Contacts of the helix formed by residues 755 - 762 (chain A) in PDB entry 6DBU
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 755 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A THR* 3.2 21.8 - - + +
747A TYR* 3.8 35.2 - - + +
748A ILE* 3.4 14.4 - - - +
754A SER* 1.3 76.6 - - - +
756A ARG* 1.3 68.0 + - - +
757A ALA* 3.5 12.3 + - - +
758A GLU* 2.5 30.1 + - - +
759A ALA* 3.6 9.5 + - - +
796A ASP* 5.3 3.4 - - - +
799A LYS* 5.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A GLY* 5.2 3.6 + - - -
745A SER 3.8 19.6 + - - -
746A THR* 3.4 22.9 + - + +
748A ILE* 3.5 29.7 - - - +
755A THR* 1.3 79.6 - - - +
757A ALA* 1.3 57.8 + - + +
759A ALA* 3.8 1.6 - - - +
760A SER* 2.9 28.2 + - - -
952A GLY 3.3 20.3 - - - +
953A LYS* 4.4 13.9 - - - +
954A ILE* 3.3 30.3 + - - +
955A THR* 5.9 1.2 - - - +
956A ASN 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A THR* 3.4 6.2 + - - +
756A ARG* 1.3 76.9 - - + +
758A GLU* 1.3 59.7 + - - +
760A SER* 2.4 26.5 + - - -
761A GLN* 2.9 22.6 + - + +
951A ASP 5.0 0.2 - - - -
952A GLY* 3.9 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A ASP 3.3 5.2 - - - +
754A SER* 3.0 17.5 - - - +
755A THR* 2.5 52.0 + - - +
757A ALA* 1.3 76.0 - - - +
759A ALA* 1.3 56.6 + - - +
761A GLN* 4.4 6.4 - - - +
762A ASN* 3.5 18.9 + - - +
766A HIS* 4.0 8.3 + - - +
799A LYS* 5.1 4.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
748A ILE* 4.3 9.0 - - + -
754A SER* 3.8 14.8 - - - -
755A THR 3.6 16.0 + - - +
756A ARG 4.2 1.1 - - - +
757A ALA 3.0 1.0 - - - -
758A GLU* 1.3 78.0 - - - +
760A SER* 1.3 61.0 + - - +
762A ASN 2.8 23.6 - - - +
763A MET* 3.4 4.5 - - - -
766A HIS* 4.0 6.5 - - + -
954A ILE* 3.0 16.8 - - + +
959A HIS* 3.9 22.4 - - - +
----------------------------------------------------------
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 ARG 2.9 18.6 + - - -
757A ALA 2.4 21.5 + - - -
759A ALA* 1.3 70.1 - - - +
761A GLN* 1.3 65.2 + - - +
763A MET* 3.9 14.6 - - - +
943A SER* 5.2 0.2 + - - -
947A LYS* 4.9 1.4 - - - -
950A TYR 2.6 33.1 + - - +
951A ASP 3.5 3.6 - - - -
952A GLY 3.4 15.5 - - - -
953A LYS 2.9 21.7 + - - -
954A ILE* 3.0 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A ALA* 2.9 21.2 + - + +
758A GLU* 4.7 5.2 - - - +
760A SER* 1.3 79.9 - - - +
762A ASN* 1.3 59.0 + - + +
763A MET* 4.1 1.0 + - - +
943A SER* 3.9 15.9 + - - -
947A LYS* 3.4 30.9 + - - +
951A ASP* 2.3 35.1 + - - +
952A GLY* 4.5 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A GLU 3.5 6.4 + - - +
759A ALA* 2.8 16.4 - - - +
761A GLN* 1.3 77.1 - - + +
763A MET* 1.3 62.4 + - - +
764A VAL* 3.6 5.2 + - - +
765A LEU* 3.5 41.4 + - - +
766A HIS* 3.3 18.9 - - + -
----------------------------------------------------------
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