Contacts of the helix formed by residues 727 - 738 (chain E) in PDB entry 3RTR
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 HIS 727 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725E LEU 4.3 0.2 + - - -
726E LYS* 1.3 70.1 - - - +
728E GLN* 1.3 65.7 + - + +
730E LEU* 3.0 7.0 + - - +
731E LEU* 2.8 54.9 + - + +
750E LYS* 4.3 26.6 + - + -
753E ILE* 4.6 12.8 - - + +
770E ASP* 2.9 41.9 + - + +
772E TYR* 3.3 37.8 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 728 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726E LYS* 3.3 3.0 - - + +
727E HIS* 1.3 84.7 - - + +
729E GLN* 1.3 57.0 + - - +
731E LEU* 3.1 27.0 + - - +
732E GLY* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 729 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722E ARG* 5.2 3.2 - - - +
725E LEU* 3.1 33.7 - - + +
726E LYS* 3.1 22.5 + - + +
728E GLN* 1.3 76.3 - - - +
730E LEU* 1.3 62.5 + - - +
732E GLY* 4.2 0.8 - - - +
733E GLU* 3.0 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 730 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715E ILE* 3.8 32.1 - - + -
718E ILE* 3.7 32.1 - - + -
719E MET* 3.8 18.4 - - + -
725E LEU* 3.7 10.5 - - + +
726E LYS 2.9 11.9 + - - +
727E HIS* 3.2 10.1 - - - +
729E GLN* 1.3 77.2 - - - +
731E LEU* 1.3 62.1 + - - +
733E GLU* 3.4 1.4 + - - +
734E VAL* 3.1 34.3 + - + +
749E ILE* 6.0 0.2 - - + -
753E ILE* 3.9 25.6 - - + -
762E LEU* 5.5 1.8 - - + -
772E TYR* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 731 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727E HIS* 2.8 40.5 + - + +
728E GLN* 3.1 27.6 + - - +
730E LEU* 1.3 80.4 - - - +
732E GLY* 1.3 60.7 + - - +
734E VAL* 3.6 5.2 + - - +
735E LEU* 3.1 35.0 + - + +
746E VAL* 4.2 35.2 - - + +
749E ILE* 3.8 34.1 - - + -
750E LYS* 6.2 1.3 - - + +
753E ILE* 5.9 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 732 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728E GLN* 3.0 19.3 + - - +
729E GLN* 4.2 1.6 - - - -
731E LEU* 1.3 77.7 - - - +
733E GLU* 1.3 60.7 + - - +
735E LEU* 3.1 25.2 + - - +
736E THR* 3.3 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 733 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718E ILE* 3.7 32.6 - - + +
722E ARG* 3.7 34.7 + - - -
725E LEU* 4.4 5.8 - - + -
729E GLN* 3.0 38.0 + - + +
730E LEU 3.6 4.9 - - - +
731E LEU 3.4 0.2 - - - -
732E GLY* 1.3 75.9 - - - +
734E VAL* 1.3 60.7 + - - +
736E THR* 3.8 7.3 + - - -
737E GLN* 3.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 734 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711E ILE* 4.6 11.2 - - + -
714E ALA* 4.3 9.0 - - + -
715E ILE* 3.7 24.2 - - + +
718E ILE* 3.4 20.0 - - + -
730E LEU* 3.1 22.2 + - + +
731E LEU 3.9 5.4 - - - +
732E GLY 3.2 0.2 - - - -
733E GLU* 1.3 75.4 - - - +
735E LEU* 1.3 65.3 + - - +
736E THR 3.2 0.9 + - - -
737E GLN* 3.7 1.6 + - - +
738E LEU* 3.4 42.1 + - + +
744E PRO* 5.0 2.5 - - + -
749E ILE* 4.3 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 735 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E LEU* 3.1 25.8 - - + +
732E GLY* 3.1 15.0 + - - +
734E VAL* 1.3 78.9 - - - +
736E THR* 1.3 52.3 + - - +
738E LEU 3.6 0.7 - - - -
739E SER* 2.8 35.0 + - - -
743E LYS* 4.3 16.8 + - - +
744E PRO* 4.4 27.3 - - + +
746E VAL* 6.0 4.3 - - + -
749E ILE* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 736 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732E GLY 3.3 12.2 + - - -
733E GLU* 4.1 9.4 - - - -
734E VAL 3.2 0.6 - - - -
735E LEU* 1.3 75.1 - - - +
737E GLN* 1.3 66.6 + - + +
738E LEU 3.2 2.0 + - - -
739E SER* 3.7 15.9 + - - -
740E SER* 4.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 737 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714E ALA* 5.2 1.1 - - + -
717E ARG* 2.7 47.4 + - - +
718E ILE* 3.2 34.2 - - - +
733E GLU* 3.8 15.5 + - - +
734E VAL 3.7 2.8 + - - +
736E THR* 1.3 78.6 - - + +
738E LEU* 1.3 69.0 + - + +
739E SER 3.5 0.2 - - - -
740E SER* 3.8 13.4 + - - -
741E ARG* 5.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 738 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710E LEU* 4.1 11.0 - - + +
711E ILE* 4.1 27.6 - - + +
714E ALA* 3.6 22.4 - - + -
717E ARG* 4.9 6.1 - - - +
734E VAL* 3.4 21.0 + - + +
735E LEU 3.6 0.9 - - - -
736E THR 3.2 0.4 - - - -
737E GLN* 1.3 88.2 - - + +
739E SER* 1.3 56.5 + - - +
740E SER 3.1 2.9 + - - -
741E ARG* 3.2 16.7 + - - +
742E PHE* 2.7 56.3 + - + +
744E PRO* 3.9 25.8 - - + -
----------------------------------------------------------
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