Contacts of the helix formed by residues 764 - 782 (chain A) in PDB entry 5J3V
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 764 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A ILE* 3.8 43.7 - - + -
763A THR* 1.3 92.3 - - + +
765A LYS* 1.3 63.2 + - - +
766A THR* 3.8 20.0 - - + +
767A LEU* 3.4 12.3 + - + +
768A LEU* 3.3 19.9 + - - +
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Residues in contact with LYS 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A THR 3.9 0.9 + - - +
764A PRO* 1.3 71.1 - - - +
766A THR* 1.3 61.7 + - + +
768A LEU* 3.1 14.1 + - + +
769A GLU* 2.8 55.1 + - + +
800A SER 5.9 0.4 - - - -
803A ASN* 3.9 28.6 - - - +
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Residues in contact with THR 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ILE* 5.7 1.4 - - - +
726A ASN* 3.2 19.5 + - - -
764A PRO* 3.8 15.7 - - + +
765A LYS* 1.3 80.3 - - + +
767A LEU* 1.3 57.8 + - - +
769A GLU* 4.2 11.7 - - - +
770A ASN* 3.3 20.6 + - - +
12C GLY* 5.1 6.5 - - - -
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Residues in contact with LEU 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PRO* 4.9 7.0 - - + -
722A ILE* 4.4 21.8 - - + -
725A CYS* 4.0 27.4 - - + +
726A ASN* 3.7 36.8 - - + +
729A THR* 4.4 4.3 - - - +
757A ILE* 4.1 15.3 - - + -
763A THR* 4.9 11.4 - - + -
764A PRO* 3.4 24.7 + - + +
765A LYS 3.1 0.6 - - - -
766A THR* 1.3 80.8 + - - +
768A LEU* 1.3 56.3 + - + +
770A ASN* 3.9 0.6 - - + -
771A THR* 2.5 48.7 + - - +
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Residues in contact with LEU 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A ILE* 3.7 17.0 - - + +
758A ILE* 3.7 32.2 - - + +
760A ARG 4.7 2.2 - - - +
762A ASN 4.6 2.9 - - - +
763A THR* 3.8 23.6 - - - +
764A PRO 3.6 12.3 - - - +
765A LYS* 3.1 16.7 + - + +
767A LEU* 1.3 76.3 - - - +
769A GLU* 1.3 65.0 + - - +
771A THR* 3.3 4.4 + - - -
772A ALA* 3.0 24.8 + - - +
796A PRO* 6.0 2.2 - - + +
800A SER* 3.6 19.2 + - - +
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Residues in contact with GLU 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A LYS* 2.8 46.8 + - + +
766A THR* 4.2 12.0 - - - +
768A LEU* 1.3 71.0 - - - +
770A ASN* 1.3 63.4 + - - +
772A ALA* 3.3 2.3 + - - +
773A ILE* 3.1 32.5 + - + +
800A SER* 3.7 17.3 - - - +
801A LEU* 4.2 4.2 - - - +
803A ASN* 4.2 3.3 - - - +
804A ILE* 3.6 35.9 - - + +
11C THR 3.0 22.6 - - - +
12C GLY* 4.9 0.4 - - - -
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Residues in contact with ASN 770 (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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726A ASN* 3.2 20.5 + - - +
729A THR* 3.9 7.0 - - + -
730A TRP* 3.5 37.2 - - - +
766A THR 3.3 14.7 + - - +
767A LEU* 3.9 3.8 - - + +
768A LEU 3.3 0.4 - - - -
769A GLU* 1.3 79.7 - - - +
771A THR* 1.3 56.0 + - - +
773A ILE* 4.1 9.8 - - - +
774A THR* 2.8 35.1 + - - -
12C GLY* 3.6 7.7 - - - -
13C GLY 2.6 34.3 + - - +
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Residues in contact with THR 771 (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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729A THR* 3.6 10.4 + - - +
754A LEU* 3.4 48.5 - - + +
757A ILE* 3.9 14.4 - - + +
758A ILE* 3.6 13.9 - - + -
767A LEU* 2.5 35.1 + - - +
768A LEU* 3.8 5.6 - - - -
769A GLU 3.2 0.2 - - - -
770A ASN* 1.3 74.9 - - - +
772A ALA* 1.3 60.8 + - - +
774A THR* 3.5 1.2 + - - -
775A ILE* 3.0 29.9 + - - +
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Residues in contact with ALA 772 (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 ILE* 4.3 6.9 - - + +
768A LEU 3.0 17.1 + - - +
769A GLU 3.6 4.3 - - - +
771A THR* 1.3 74.9 - - - +
773A ILE* 1.3 59.6 + - - +
775A ILE* 3.4 1.3 + - - +
776A GLY* 2.8 24.9 + - - -
797A TRP* 2.9 44.1 + - + +
800A SER* 4.6 2.5 - - - +
801A LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 773 (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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769A GLU* 3.1 23.3 + - + +
770A ASN* 4.1 10.5 - - - +
772A ALA* 1.3 75.4 - - - +
774A THR* 1.3 53.7 + - - +
776A GLY* 3.2 0.9 + - - -
777A ARG* 2.8 67.6 + - + +
801A LEU* 4.5 11.0 - - + -
804A ILE* 5.3 4.3 - - + -
809A GLU* 3.7 45.3 - - + +
810A LYS* 5.7 0.7 - - - -
813A ALA* 3.9 12.4 - - + +
11C THR* 4.7 4.0 - - - -
12C GLY* 4.5 14.1 - - - +
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Residues in contact with THR 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A THR* 2.7 39.3 + - + +
730A TRP* 4.1 2.9 + - - -
732A ILE* 3.9 15.9 - - + -
733A GLY* 3.5 26.0 - - - +
754A LEU* 4.0 15.9 - - + -
770A ASN* 2.8 22.0 + - - -
771A THR 3.8 2.5 - - - -
773A ILE* 1.3 79.3 - - - +
775A ILE* 1.3 57.2 + - - +
777A ARG* 3.3 2.6 + - - +
778A LEU* 2.8 29.5 + - + +
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Residues in contact with ILE 775 (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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751A LEU* 5.1 4.9 - - + +
754A LEU* 3.7 39.5 - - + -
755A VAL* 4.1 14.8 - - + +
758A ILE* 3.6 25.8 - - + -
771A THR 3.0 18.1 + - - +
772A ALA* 3.7 5.8 - - - +
774A THR* 1.3 75.0 - - - +
776A GLY* 1.3 53.7 + - - +
778A LEU* 3.1 9.2 + - + +
779A GLY* 2.8 32.6 + - - -
786A VAL* 4.5 7.9 - - + +
793A PHE* 3.8 35.9 - - + -
797A TRP* 4.7 2.0 - - - +
820A MET* 4.2 4.8 - - + +
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Residues in contact with GLY 776 (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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772A ALA 2.8 16.2 + - - -
773A ILE 3.2 3.6 + - - -
775A ILE* 1.3 78.1 - - - +
777A ARG* 1.3 56.6 + - - +
779A GLY* 3.3 1.0 + - - -
780A TYR* 3.0 23.7 + - - +
797A TRP* 4.3 4.2 - - - +
812A SER 4.3 2.9 - - - -
813A ALA* 3.8 22.7 - - - -
816A GLY* 3.4 12.2 - - - -
820A MET* 4.5 9.2 - - - -
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Residues in contact with ARG 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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730A TRP* 5.0 5.1 - - - +
733A GLY* 3.5 29.2 - - - +
734A GLU* 2.7 39.2 + - - +
736A SER* 4.0 6.2 - - - -
737A ILE* 3.4 28.3 - - + +
773A ILE* 2.8 36.1 + - + +
774A THR* 3.7 4.7 - - - +
776A GLY* 1.3 74.3 - - - +
778A LEU* 1.3 60.4 + - - +
779A GLY 3.4 0.2 - - - -
780A TYR* 3.6 6.7 + - - +
781A VAL* 3.3 28.3 + - - +
808A GLU* 5.0 6.9 + - - +
809A GLU* 3.9 28.5 + - - +
812A SER* 3.3 35.0 + - - +
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Residues in contact with LEU 778 (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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732A ILE* 4.2 7.6 - - + -
736A SER* 3.2 22.4 - - - +
743A MET* 3.8 27.1 - - + -
747A ILE* 4.1 21.0 - - + +
750A VAL* 4.5 7.0 - - + -
751A LEU* 5.5 7.0 - - + +
754A LEU* 3.7 28.9 - - + -
774A THR* 2.8 25.7 + - + +
775A ILE* 3.4 8.1 - - + +
777A ARG* 1.3 78.3 - - - +
779A GLY* 1.3 61.1 + - - +
781A VAL* 3.3 4.9 - - + +
782A CYS* 3.3 25.1 + - - +
786A VAL* 3.7 12.3 - - + +
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Residues in contact with GLY 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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775A ILE 2.8 15.3 + - - -
776A GLY 3.3 2.6 + - - -
778A LEU* 1.3 76.6 - - - +
780A TYR* 1.3 62.6 + - - +
782A CYS 4.1 0.2 - - - -
783A PRO* 3.4 26.9 - - - +
786A VAL* 3.9 10.7 - - - +
816A GLY 4.2 8.5 - - - +
819A THR* 4.3 1.9 - - - -
820A MET* 3.7 23.5 - - - +
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Residues in contact with TYR 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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776A GLY 3.0 16.5 + - - +
777A ARG* 3.8 8.5 - - - +
778A LEU 3.3 0.4 - - - -
779A GLY* 1.3 81.2 - - - +
781A VAL* 1.3 73.1 + - + +
783A PRO* 4.4 2.1 - - - +
812A SER 4.6 3.6 - - - +
815A ARG* 3.4 52.1 - - + -
816A GLY* 3.6 9.9 - - - +
819A THR* 3.7 18.9 - - + +
852A MET* 6.0 2.0 - - + -
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Residues in contact with VAL 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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736A SER* 3.4 30.5 - - - +
737A ILE* 4.7 6.1 - - + +
740A GLY* 3.2 29.2 - - - +
741A ILE* 3.9 14.9 + - - +
743A MET* 4.4 6.7 - - + -
777A ARG 3.3 20.2 - - - +
778A LEU* 3.3 13.5 - - + +
780A TYR* 1.3 95.7 - - + +
782A CYS* 1.3 71.3 + - - +
783A PRO* 3.8 5.0 - - - +
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Residues in contact with CYS 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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740A GLY 3.6 16.6 - - - -
741A ILE* 3.6 25.1 - - + -
743A MET 4.2 2.2 - - - -
744A GLN* 3.6 20.2 - - + -
747A ILE* 3.5 19.5 - - + -
778A LEU 3.3 2.0 + - - -
779A GLY 3.8 2.7 - - - -
781A VAL* 1.3 92.5 - - - +
783A PRO* 1.3 67.1 - - - +
784A GLN* 3.2 3.7 + - - +
785A GLU* 3.6 12.1 + - - +
786A VAL* 3.2 21.5 - - - +
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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
------------------------------------------------------------
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