Contacts of the helix formed by residues 746 - 758 (chain W) in PDB entry 5O9G
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 PRO 746 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-17I T 5.1 9.0 - - - +
434W LEU* 6.2 0.2 - - - -
744W THR 3.8 3.3 - - - +
745W VAL* 1.3 94.2 - - + +
747W SER* 1.3 64.8 - - - +
748W ALA* 4.2 9.4 - - + +
749W GLN* 3.5 15.6 + - + +
750W ARG* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 747 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-17I T 4.9 2.1 + - - -
434W LEU* 3.5 38.8 + - - +
435W SER* 5.0 1.1 - - - -
438W PRO* 5.6 4.5 - - - -
457W MET* 6.4 2.0 - - - -
746W PRO* 1.3 74.1 - - - +
748W ALA* 1.3 60.5 + - - +
750W ARG* 3.6 11.4 - - - -
751W ARG* 2.9 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 748 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313W ARG* 5.2 20.2 - - + +
746W PRO* 3.3 10.5 - - + +
747W SER* 1.3 78.6 - - - +
749W GLN* 1.3 56.0 + - - +
751W ARG* 4.4 2.9 - - - +
752W ILE* 3.2 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 749 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276W ARG* 6.0 3.6 - - - +
280W GLU* 3.9 18.1 + - - +
745W VAL* 4.2 25.6 - - + -
746W PRO* 3.5 18.3 + - + +
747W SER 3.1 0.4 - - - -
748W ALA* 1.3 78.7 - - - +
750W ARG* 1.3 60.8 + - - +
751W ARG 3.2 1.6 - - - -
752W ILE* 3.2 11.9 + - - +
753W SER* 2.9 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 750 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-18I C 3.3 21.0 + - - -
-17I T 5.7 0.6 + - - -
434W LEU* 4.5 7.2 - - - +
435W SER* 3.2 34.5 + - - +
740W ARG 6.1 0.2 - - - -
741W LEU* 3.5 37.4 - - + +
742W ASP 4.0 16.3 + - - -
743W GLY* 5.0 1.0 - - - -
745W VAL* 4.2 17.2 + - + -
746W PRO 3.3 20.2 + - - +
747W SER* 3.6 17.7 - - - +
749W GLN* 1.3 78.5 - - - +
751W ARG* 1.3 64.4 + - + +
753W SER* 3.7 7.9 - - - -
754W ILE* 2.9 39.7 + - + +
773W ALA* 4.1 19.2 + - - +
776W LEU* 5.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 751 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313W ARG* 4.7 20.2 - - - +
435W SER* 2.3 31.5 + - - +
436W THR* 3.6 0.6 - - - +
438W PRO* 3.4 29.8 - - + +
439W ALA* 3.1 40.7 - - - +
442W ASP* 5.6 1.4 + - - -
747W SER* 2.9 27.0 + - - +
748W ALA 4.7 1.8 - - - +
750W ARG* 1.3 79.8 - - + +
752W ILE* 1.3 59.9 + - - +
754W ILE* 4.8 9.1 - - - +
755W ASP* 2.9 51.3 + - - +
778W ILE* 3.1 28.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 752 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276W ARG* 3.4 39.9 - - - +
279W ASP 5.7 1.6 - - - +
280W GLU* 3.8 35.9 - - + +
313W ARG* 4.7 18.2 - - + -
748W ALA 3.2 19.3 - - - +
749W GLN* 3.2 16.2 + - - +
751W ARG* 1.3 75.8 - - - +
753W SER* 1.3 59.5 + - - +
755W ASP* 3.8 5.3 - - - +
756W HIS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 753 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739W GLN* 2.6 53.9 + - - +
740W ARG 4.7 8.4 + - - -
741W LEU* 6.1 1.1 - - - -
749W GLN* 2.9 31.9 + - - +
750W ARG* 3.7 9.3 - - - -
752W ILE* 1.3 77.9 - - - +
754W ILE* 1.3 57.0 + - - +
756W HIS* 3.2 2.2 + - - +
757W PHE 2.9 14.7 + - - -
767W PHE* 4.7 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 754 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741W LEU* 4.3 20.0 - - + -
750W ARG* 2.9 26.6 + - + +
751W ARG* 4.2 9.6 - - - +
753W SER* 1.3 75.5 - - - +
755W ASP* 1.3 65.1 + - - +
757W PHE* 3.1 6.9 + - + +
758W ASN* 3.1 48.6 + - - +
767W PHE* 4.3 18.4 - - + -
778W ILE* 3.9 44.9 - - + -
779W ASN 4.9 2.9 - - - +
780W LEU* 5.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 755 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313W ARG* 4.2 18.0 + - - -
751W ARG* 2.9 40.9 + - - +
752W ILE* 4.0 5.5 - - - +
754W ILE* 1.3 77.7 - - - +
756W HIS* 1.3 59.2 + - - +
758W ASN* 4.0 16.9 + - - +
759W SER* 3.7 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 756 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276W ARG* 4.5 20.0 - - - +
739W GLN* 4.2 5.9 + - - +
752W ILE* 2.9 19.3 + - + +
753W SER* 3.6 6.5 - - - +
754W ILE 3.1 0.2 - - - -
755W ASP* 1.3 76.8 - - - +
757W PHE* 1.3 62.3 + - - +
759W SER* 3.6 14.2 + - - -
762W SER* 3.5 22.5 - - - -
763W ASN* 4.2 10.8 - - - -
764W ASP* 3.1 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 757 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713W ARG* 4.1 15.9 + - + -
715W LEU* 4.5 3.4 - - + -
739W GLN* 3.5 15.0 - - - +
753W SER 2.9 8.7 + - - +
754W ILE* 3.1 6.5 + - + +
756W HIS* 1.3 75.0 - - - +
758W ASN* 1.3 62.6 + - - +
759W SER 3.1 11.2 + - - +
762W SER* 3.4 16.5 + - - -
764W ASP* 3.1 34.5 - - + -
765W PHE 5.0 1.1 - - - -
766W VAL 4.9 0.2 - - - -
767W PHE* 3.7 37.0 - + + -
780W LEU* 3.5 37.0 - - + -
782W THR* 3.2 29.9 + - - -
783W ALA* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 758 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754W ILE* 3.1 36.0 + - - +
755W ASP* 4.0 14.5 + - - +
756W HIS 3.4 0.4 - - - -
757W PHE* 1.3 84.4 - - - +
759W SER* 1.3 63.4 + - - +
760W PRO* 3.6 4.3 - - - +
778W ILE* 6.0 0.4 - - - +
779W ASN 4.5 11.0 + - - +
780W LEU* 4.8 1.4 - - - +
781W MET* 4.7 11.7 + - - +
782W THR* 4.5 14.7 + - - +
----------------------------------------------------------
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