Contacts of the helix formed by residues 745 - 754 (chain A) in PDB entry 1Q6T
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 ASP 745 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A ARG* 4.8 1.2 - - - +
743A SER 3.3 7.6 + - - +
744A VAL* 1.3 72.9 - - - +
746A ILE* 1.3 57.2 + - - +
747A LYS* 3.3 24.0 + - - +
748A LYS* 2.8 56.4 + - + +
749A VAL* 3.0 16.2 + - - +
771A TYR* 4.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LEU* 3.6 31.1 - - + +
731A CYS* 3.8 12.8 - - - -
735A MET* 5.5 3.1 - - + -
744A VAL* 3.4 12.2 + - + +
745A ASP* 1.3 73.4 + - - +
747A LYS* 1.3 55.9 + - - +
749A VAL* 3.2 8.2 + - - +
750A LEU* 2.8 28.6 + - - +
767A LEU* 4.4 3.1 - - + -
770A SER* 4.5 0.7 - - - +
771A TYR* 3.5 66.2 + - + +
774A VAL* 4.2 25.4 - - + -
775A ILE* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE* 5.2 8.5 - - + -
522A ASP* 3.0 28.3 + - - +
523A ILE* 3.5 36.4 - - + +
526A GLU* 5.8 3.9 - - - +
745A ASP* 3.1 16.4 + - - +
746A ILE* 1.3 78.2 - - - +
748A LYS* 1.3 64.9 + - - +
750A LEU* 3.3 2.5 + - - +
751A LEU* 3.1 38.1 + - + +
771A TYR* 4.0 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A ASP* 2.8 35.7 + - + +
747A LYS* 1.3 84.0 - - + +
749A VAL* 1.3 57.3 + - + +
751A LEU* 3.2 12.3 + - + +
752A GLU* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A MET* 3.7 10.2 - - + +
727A LEU* 3.8 13.5 - - + -
730A THR* 3.7 29.8 - - + -
731A CYS* 4.0 15.7 - - - -
734A LEU* 3.9 23.1 - - + -
738A ARG* 5.9 1.8 - - - +
744A VAL* 4.4 3.6 - - + -
745A ASP 3.0 17.8 + - - +
746A ILE 3.7 5.6 - - - +
748A LYS* 1.3 75.1 - - + +
750A LEU* 1.3 59.0 + - - +
752A GLU* 3.3 7.1 + - - +
753A MET* 2.9 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A TYR* 5.4 3.8 - - + -
523A ILE* 4.1 25.6 - - + -
727A LEU* 3.9 10.3 - - + +
746A ILE 2.8 16.9 + - - +
747A LYS* 3.7 5.6 - - - +
749A VAL* 1.3 77.8 - - - +
751A LEU* 1.3 53.4 + - - +
753A MET* 3.2 12.7 + - + +
754A ARG* 2.7 37.2 + - + +
760A LEU* 3.4 42.0 - - + +
761A ILE* 4.0 21.8 - - + -
767A LEU* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.8 34.5 - - + +
526A GLU* 4.1 16.2 - - + +
527A ALA* 3.9 23.6 - - + +
528A SER* 4.7 1.7 + - - -
747A LYS* 3.1 36.8 + - + +
748A LYS* 3.2 12.5 + - + +
750A LEU* 1.3 75.1 - - - +
752A GLU* 1.3 66.7 + - - +
754A ARG* 3.2 11.7 + - - +
755A LYS* 3.4 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A LYS 4.6 2.5 - - - +
574A MET* 3.9 22.0 - - + -
575A GLU* 5.6 8.3 - - - +
748A LYS* 3.0 13.4 + - + +
749A VAL* 3.5 12.3 - - - +
751A LEU* 1.3 74.9 - - - +
753A MET* 1.3 63.9 + - - +
755A LYS* 2.8 59.6 + - - +
756A PHE* 3.5 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ILE* 3.7 16.3 - - + +
574A MET* 3.6 22.9 - - + +
581A TYR* 5.5 0.2 - - - -
583A LEU* 6.1 0.4 - - - -
723A GLY 4.6 3.4 - - - +
726A CYS* 4.0 17.3 - - - +
727A LEU* 3.3 59.5 - - + -
730A THR* 5.0 2.9 - - - -
749A VAL* 2.9 19.0 + - + +
750A LEU* 3.5 12.3 - - + +
752A GLU* 1.3 73.0 - - - +
754A ARG* 1.3 55.4 + - - +
755A LYS 3.0 5.4 - - - -
756A PHE* 3.0 27.9 + - - +
757A ARG 3.6 2.3 + - - -
760A LEU* 3.4 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A TYR* 3.9 13.9 + - - -
523A ILE* 4.3 16.0 - - - +
524A ARG* 4.0 19.2 - - - +
527A ALA* 3.9 25.4 - - + +
528A SER* 4.1 10.1 - - - +
552A PHE* 3.6 12.3 - - - -
750A LEU* 2.7 27.8 + - + +
751A LEU* 3.2 8.9 + - - +
753A MET* 1.3 71.7 - - - +
755A LYS* 1.3 61.0 + - - +
756A PHE 3.2 0.4 - - - -
757A ARG 3.5 16.1 - - - +
758A MET* 4.7 1.4 - - - -
759A GLY* 3.3 22.4 - - - +
760A LEU* 2.8 50.4 + - + +
761A ILE 2.9 16.6 + - - -
762A GLN* 4.5 1.6 - - - +
801A 600 3.7 21.8 + - - -
----------------------------------------------------------
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