Contacts of the helix formed by residues 764 - 782 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B ILE* 3.7 38.6 - - + -
762B ASN 3.5 8.5 - - - +
763B THR* 1.3 97.2 - - + +
765B LYS* 1.3 65.7 + - - +
766B THR* 3.4 13.2 - - - +
767B LEU* 3.5 11.3 + - + -
768B LEU* 3.3 19.4 + - - +
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Residues in contact with LYS 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B THR 5.6 1.1 - - - +
764B PRO* 1.3 73.3 - - - +
766B THR* 1.3 66.8 + - + +
768B LEU* 3.1 13.5 + - + +
769B GLU* 3.0 37.0 + - - +
803B ASN* 5.8 3.8 - - - +
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Residues in contact with THR 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ILE* 5.5 3.6 - - - +
726B ASN* 3.1 20.0 + - - -
764B PRO* 4.3 8.8 - - - +
765B LYS* 1.3 78.6 - - + +
767B LEU* 1.3 62.1 + - - +
769B GLU* 3.7 17.3 - - - +
770B ASN* 3.3 19.9 + - - +
12D GLY* 5.7 0.3 - - - -
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Residues in contact with LEU 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B PRO* 4.9 12.6 - - + +
722B ILE* 4.6 19.7 - - + -
725B CYS* 4.2 21.3 - - + +
726B ASN* 3.5 37.9 - - + +
729B THR* 4.4 4.7 - - + +
757B ILE* 4.1 12.1 - - + -
763B THR* 3.7 21.3 - - + -
764B PRO* 3.5 19.4 + - + +
765B LYS 3.2 0.6 - - - -
766B THR* 1.3 80.3 + - - +
768B LEU* 1.3 56.3 + - - +
769B GLU 3.2 0.2 - - - -
770B ASN* 3.4 0.9 + - - -
771B THR* 2.7 48.3 + - - +
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Residues in contact with LEU 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B ILE* 3.7 4.5 - - + +
758B ILE* 3.7 41.6 - - + +
760B ARG 4.9 3.8 - - - +
763B THR* 3.7 37.0 - - + +
764B PRO 3.3 11.0 + - - +
765B LYS* 3.1 13.8 + - + +
767B LEU* 1.3 77.0 - - - +
769B GLU* 1.3 58.4 + - - +
771B THR* 3.7 3.6 - - - -
772B ALA* 2.9 31.0 + - - +
796B PRO* 5.7 4.0 - - + -
800B SER* 3.6 19.3 + - - +
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Residues in contact with GLU 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B LYS* 3.0 30.4 + - - +
766B THR* 3.7 19.8 - - - +
767B LEU 3.2 0.2 - - - -
768B LEU* 1.3 77.1 - - - +
770B ASN* 1.3 58.8 + - - +
772B ALA* 3.4 2.3 + - - +
773B ILE* 2.9 36.8 + - + +
800B SER* 3.7 15.8 - - - +
801B LEU* 4.0 3.5 - - - +
803B ASN* 4.9 3.6 - - - +
804B ILE* 3.6 33.7 - - + +
11D THR 3.3 20.8 - - - +
12D GLY* 4.9 1.3 - - - -
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Residues in contact with ASN 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ASN* 2.9 33.8 + - - +
729B THR* 3.7 16.6 - - - +
730B TRP* 4.1 15.4 - - + +
766B THR* 3.3 10.7 + - - +
767B LEU 3.9 2.5 - - - +
769B GLU* 1.3 76.7 - - - +
771B THR* 1.3 58.2 + - - +
773B ILE* 3.8 10.2 - - - +
774B THR* 2.7 38.5 + - - -
12D GLY* 3.2 30.5 - - - -
13D GLY 3.3 17.0 + - - +
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Residues in contact with THR 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B THR* 4.3 10.6 + - - +
754B LEU* 3.4 36.8 - - + +
757B ILE* 3.8 15.7 - - + +
758B ILE* 3.8 18.6 - - + +
767B LEU* 2.7 31.6 + - - +
768B LEU* 3.7 8.3 - - - -
770B ASN* 1.3 77.9 - - - +
772B ALA* 1.3 57.1 + - - +
774B THR* 3.7 4.5 - - - -
775B ILE* 3.0 41.1 + - + +
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Residues in contact with ALA 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ILE* 4.1 12.1 - - + +
768B LEU 2.9 18.4 + - - +
769B GLU 3.7 3.1 - - - +
771B THR* 1.3 76.2 - - - +
773B ILE* 1.3 59.9 + - - +
775B ILE* 3.4 1.5 + - - +
776B GLY* 2.8 25.3 + - - -
797B TRP* 3.1 38.1 + - + +
800B SER* 4.6 2.0 - - - +
801B LEU* 3.7 22.2 - - + +
813B ALA* 4.7 0.2 - - - +
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Residues in contact with ILE 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B TRP* 6.3 0.7 - - + -
733B GLY* 6.2 0.4 - - - -
769B GLU* 2.9 26.1 + - + +
770B ASN* 3.8 9.0 - - - +
772B ALA* 1.3 74.8 - - - +
774B THR* 1.3 54.8 + - - +
776B GLY* 3.3 0.9 + - - -
777B ARG* 2.7 66.8 + - - +
801B LEU* 4.3 13.5 - - + -
804B ILE* 5.0 6.5 - - + -
809B GLU* 3.7 42.0 - - + +
810B LYS* 5.4 0.9 - - - -
812B SER* 4.9 0.2 - - - +
813B ALA* 4.2 12.3 - - + +
11D THR 4.9 2.2 - - - -
12D GLY* 4.5 17.7 - - - +
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Residues in contact with THR 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B THR* 2.5 34.3 + - - +
730B TRP* 4.0 2.6 + - - -
732B ILE* 3.9 12.3 - - + -
733B GLY* 3.5 24.4 + - - +
754B LEU* 3.7 22.9 - - + -
770B ASN 2.7 23.5 + - - -
771B THR* 3.7 5.2 - - - -
773B ILE* 1.3 75.3 - - - +
775B ILE* 1.3 55.5 + - - +
777B ARG* 3.0 2.1 + - - +
778B LEU* 2.7 40.3 + - + +
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Residues in contact with ILE 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B LEU* 4.7 8.3 - - + -
754B LEU* 3.8 40.8 - - + +
755B VAL* 4.3 7.6 - - + +
758B ILE* 4.5 15.0 - - + -
771B THR* 3.0 30.9 + - + +
772B ALA* 3.7 4.3 - - - +
774B THR* 1.3 75.1 - - - +
776B GLY* 1.3 57.6 + - - +
778B LEU* 3.2 10.8 + - - +
779B GLY* 2.9 24.9 + - - -
786B VAL* 4.2 11.8 - - + +
793B PHE* 3.6 44.2 - - + -
797B TRP* 4.9 0.9 - - + -
820B MET* 5.3 0.9 - - - +
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Residues in contact with GLY 776 (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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772B ALA 2.8 16.7 + - - -
773B ILE 3.6 1.6 - - - -
775B ILE* 1.3 77.3 - - - +
777B ARG* 1.3 59.6 + - - +
779B GLY* 3.3 1.6 + - - -
780B TYR* 3.2 19.6 + - - +
797B TRP* 4.3 6.7 - - - +
812B SER 4.3 0.3 - - - +
813B ALA* 4.0 22.9 - - - -
816B GLY* 3.2 15.9 - - - -
817B ILE* 4.9 5.2 - - - -
820B MET* 6.0 1.1 - - - -
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Residues in contact with ARG 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B TRP* 4.9 7.1 + - - -
733B GLY* 3.3 30.3 + - - +
734B GLU* 3.4 27.3 + - - +
736B SER* 3.9 4.7 - - - -
737B ILE* 3.6 33.3 - - + +
773B ILE* 2.7 39.5 + - - +
774B THR* 3.0 7.2 + - - +
776B GLY* 1.3 70.0 - - - +
778B LEU* 1.3 64.7 + - - +
780B TYR* 3.8 7.0 + - + +
781B VAL* 3.5 25.2 + - + +
808B GLU* 4.5 2.8 + - - +
809B GLU* 3.5 24.0 + - - -
812B SER* 2.9 39.4 + - - -
813B ALA* 4.8 0.4 - - - +
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Residues in contact with LEU 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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732B ILE* 4.3 10.8 - - + -
736B SER* 3.2 23.1 - - - +
743B MET* 4.1 8.3 - - + -
747B ILE* 3.7 27.3 - - + +
750B VAL* 4.4 11.9 - - + -
751B LEU* 4.6 15.5 - - + +
754B LEU* 3.8 29.2 - - + -
774B THR* 2.7 28.6 + - + +
775B ILE* 3.4 9.0 - - - +
777B ARG* 1.3 72.7 - - - +
779B GLY* 1.3 57.0 + - - +
781B VAL* 3.5 2.6 + - - +
782B CYS* 3.0 31.2 + - - +
786B VAL* 3.8 12.4 - - + +
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Residues in contact with GLY 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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775B ILE 2.9 11.7 + - - -
776B GLY 3.3 3.7 + - - -
777B ARG 3.2 0.4 - - - -
778B LEU* 1.3 74.4 - - - +
780B TYR* 1.3 63.8 + - - +
781B VAL 3.1 2.0 - - - -
782B CYS 4.3 0.2 - - - -
783B PRO* 3.1 29.8 - - - +
786B VAL* 4.0 6.9 - - - +
816B GLY 4.3 1.1 - - - -
819B THR* 3.5 6.5 + - - -
820B MET* 3.6 27.8 - - - +
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Residues in contact with TYR 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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776B GLY 3.2 10.2 + - - +
777B ARG* 4.1 7.6 - - + +
778B LEU 3.5 0.4 - - - -
779B GLY* 1.3 76.0 - - - +
781B VAL* 1.3 70.8 + - + +
783B PRO* 4.3 6.1 - - - +
812B SER 4.6 4.7 - - - +
815B ARG* 3.6 45.2 - - + -
816B GLY* 3.5 13.1 - - - +
819B THR* 3.6 21.3 + - + +
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Residues in contact with VAL 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B SER* 3.3 28.5 - - - +
737B ILE* 4.6 3.4 - - - +
740B GLY* 3.1 36.8 - - - +
741B ILE* 4.0 11.6 - - - +
743B MET* 3.9 10.1 - - + -
777B ARG* 3.5 19.5 + - + +
778B LEU* 3.5 3.6 + - - +
779B GLY 3.1 0.6 - - - -
780B TYR* 1.3 90.1 - - + +
782B CYS* 1.3 73.3 + - + +
783B PRO* 3.4 7.8 - - - +
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Residues in contact with CYS 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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741B ILE* 3.6 20.2 - - + -
743B MET* 4.2 2.7 - - - -
744B GLN* 3.6 36.6 - - - -
747B ILE* 4.5 6.3 - - + -
778B LEU 3.0 10.3 + - - +
779B GLY 3.5 2.9 - - - -
781B VAL* 1.3 95.2 - - - +
783B PRO* 1.3 65.0 - - - +
784B GLN 3.4 2.7 - - - -
785B GLU* 3.3 22.8 + - + -
786B VAL* 3.3 21.0 - - - +
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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
------------------------------------------------------------
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