795B ASN* 3.0 22.7 + - - +
1303B MG 3.9 12.6 - - - -
5E G 3.1 42.6 + - - +
6E A 4.4 10.2 + - - +
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Residues in contact with LEU 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B PHE* 4.3 16.8 - - + -
742B GLN* 3.5 40.6 - - + +
745B VAL* 4.0 32.1 - - + -
746B LEU* 5.5 3.6 - - + +
783B THR* 2.9 26.5 + - + +
784B ILE* 3.2 5.8 + - - +
786B ASN* 1.3 77.2 - - - +
788B ALA* 1.3 59.9 + - - +
795B ASN* 3.6 9.1 + - - +
798B ASN* 3.6 15.2 - - - +
799B LEU* 3.6 20.5 + - + +
800B LEU* 3.8 18.1 + - + +
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Residues in contact with ALA 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B ILE 3.2 8.5 + - - +
785B VAL 3.2 2.2 + - - -
787B LEU* 1.3 76.7 - - - +
789B GLN* 1.3 68.4 + - - +
798B ASN* 3.6 5.3 - - - +
800B LEU* 3.3 28.0 - - + +
801B GLN 4.0 1.8 - - - +
802B PRO* 3.4 31.5 - - - +
806B PHE* 3.6 31.0 - - + -
824B THR* 4.3 1.6 - - - +
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Residues in contact with GLN 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785B VAL* 3.2 29.5 + - - +
786B ASN* 3.5 23.5 + - - +
787B LEU 3.5 2.0 - - - -
788B ALA* 1.3 79.2 - - - +
790B ASN* 1.3 59.2 + - - +
791B PHE* 3.6 26.5 - - + -
794B SER* 3.3 17.1 + - - +
795B ASN* 2.7 25.6 + - - +
798B ASN* 3.5 6.1 - - - +
802B PRO* 5.0 2.5 - - - -
806B PHE* 2.8 33.2 + - + +
812B GLY 5.5 0.3 - - - +
813B GLY* 4.0 14.6 + - - -
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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