Contacts of the helix formed by residues 953 - 960 (chain A) in PDB entry 6S1M
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 ASP 953 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ILE* 3.7 9.8 + - + +
927A ILE 3.9 5.4 - - - +
928A SER* 3.7 31.5 + - - +
929A ALA 5.0 2.0 + - - +
938A LYS* 3.5 22.0 + - - -
952A ILE* 1.3 71.9 - - - +
954A THR* 1.3 62.7 + - - +
955A GLN* 3.3 10.9 + - - +
956A TYR* 3.3 31.0 + - + +
957A TYR* 3.2 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A LEU* 3.7 40.6 - - + +
872A LEU* 4.2 13.6 + - - +
874A ASN* 3.9 15.0 - - - +
952A ILE* 3.2 17.5 + - + +
953A ASP* 1.3 73.1 + - - +
955A GLN* 1.3 60.8 + - - +
957A TYR* 3.7 5.1 + - + +
958A LEU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LEU* 5.1 4.3 - - - +
953A ASP* 3.2 8.8 + - - +
954A THR* 1.3 81.0 + - - +
956A TYR* 1.3 60.2 + - - +
958A LEU* 3.6 29.2 - - - +
959A GLU* 3.0 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A ILE* 4.9 5.3 - - + +
924A TYR* 5.8 1.2 - - - -
926A ILE* 3.6 43.4 - - + +
935A ALA* 4.5 18.2 - - + +
938A LYS* 4.4 11.0 - - - +
953A ASP* 3.3 29.8 + - + +
955A GLN* 1.3 77.8 - - - +
957A TYR* 1.3 70.5 + + - +
960A GLN* 2.9 82.4 + - + +
961A GLN* 3.3 29.8 + - - -
8T G 4.2 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A CYS* 3.6 25.6 - - - -
839A LEU* 6.0 1.8 - - + -
871A LEU* 4.7 14.6 - - + -
881A LEU* 2.9 44.3 + - + +
883A ILE* 4.5 4.5 - - + +
925A VAL* 3.9 3.1 - - - +
926A ILE* 3.5 30.7 + - + +
952A ILE* 3.6 26.7 - - + -
953A ASP 3.2 23.3 + - - +
954A THR* 4.0 6.3 - - + +
956A TYR* 1.3 88.7 - + - +
958A LEU* 1.3 62.1 + - - +
961A GLN* 3.6 26.6 - - + +
962A LEU* 3.2 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A ILE* 4.0 27.8 - - + -
871A LEU* 4.7 6.0 - - + +
872A LEU* 4.0 30.1 - - + -
954A THR 3.0 19.3 + - - +
955A GLN* 3.3 26.7 + - - +
956A TYR 3.2 0.4 - - - -
957A TYR* 1.3 78.4 - - - +
959A GLU* 1.3 59.7 + - - +
962A LEU* 3.8 17.1 - - + +
963A ALA* 3.4 24.1 + - + +
990A ARG* 4.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A GLN* 3.0 44.9 + - - +
958A LEU* 1.3 78.1 - - + +
960A GLN* 1.3 81.5 + - + +
963A ALA* 3.9 16.2 + - + +
964A LYS* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 960 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A ALA* 5.5 3.8 - - - +
956A TYR* 2.9 56.6 + - + +
959A GLU* 1.3 97.6 - - + +
961A GLN* 1.3 66.0 + - - +
964A LYS* 4.2 22.3 - - - +
7T C 5.4 4.9 + - - +
8T G 3.9 37.1 + - - +
9T T 5.9 0.6 + - - -
----------------------------------------------------------
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