Contacts of the helix formed by residues 726 - 737 (chain A) in PDB entry 3GQL
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 726 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A SER* 5.6 5.4 - - - +
721A LYS* 3.7 1.5 - - - -
724A ASN 4.0 5.6 - - - +
725A CYS* 1.3 81.3 - - - +
727A ASN* 1.3 68.4 + - - +
728A GLU* 3.1 9.6 + - - +
729A LEU* 3.1 38.6 + - + +
730A TYR* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LYS* 3.4 22.0 - - - +
726A THR* 1.3 76.7 - - - +
728A GLU* 1.3 81.5 + - - +
730A TYR* 3.4 2.6 + - - +
731A MET* 3.1 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A THR* 3.1 6.9 + - - +
727A ASN* 1.3 92.4 - - - +
729A LEU* 1.3 59.8 + - + +
731A MET* 2.9 23.5 + - - +
732A MET* 3.0 12.4 + - + +
756A ARG* 3.0 27.9 + - - +
757A ILE* 3.4 39.6 - - + +
760A LEU* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A VAL* 4.0 14.6 - - + -
690A LEU* 4.9 2.8 - - + +
694A PHE* 3.3 43.1 - - + -
725A CYS* 3.9 13.5 - - - -
726A THR* 3.1 29.9 + - + +
728A GLU* 1.3 76.2 - - + +
730A TYR* 1.3 61.5 + - - +
732A MET* 3.4 11.3 + - - +
733A MET* 3.1 26.4 + - - +
754A LEU* 4.3 17.3 - - + -
757A ILE* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A TRP* 5.8 0.2 - + - -
719A MET 2.8 25.3 + - - -
720A ASP* 3.9 2.7 - - - -
721A LYS* 3.3 59.0 + - + -
722A PRO* 4.2 0.4 - - + -
725A CYS* 4.0 2.9 - - - -
726A THR 3.3 18.2 + - - +
727A ASN 3.7 3.8 - - - +
728A GLU 3.1 1.0 - - - -
729A LEU* 1.3 80.5 - - - +
731A MET* 1.3 64.6 + - - +
733A MET* 3.3 23.2 - - + +
734A ARG* 2.8 72.6 + - + +
737A TRP* 4.7 2.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 3.1 20.3 + - + +
728A GLU* 2.9 10.8 + - - +
730A TYR* 1.3 80.3 - - + +
732A MET* 1.3 66.6 + - - +
734A ARG* 3.0 9.7 + - - +
735A ASP* 2.9 35.2 + - - +
518C SER* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 4.1 16.6 - - + -
728A GLU* 3.0 10.8 + - + +
729A LEU* 3.4 15.3 - - - +
731A MET* 1.3 75.6 - - - +
733A MET* 1.3 64.0 + - - +
735A ASP* 3.1 13.1 + - - +
736A CYS* 3.1 22.1 + - - -
745A PRO* 5.1 0.2 - - - +
750A LEU* 3.7 26.0 - - + -
753A ASP* 3.5 34.1 - - + +
754A LEU* 3.5 31.0 - - + -
757A ILE* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A GLY* 4.0 15.0 - - - +
690A LEU* 3.7 32.5 - - + +
691A TRP* 3.9 13.9 - - - +
694A PHE* 3.7 24.2 - - + -
722A PRO* 4.2 9.0 - - + -
725A CYS* 4.0 10.8 - - - -
729A LEU 3.1 13.4 + - - +
730A TYR* 3.3 34.8 - - + +
732A MET* 1.3 79.7 - - - +
734A ARG* 1.3 58.6 + - - +
736A CYS* 3.7 7.8 - - - +
737A TRP* 3.0 51.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A GLY 5.1 3.8 + - - -
718A ARG* 3.9 28.6 - - - +
730A TYR* 2.8 64.0 + - + +
731A MET* 3.0 16.0 + - - +
733A MET* 1.3 76.2 - - - +
735A ASP* 1.3 66.7 + - - +
737A TRP* 3.2 37.4 + - - +
738A HIS* 3.6 2.8 + - - +
518C SER* 4.8 23.0 + - - +
519C ASP* 5.1 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A MET* 2.9 27.6 + - - +
732A MET* 3.4 10.1 - - - +
734A ARG* 1.3 74.7 - - - +
736A CYS* 1.3 66.9 + - - +
738A HIS* 2.9 28.0 + - - +
743A GLN 4.8 1.1 - - - +
744A ARG* 3.6 0.5 - - - +
745A PRO* 3.5 28.8 - - + +
518C SER* 3.8 22.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A VAL* 3.7 43.5 - - - +
684A TRP* 3.6 8.4 - - - -
686A PHE* 4.0 11.9 - - - -
687A GLY* 3.8 13.7 - - - -
690A LEU* 4.7 1.3 - - - -
732A MET 3.1 15.4 + - - -
733A MET* 3.7 9.2 - - - +
735A ASP* 1.3 77.8 - - - +
737A TRP* 1.3 59.0 + - - +
744A ARG* 2.8 26.9 + - - -
745A PRO* 3.7 3.6 - - - +
750A LEU* 4.0 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A TRP* 3.2 40.5 + + + -
687A GLY* 3.5 10.1 - - - -
688A VAL* 3.2 45.7 - - + +
691A TRP* 4.3 7.9 - + + -
701A TYR* 5.5 2.9 - - - -
718A ARG* 2.9 50.9 + - + +
719A MET* 3.9 43.7 - - + -
730A TYR* 4.7 1.3 - + - -
733A MET* 3.0 38.3 + - + +
734A ARG* 3.2 31.3 + - - +
735A ASP 3.1 1.4 - - - -
736A CYS* 1.3 76.2 - - - +
738A HIS* 1.3 63.7 + - - -
739A ALA 3.4 0.2 + - - -
----------------------------------------------------------
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