Contacts of the helix formed by residues 742 - 765 (chain A) in PDB entry 3NC0
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 GLN 742 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A VAL* 3.0 42.3 - - - +
740A THR 3.2 1.8 + - - -
741A LYS* 1.3 77.9 - - - +
743A PRO* 1.3 80.6 - - + +
744A LEU* 3.4 3.9 + - + +
745A ILE* 3.4 11.2 + - + +
746A ARG* 3.2 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A GLN* 1.3 91.1 - - + +
744A LEU* 1.3 65.7 + - - +
746A ARG* 3.2 5.7 + - + +
747A SER* 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LYS* 3.6 36.6 - - + +
682A PRO* 3.9 30.7 - - + -
685A VAL* 4.6 5.8 - - + -
727A ASN* 5.6 1.6 - - - +
742A GLN* 3.4 5.1 + - + +
743A PRO* 1.3 79.9 - - + +
745A ILE* 1.3 63.0 + - + +
747A SER* 3.1 11.9 + - - -
748A MET* 2.9 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 4.9 3.4 - - - +
728A ILE* 4.2 27.4 - - + -
731A ALA* 4.2 16.4 - - + -
739A VAL* 3.3 38.8 - - + +
740A THR* 3.6 24.0 - - + +
742A GLN* 3.4 10.2 + - + +
743A PRO 3.3 0.6 - - - -
744A LEU* 1.3 80.3 - - + +
746A ARG* 1.3 59.8 + - - +
748A MET* 2.9 14.8 + - - +
749A ARG* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASP 5.3 3.1 - - - +
437A GLN* 2.8 67.7 + - - +
438A GLY* 4.3 5.3 - - - +
740A THR 3.1 23.5 + - - +
741A LYS* 3.2 38.3 - - - +
742A GLN 3.2 23.0 + - - +
743A PRO* 3.2 7.9 + - + +
745A ILE* 1.3 79.0 - - - +
747A SER* 1.3 59.5 + - - +
749A ARG* 3.5 7.0 - - - +
750A THR* 3.0 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A PRO* 4.6 2.8 + - - -
685A VAL* 3.2 32.7 + - - +
686A LYS* 4.1 6.8 + - - +
743A PRO 2.9 14.7 + - - -
744A LEU* 3.2 16.4 - - - -
745A ILE 3.0 0.2 - - - -
746A ARG* 1.3 76.6 - - - +
748A MET* 1.3 57.8 + - - +
750A THR* 3.0 26.4 + - - -
751A VAL* 3.4 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LEU 3.6 22.4 - - - +
680A LYS* 3.7 17.3 - - + -
685A VAL* 4.2 16.2 - - + -
724A LEU* 3.9 20.4 - - + +
727A ASN* 3.5 34.5 - - - +
728A ILE* 3.7 24.5 - - + -
744A LEU* 2.9 39.3 + - + +
745A ILE* 3.5 11.4 - - - +
747A SER* 1.3 70.1 - - - +
749A ARG* 1.3 66.5 + - - +
750A THR 3.1 1.7 + - - -
751A VAL* 3.4 4.2 + - - +
752A LYS* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 3.6 11.7 - - - +
728A ILE* 3.8 30.7 - - - +
732A ILE* 4.3 0.4 - - - +
740A THR* 4.1 20.1 - - - +
745A ILE* 2.8 31.2 + - - +
746A ARG* 3.5 14.4 - - - +
747A SER 3.3 0.2 - - - -
748A MET* 1.3 75.5 - - - +
750A THR* 1.3 58.3 + - - +
752A LYS* 3.2 16.4 + - + +
753A ARG* 2.9 49.0 + - - +
794A ALA 3.5 22.6 + - - -
795A ALA* 3.4 23.2 + - - +
796A ARG 5.1 3.8 + - - -
797A GLU* 4.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 3.5 17.1 + - + +
439A GLU* 3.4 28.0 + - - +
689A GLY* 4.7 12.8 - - - -
693A LYS* 4.5 7.2 - - - +
746A ARG 3.0 13.7 + - - -
747A SER* 3.0 13.6 + - - -
749A ARG* 1.3 77.3 - - - +
751A VAL* 1.3 60.9 + - - +
753A ARG* 3.9 4.8 - - - +
754A GLU* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 3.8 31.6 - - + +
688A LEU* 3.9 10.5 - - + -
689A GLY* 3.8 16.6 - - - +
692A LEU* 3.4 19.4 - - + +
717A MET* 6.4 0.2 - - + -
720A VAL* 4.2 16.4 - - + -
721A TYR* 5.2 2.9 - - - -
724A LEU* 3.3 33.0 - - + -
747A SER 3.4 2.6 + - - +
748A MET 3.4 1.6 + - - +
750A THR* 1.3 77.1 - - - +
752A LYS* 1.3 55.0 + - - +
755A THR* 2.6 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A TYR* 3.7 45.9 + - + +
724A LEU* 4.5 5.6 - - + -
725A SER* 3.2 35.1 + - - +
728A ILE* 3.9 24.2 - - + +
748A MET 3.3 10.8 - - - +
749A ARG* 3.3 16.3 - - - +
750A THR 3.1 0.2 - - - -
751A VAL* 1.3 78.6 - - - +
753A ARG* 1.3 57.3 + - - +
755A THR* 3.2 4.3 + - - -
756A LEU* 3.0 34.3 + - + +
791A ASN* 4.1 3.6 - - - +
795A ALA 4.0 18.6 + - - -
797A GLU* 4.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASP* 3.3 37.0 + - - -
437A GLN* 2.6 37.8 + - - +
749A ARG* 2.9 33.2 + - - +
750A THR* 4.0 5.4 - - - +
752A LYS* 1.3 76.3 - - - +
754A GLU* 1.3 61.4 + - + +
756A LEU* 3.2 10.9 + - - +
757A LYS* 2.9 31.1 + - + +
797A GLU* 3.8 32.1 + - - +
799A GLU* 4.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A GLY 4.7 1.8 - - - +
692A LEU* 4.0 21.7 - - + +
693A LYS* 2.7 52.1 + - + +
696A VAL* 3.6 22.2 - - + +
750A THR* 3.0 27.8 + - + +
751A VAL* 4.4 0.9 - - - +
753A ARG* 1.3 76.0 - - + +
755A THR* 1.3 60.1 + - - +
757A LYS* 3.4 29.9 + - - +
758A LEU* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LEU* 3.2 17.7 - - - +
717A MET* 3.9 26.8 + - + +
718A LEU* 4.7 2.2 - - + -
721A TYR* 3.7 31.4 - - + +
751A VAL* 2.6 29.2 + - - +
752A LYS 3.3 5.8 - - - -
754A GLU* 1.3 77.6 - - - +
756A LEU* 1.3 56.1 + - - +
758A LEU* 3.5 3.9 + - - +
759A ILE* 3.0 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A TYR* 4.2 10.8 - - + +
752A LYS 3.0 19.3 + - - +
753A ARG* 3.5 8.5 - - - +
754A GLU 3.1 0.2 - - - -
755A THR* 1.3 75.4 - - + +
757A LYS* 1.3 65.4 + - - +
759A ILE* 3.8 8.7 - - + +
760A SER* 2.9 25.8 + - - -
780A LEU* 6.3 0.2 - - + -
784A VAL* 4.0 29.8 - - + -
797A GLU* 3.7 29.6 - - + -
799A GLU* 3.9 11.0 - - + -
800A VAL* 3.9 19.7 - - + +
803A THR* 3.4 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A LYS* 5.3 2.2 - - - +
696A VAL* 4.3 18.5 - - + +
753A ARG* 2.9 16.2 + - + +
754A GLU* 3.4 39.0 + - - +
756A LEU* 1.3 75.5 - - - +
758A LEU* 1.3 52.8 + - - +
760A SER* 3.4 5.3 + - - -
761A GLY* 2.6 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LEU* 4.5 6.3 - - + -
695A ASN* 3.6 47.1 - - + +
696A VAL* 4.0 11.4 - - + +
699A CYS* 4.0 17.5 - - + -
706A PHE* 4.1 9.4 - - + -
710A LEU* 4.1 20.3 - - + +
713A ILE* 4.8 4.5 - - + -
717A MET* 3.9 24.0 - - + -
754A GLU 2.8 17.0 + - - +
755A THR* 3.6 6.1 - - - +
757A LYS* 1.3 77.6 - - - +
759A ILE* 1.3 62.9 + - - +
761A GLY* 4.9 0.7 - - - -
762A TRP* 3.1 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LEU* 5.4 3.1 - - - -
714A TYR* 3.7 30.3 - - + +
717A MET* 4.1 6.7 - - + -
718A LEU* 3.8 20.4 - - + -
755A THR* 3.0 30.2 + - + +
756A LEU* 3.3 11.2 + - + +
758A LEU* 1.3 77.4 - - - +
760A SER* 1.3 62.9 + - - +
762A TRP* 4.1 2.9 - - - +
763A VAL* 3.3 34.8 + - + +
780A LEU* 3.5 38.4 - - + -
784A VAL* 4.7 5.8 - - + -
803A THR* 4.7 8.7 - - + -
807A ILE* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A LEU 2.9 18.6 + - - -
757A LYS* 3.4 6.6 + - - -
759A ILE* 1.3 76.2 - - - +
761A GLY* 1.3 67.9 + - - +
762A TRP 3.2 0.7 + - - -
763A VAL* 3.5 4.6 + - - -
764A SER* 3.0 28.9 + - - -
803A THR* 3.9 33.8 + - - -
806A ILE* 4.1 23.5 - - - +
807A ILE* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A VAL* 6.4 0.4 - - - -
699A CYS* 4.3 4.4 - - - -
757A LYS 2.6 25.9 + - - -
758A LEU* 3.9 1.6 - - - -
760A SER* 1.3 75.9 + - - +
762A TRP* 1.3 59.1 + - - +
764A SER* 3.9 8.8 - - - -
765A ARG* 2.6 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A CYS* 3.7 24.2 - - - -
703A GLY 4.3 8.5 - - - -
704A HIS* 3.3 36.2 + + - +
706A PHE* 4.6 3.8 - + + -
707A VAL* 3.8 32.4 - - + +
710A LEU* 3.8 22.4 - - + -
758A LEU* 3.1 17.5 + - + +
759A ILE 4.1 1.1 - - - +
761A GLY* 1.3 76.3 - - - +
763A VAL* 1.3 102.0 + - + +
764A SER 2.9 1.8 - - - -
765A ARG* 2.8 17.5 + - + -
766A SER* 2.9 21.1 + - - -
771A MET* 4.5 2.0 - - + -
772A VAL* 3.6 33.2 - - + -
776A PHE* 4.0 28.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A TYR* 6.0 0.2 - - - +
759A ILE* 3.3 24.3 + - + +
760A SER 4.2 3.1 - - - +
762A TRP* 1.3 99.8 - - + +
764A SER* 1.3 59.5 + - - +
766A SER* 2.7 22.1 + - - +
772A VAL* 4.1 20.9 - - + -
776A PHE* 5.6 4.5 - - + +
777A VAL* 6.1 2.2 - - + -
780A LEU* 6.2 1.6 - - + -
806A ILE* 5.8 0.9 - - + -
807A ILE* 4.3 29.2 - - + -
810A LYS* 3.1 30.0 - - + -
811A LEU* 4.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A SER 3.0 21.3 + - - -
761A GLY* 3.9 8.9 - - - -
762A TRP 2.9 0.4 - - - -
763A VAL* 1.3 77.2 - - - +
765A ARG* 1.3 65.6 + - - +
806A ILE* 3.2 22.8 - - - +
810A LYS* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A VAL 5.6 0.4 + - - -
699A CYS* 4.3 10.1 + - - -
700A LYS* 3.6 57.4 + - - +
703A GLY* 4.6 14.8 - - - -
704A HIS* 3.6 20.7 + - - +
761A GLY* 2.6 38.2 + - - +
762A TRP* 2.8 12.8 + - + +
764A SER* 1.3 78.6 - - - +
766A SER* 1.3 62.8 + - - +
767A ASN* 4.9 1.2 - - - +
810A LYS* 4.8 0.4 - - - +
----------------------------------------------------------
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