Contacts of the helix formed by residues 710 - 733 (chain A) in PDB entry 6V3O
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 LYS 710 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A VAL* 6.1 2.2 - - + -
708A SER 3.4 3.7 + - - +
709A PRO* 1.3 75.4 - - - +
711A PRO* 1.3 76.4 - - + +
712A GLU* 3.4 22.1 + - - +
713A TRP* 3.3 52.6 + - + +
714A ARG* 3.1 20.5 + - - +
814A GLU* 5.1 8.9 + - - -
818A GLU* 3.8 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A PRO 4.4 2.2 - - - +
710A LYS* 1.3 87.3 - - + +
712A GLU* 1.3 69.3 + - - +
714A ARG* 3.0 13.9 + - + +
715A LYS* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LYS* 3.9 23.2 + - - +
711A PRO* 1.3 85.1 - - - +
713A TRP* 1.3 79.1 + - + +
715A LYS* 4.0 7.0 - - - +
716A LEU* 3.0 27.9 + - - +
811A VAL* 4.6 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A VAL* 4.5 9.9 - - + -
708A SER 4.5 4.3 - - - -
709A PRO* 3.9 6.3 - - + -
710A LYS* 3.3 55.6 + - + +
711A PRO 3.2 0.6 - - - -
712A GLU* 1.3 87.0 - - + +
714A ARG* 1.3 64.7 + - - +
716A LEU* 3.4 1.9 + - - +
717A MET* 3.0 29.8 + - - +
811A VAL* 3.9 12.5 + - + +
814A GLU* 4.5 5.9 + - + +
815A MET* 3.4 39.4 - - + +
818A GLU* 3.7 43.7 - - + -
819A TRP* 3.5 52.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 3.9 31.5 - - + -
618A TYR* 4.7 0.2 - - - -
619A ARG* 4.7 7.5 - - - +
622A GLU* 2.7 41.4 + - - -
709A PRO* 4.0 37.6 + - + +
710A LYS 3.1 11.6 + - - +
711A PRO* 3.0 13.5 + - + +
713A TRP* 1.3 77.5 - - - +
715A LYS* 1.3 57.1 + - - +
717A MET* 3.2 4.0 + - - +
718A ASP* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A PRO 3.0 15.6 + - - +
712A GLU* 4.0 7.2 - - - +
714A ARG* 1.3 75.8 - - - +
716A LEU* 1.3 68.5 + - - +
718A ASP* 3.1 12.8 + - + +
719A GLU* 2.7 66.2 + - + +
808A ASN* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A GLU 3.0 17.6 + - - +
713A TRP* 3.8 4.7 - - - +
715A LYS* 1.3 80.3 - - - +
717A MET* 1.3 56.9 + - - +
719A GLU* 3.8 17.6 - - + +
720A MET* 2.9 43.2 + - + +
801A ALA* 4.2 12.8 - - + -
808A ASN* 3.8 37.9 - - + +
811A VAL* 3.9 22.9 - - + -
812A LEU* 3.6 33.0 - - + -
815A MET* 4.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 4.2 26.2 - - + -
615A TRP* 3.5 50.6 - - + -
713A TRP 3.0 18.5 + - - +
714A ARG 3.5 4.5 - - - +
716A LEU* 1.3 76.8 - - - +
718A ASP* 1.3 64.7 + - - +
720A MET* 3.9 9.4 - - + +
721A ALA* 2.9 26.8 + - + +
815A MET* 4.1 6.5 - - + -
819A TRP* 3.9 18.8 - - + -
821A PHE* 4.0 14.4 - - + -
822A PHE* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 2.8 25.7 + - - +
619A ARG* 4.5 10.3 + - - -
714A ARG* 2.9 23.5 + - - +
715A LYS* 3.1 13.9 + - + +
717A MET* 1.3 77.8 - - - +
719A GLU* 1.3 63.2 + - + +
721A ALA* 3.4 9.8 + - - +
722A VAL* 3.5 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LYS* 2.7 56.6 + - + +
716A LEU* 3.8 17.4 - - + +
718A ASP* 1.3 76.2 - - + +
720A MET* 1.3 62.7 + - - +
722A VAL* 3.3 15.6 + - - +
723A VAL* 3.4 17.3 + - - +
800A PHE* 3.9 27.4 - - + -
804A LYS* 4.8 15.3 + - - +
808A ASN* 5.1 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 3.8 20.6 - - + -
716A LEU* 2.9 28.4 + - + +
717A MET* 4.0 12.1 - - - +
719A GLU* 1.3 75.7 - - + +
721A ALA* 1.3 57.5 + - - +
723A VAL* 3.3 5.3 + - - +
724A ALA* 2.9 32.3 + - - +
797A ALA* 3.6 28.0 - - + +
798A PHE* 3.3 40.4 - - + -
800A PHE* 5.0 2.5 - - + -
801A ALA* 4.1 21.3 - - + -
812A LEU* 4.3 18.6 - - + -
822A PHE* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 5.3 3.1 - - - +
612A SER* 3.1 25.5 + - - +
615A TRP* 4.3 15.7 - - + -
717A MET* 2.9 19.7 + - + +
718A ASP* 3.6 6.5 - - - +
719A GLU 3.2 0.4 - - - -
720A MET* 1.3 78.1 - - - +
722A VAL* 1.3 63.1 + - + +
724A ALA* 4.5 1.3 - - - -
725A THR* 3.0 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A ASP 3.5 15.0 - - - +
719A GLU* 3.3 8.0 + - - +
720A MET 3.3 0.6 - - - -
721A ALA* 1.3 76.6 - - + +
723A VAL* 1.3 60.4 + - + +
725A THR* 3.9 4.3 - - - -
726A GLU* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A GLU 3.5 14.4 - - - +
720A MET 3.3 5.7 + - - +
722A VAL* 1.3 79.1 - - + +
724A ALA* 1.3 64.0 + - - +
726A GLU* 3.3 14.6 + - - +
727A GLU* 3.1 22.8 + - + +
796A ALA* 3.8 32.7 - - + +
797A ALA* 4.4 4.9 - - - -
800A PHE* 3.7 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA 4.7 1.3 - - - +
609A GLY* 6.0 1.6 - - - -
611A LEU* 4.4 15.5 - - + +
612A SER* 3.6 13.7 - - - +
720A MET 2.9 18.3 + - - +
721A ALA 4.4 0.2 - - - -
723A VAL* 1.3 73.9 - - - +
725A THR* 1.3 60.6 + - - +
727A GLU 3.2 1.4 + - - -
728A TYR* 2.9 31.7 + - - +
793A GLY* 3.4 34.1 - - - +
797A ALA* 4.0 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.5 3.6 - - + +
608A ALA* 3.5 23.7 + - + +
612A SER* 2.8 29.0 + - - -
721A ALA 3.0 13.7 + - - -
722A VAL* 3.9 4.9 - - - -
724A ALA* 1.3 75.1 - - - +
726A GLU* 1.3 58.4 + - - +
728A TYR* 3.7 1.0 - - - +
729A ARG* 2.9 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A VAL* 3.0 21.5 + - + +
723A VAL* 3.6 16.1 - - - +
724A ALA 3.2 0.2 - - - -
725A THR* 1.3 78.2 - - - +
727A GLU* 1.3 58.0 + - - +
729A ARG* 3.9 4.1 - - - +
730A SER* 3.0 28.6 + - - -
734A LYS* 4.5 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A VAL* 3.1 15.1 + - + +
724A ALA 4.2 1.6 - - - +
726A GLU* 1.3 75.4 - - - +
728A TYR* 1.3 67.4 + - - +
730A SER* 3.1 26.0 + - - +
731A VAL* 3.5 15.1 + - + +
792A LEU* 4.5 14.5 - - - +
793A GLY* 4.8 8.0 + - - -
796A ALA* 3.1 32.3 + - + +
863A LYS* 4.5 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLY 3.6 6.1 - - - -
606A LYS* 2.8 39.6 + - - +
607A ASP 3.8 6.3 - - - -
608A ALA* 3.7 8.1 - - - -
609A GLY* 3.4 37.0 - - - +
724A ALA 2.9 17.8 + - - +
725A THR 3.7 3.1 - - - +
727A GLU* 1.3 79.6 - - - +
729A ARG* 1.3 65.4 + - + +
731A VAL* 3.3 2.3 + - - +
732A VAL* 3.1 46.9 + - + +
733A VAL* 5.6 0.7 - - + -
769A ILE* 5.2 0.2 - - - +
777A TRP* 3.5 26.2 + + - -
788A LEU* 6.4 0.2 - - + -
789A PRO* 4.8 12.8 - - + -
792A LEU* 3.8 40.7 - - + +
793A GLY* 4.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.3 6.9 - - - +
607A ASP* 3.6 41.2 + - - +
608A ALA* 3.7 17.8 - - - +
725A THR* 2.9 37.9 + - + +
726A GLU* 4.1 3.4 - - - +
728A TYR* 1.3 79.4 - - + +
730A SER* 1.3 57.6 + - - +
732A VAL* 4.1 6.3 - - - -
733A VAL* 3.0 26.1 + - + +
734A LYS* 3.0 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A GLU* 3.0 21.0 + - - -
727A GLU* 3.1 20.6 + - - +
728A TYR 3.2 0.6 - - - -
729A ARG* 1.3 75.7 - - - +
731A VAL* 1.3 67.2 + - - +
734A LYS* 3.8 20.1 - - - +
735A GLU* 3.6 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A GLU* 3.8 15.0 - - + +
728A TYR 3.3 2.9 + - - +
729A ARG 3.2 0.2 - - - -
730A SER* 1.3 91.0 + - - +
732A VAL* 1.3 61.2 + - - +
733A VAL 3.6 0.2 - - - -
735A GLU* 3.4 12.8 - - - +
738A PHE* 3.3 33.3 - - + +
788A LEU* 5.6 0.2 - - + -
792A LEU* 4.2 17.7 - - + -
856A PHE* 3.9 19.3 - - + -
860A LEU* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LYS 5.4 0.2 - - - +
728A TYR* 3.1 49.0 + - + +
731A VAL* 1.3 79.3 - - + +
733A VAL* 1.3 75.0 + - + +
735A GLU 5.1 0.2 - - - +
738A PHE* 3.4 41.7 - - + +
739A VAL* 5.4 3.3 - - - +
769A ILE* 3.5 28.6 + - + +
777A TRP* 3.7 15.7 - - + -
788A LEU* 6.0 0.2 - - + -
792A LEU* 5.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ASP 5.6 1.8 - - - +
728A TYR* 5.6 1.3 - - + -
729A ARG* 3.0 31.6 + - + +
732A VAL* 1.3 96.3 - - + +
734A LYS* 1.3 69.6 + - + +
735A GLU 3.3 7.0 + - - +
736A ALA* 5.6 0.5 - - - -
769A ILE* 6.1 2.0 - - + -
770A THR* 5.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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