Contacts of the helix formed by residues 727 - 735 (chain A) in PDB entry 3L7A
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 ASN 727 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 5.1 1.6 - - - +
725A GLY 3.4 7.0 + - - +
726A TYR* 1.3 77.3 - - - +
728A ALA* 1.3 63.6 + - - +
729A GLN* 3.3 23.3 + - - +
730A GLU* 3.3 40.2 + - + +
731A TYR* 3.7 8.7 - - - -
766A MET 5.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A TYR* 3.9 30.7 + - + +
727A ASN* 1.3 74.1 + - - +
729A GLN* 1.3 63.4 + - - +
731A TYR* 3.1 13.8 + - - +
732A TYR* 3.3 9.4 + - - +
765A LEU 3.3 26.2 - - - +
766A MET* 3.6 18.4 + - - +
774A PHE* 3.5 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 3.2 19.1 + - - +
728A ALA* 1.3 78.1 - - - +
730A GLU* 1.3 55.8 + - - +
732A TYR* 3.2 24.0 + - - +
733A ASP* 2.8 62.9 + - - +
766A MET* 3.5 25.3 + - - +
767A HIS* 5.4 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A ARG* 5.0 9.0 + - - -
727A ASN* 3.3 31.4 + - - +
728A ALA 3.2 0.2 - - - -
729A GLN* 1.3 78.7 - - - +
731A TYR* 1.3 72.2 + - + +
733A ASP* 3.3 6.0 + - - +
734A ARG* 2.8 74.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 4.1 16.5 - - + +
724A ARG* 4.9 4.9 + - - -
726A TYR* 3.7 27.1 - + - -
727A ASN 3.7 15.7 - - - -
728A ALA* 3.1 8.8 + - - +
730A GLU* 1.3 87.9 + - + +
732A TYR* 1.3 65.3 + - - +
734A ARG* 3.2 2.0 + - - +
735A ILE* 3.0 46.4 + - + +
738A LEU* 4.0 8.1 - - + -
774A PHE* 3.8 29.8 - - + -
775A ALA* 3.7 29.6 + - - +
778A GLU* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A ALA 3.3 8.5 + - - +
729A GLN* 3.2 32.2 + - - +
731A TYR* 1.3 79.4 - - - +
733A ASP* 1.3 65.1 + - - +
735A ILE 3.8 2.6 - - - +
738A LEU* 4.1 10.9 - - - +
739A ARG* 3.1 59.4 + - + +
742A ILE* 3.7 36.7 - - + +
743A GLU* 3.5 24.3 + - + +
766A MET* 3.8 31.9 - - + -
774A PHE* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A GLN* 2.8 53.3 + - - +
730A GLU* 3.6 7.9 + - - +
731A TYR 3.2 0.2 - - - -
732A TYR* 1.3 85.7 - - - +
734A ARG* 1.3 59.0 + - + +
739A ARG* 2.8 22.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
730A GLU* 2.8 60.7 + - - +
731A TYR* 3.2 2.9 + - - +
733A ASP* 1.3 82.4 - - + +
735A ILE* 1.3 66.0 + - + +
736A PRO* 3.6 9.9 - - - +
739A ARG* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A TYR* 3.0 38.0 + - + +
732A TYR 3.8 4.9 - - - +
733A ASP 3.6 0.8 - - - -
734A ARG* 1.3 86.9 - - + +
736A PRO* 1.3 66.8 - - + +
737A GLU* 4.2 5.4 - - + +
738A LEU* 3.1 34.1 + - + +
739A ARG* 3.1 19.9 + - - -
774A PHE 5.0 2.9 - - - +
777A TYR* 3.9 18.2 - - + -
778A GLU* 3.7 40.4 - - + +
----------------------------------------------------------
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