Contacts of the helix formed by residues 744 - 761 (chain A) in PDB entry 3ODX
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 THR 744 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A LYS* 5.0 2.9 - - - +
742A ALA* 3.6 9.5 - - - +
743A GLN* 1.3 77.9 - - + +
745A VAL* 1.3 66.3 + - - +
746A SER* 3.3 26.4 + - - +
747A GLU* 3.0 37.5 + - + +
748A ARG* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A HIS* 3.5 36.1 - - + +
723A LYS* 4.1 18.0 - - + +
743A GLN 4.2 0.4 + - - -
744A THR* 1.3 73.7 + - - +
746A SER* 1.3 60.3 + - - +
748A ARG* 3.0 41.5 - - - +
749A LYS* 3.1 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A THR* 3.3 20.2 + - - +
745A VAL* 1.3 80.2 - - - +
747A GLU* 1.3 65.8 + - - +
749A LYS* 3.2 16.0 - - - +
750A ASN* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A ALA* 4.0 7.0 - - + +
743A GLN* 4.1 13.5 + - - +
744A THR* 3.0 35.2 + - + +
745A VAL 3.3 0.4 - - - -
746A SER* 1.3 84.1 + - - +
748A ARG* 1.3 52.6 + - - +
750A ASN* 3.1 16.3 + - - +
751A TRP* 2.7 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLU* 2.9 45.5 + - - +
718A VAL 5.6 0.4 - - - -
722A HIS* 2.9 37.0 + - - +
723A LYS 3.4 27.8 - - - +
724A ALA 3.3 15.6 + - - -
725A PHE* 3.8 16.9 - - + +
742A ALA* 3.6 11.8 - - + +
744A THR 3.4 2.4 + - - -
745A VAL* 3.0 38.0 + - - +
747A GLU* 1.3 74.3 - - - +
749A LYS* 1.3 84.5 + - - +
751A TRP* 3.8 8.6 - - - +
752A CYS* 3.3 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLU* 5.1 7.9 + - - -
745A VAL* 3.1 26.3 + - + +
746A SER* 3.2 15.5 - - - +
747A GLU 3.2 0.2 - - - -
748A ARG* 1.3 102.8 - - - +
750A ASN* 1.3 63.3 - - - +
752A CYS* 3.4 3.7 + - - +
753A ALA* 3.1 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A HIS* 3.8 30.3 + - - -
746A SER 2.9 14.3 + - - +
747A GLU* 3.1 23.1 + - - +
749A LYS* 1.3 76.9 - - - +
751A TRP* 1.3 59.6 + - - +
753A ALA* 3.3 7.6 - - - +
754A LEU* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A HIS* 3.7 32.2 - + + -
651A GLU* 3.7 2.5 - - - -
652A GLY* 3.6 32.3 - - - -
654A LEU* 3.2 45.6 - - + +
668A VAL* 3.6 34.1 - - + -
670A LEU* 4.7 13.7 - - + -
675A LEU* 5.7 0.2 - - + -
725A PHE* 3.8 19.7 - + + -
742A ALA* 4.5 3.3 - - + +
747A GLU* 2.7 45.1 + - + +
748A ARG* 4.0 5.2 - - - +
749A LYS 3.3 0.6 - - - -
750A ASN* 1.3 71.1 - - - +
752A CYS* 1.3 60.5 + - - +
754A LEU* 3.1 7.3 + - + +
755A ILE* 2.8 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A THR* 3.2 29.8 + - - +
716A ARG 4.7 4.7 - - - -
725A PHE* 3.5 38.1 - - - -
748A ARG* 3.3 20.9 - - - +
749A LYS* 3.4 6.8 + - - +
751A TRP* 1.3 70.1 - - - +
753A ALA* 1.3 61.3 + - - +
755A ILE* 4.7 0.4 - - - -
756A THR* 2.5 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A LYS 3.1 12.2 + - - +
750A ASN* 3.3 16.2 - - - +
752A CYS* 1.3 80.8 - - - +
754A LEU* 1.3 63.7 + - + +
756A THR* 3.1 11.4 + - - -
757A GLU* 3.2 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A VAL* 4.7 9.9 - - + +
650A HIS* 3.3 50.5 - - + +
670A LEU* 3.8 10.5 - - + -
750A ASN* 3.0 26.8 + - - +
751A TRP* 3.1 5.3 + - + +
753A ALA* 1.3 78.9 - - + +
755A ILE* 1.3 62.3 + - - +
757A GLU* 3.4 17.9 + - - +
758A THR* 2.6 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A LEU* 4.0 16.4 - - + -
675A LEU* 4.0 24.7 - - + -
710A LEU* 3.9 23.1 - - + +
713A ALA* 4.2 12.6 - - + -
714A MET 5.2 0.2 - - - +
715A THR* 3.9 26.5 - - + -
725A PHE* 4.3 11.4 - - + -
727A VAL* 4.2 17.7 - - + -
740A LEU* 6.2 0.9 - - + -
751A TRP* 2.8 36.9 + - + +
754A LEU* 1.3 70.8 - - - +
756A THR* 1.3 53.7 + - + +
758A THR* 2.8 6.9 + - - -
759A ALA* 2.6 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A ALA 5.7 0.4 - - - +
714A MET* 4.4 7.2 - - + -
715A THR* 3.2 42.6 + - + +
752A CYS 2.5 26.1 + - - -
753A ALA* 3.1 8.1 + - - -
755A ILE* 1.3 74.1 - - - +
757A GLU* 1.3 55.5 + - - +
759A ALA* 3.7 7.9 - - - +
760A GLY* 2.9 25.1 + - - -
548B ARG* 5.4 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A ALA* 3.2 21.9 + - - +
754A LEU* 3.6 21.3 - - - +
756A THR* 1.3 76.7 - - - +
758A THR* 1.3 60.9 + - - +
760A GLY* 3.4 2.0 + - - -
761A SER* 3.1 29.6 + - - +
548B ARG* 5.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A VAL* 3.9 22.4 - - + +
670A LEU* 3.7 16.3 - - + +
671A LEU 3.9 12.6 - - - +
672A ASP* 3.4 24.0 - - - +
710A LEU* 4.3 3.1 - - + -
754A LEU* 2.6 21.3 + - - +
755A ILE 2.8 9.8 + - - -
757A GLU* 1.3 70.5 - - - +
759A ALA* 1.3 67.0 + - - -
761A SER* 3.1 16.1 + - - -
762A LEU* 3.0 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LEU* 4.0 34.5 - - + +
711A THR* 5.1 2.8 - - - -
713A ALA* 4.1 22.4 - - + +
755A ILE 2.6 20.9 + - - +
756A THR* 3.7 10.3 - - - +
758A THR* 1.3 73.2 - - - +
760A GLY* 1.3 62.4 + - - +
762A LEU* 3.2 21.8 + - - +
550B ARG* 5.5 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A THR 2.9 20.4 + - - -
757A GLU 3.7 2.0 - - - -
758A THR 3.2 0.4 - - - -
759A ALA* 1.3 70.6 - - - +
761A SER* 1.3 52.3 + - - +
762A LEU 2.8 25.1 + - - +
547B PRO* 3.4 14.1 - - - +
548B ARG* 4.1 29.7 + - - -
550B ARG* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A GLU* 3.1 15.8 + - - +
758A THR* 3.2 17.7 - - - -
760A GLY* 1.3 72.3 - - - +
762A LEU* 1.3 62.2 + - - +
763A LYS* 3.9 2.3 + - - +
547B PRO* 4.2 18.1 - - - +
----------------------------------------------------------
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