Contacts of the helix formed by residues 971 - 980 (chain A) in PDB entry 4Q0R
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 971 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A ARG 4.8 0.9 - - - +
969A GLY 4.2 4.3 - - - +
970A TRP* 1.3 90.8 - - + +
972A HIS* 1.3 66.2 + - + +
973A GLU* 3.2 13.5 - - + +
974A LYS* 3.6 30.7 - - + +
975A SER* 3.2 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 972 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A ASP* 5.5 6.7 + - - -
961A ARG* 3.9 35.0 + - + +
962A SER* 4.4 9.6 + - - -
965A LYS* 4.4 12.9 - - + +
971A PRO* 1.3 77.8 - - + +
973A GLU* 1.3 61.4 + - - +
975A SER* 4.5 5.2 - - - -
976A ASP* 3.0 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 973 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A PRO* 3.2 10.2 - - + +
972A HIS* 1.3 77.7 - - - +
974A LYS* 1.3 65.8 + - - +
976A ASP* 3.4 3.8 + - - +
977A GLU* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 974 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A TRP* 3.6 47.3 - - + +
971A PRO* 3.6 24.9 - - + +
973A GLU* 1.3 78.7 - - - +
975A SER* 1.3 68.6 + - - +
977A GLU* 3.4 11.4 + - - +
978A ILE* 3.6 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 975 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 5.8 1.3 - - - -
961A ARG* 3.9 28.5 + - - -
964A MSE 3.8 15.0 - - - +
970A TRP* 3.4 25.1 - - - -
971A PRO 3.2 18.5 + - - -
972A HIS 4.3 0.9 - - - -
973A GLU 3.4 0.2 - - - -
974A LYS* 1.3 81.3 - - - +
976A ASP* 1.3 63.8 + - - +
978A ILE* 3.5 2.8 + - - +
979A LEU* 3.3 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 976 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A LEU* 4.2 9.2 - - - +
961A ARG* 4.0 18.4 - - - +
972A HIS* 3.0 27.6 + - - +
973A GLU* 3.9 2.7 - - - +
975A SER* 1.3 76.2 - - - +
977A GLU* 1.3 58.4 + - - +
979A LEU* 4.7 3.7 - - - +
980A ILE* 2.9 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A GLU 3.1 17.7 + - - +
974A LYS* 3.8 7.2 - - - +
975A SER 3.3 0.6 + - - -
976A ASP* 1.3 76.4 - - - +
978A ILE* 1.3 61.2 + - + +
980A ILE* 5.3 0.4 - - - -
981A PRO* 3.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 978 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 4.8 5.2 - - + -
63A CYS* 4.3 26.7 - - + -
970A TRP* 4.1 26.5 - - + -
974A LYS* 3.6 21.8 - - + +
975A SER 3.5 3.8 + - - +
976A ASP 3.3 0.4 - - - -
977A GLU* 1.3 77.1 - - + +
979A LEU* 1.3 69.2 + - + +
981A PRO* 3.3 15.3 - - - +
982A LEU* 4.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 979 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.4 33.7 - - + -
63A CYS* 4.0 15.7 - - - -
782A PHE* 4.2 11.9 - - + -
957A LEU* 4.8 14.8 - - + +
960A LEU* 3.7 39.0 - - + -
961A ARG 5.0 2.2 - - - +
975A SER* 3.3 24.7 + - - +
976A ASP* 4.3 3.6 - - - +
978A ILE* 1.3 79.0 - - + +
980A ILE* 1.3 56.0 + - - +
982A LEU* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 980 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A LEU* 6.4 1.8 - - - -
976A ASP* 2.9 28.8 + - + +
977A GLU* 5.3 0.2 - - - -
979A LEU* 1.3 72.1 - - - +
981A PRO* 1.4 67.9 - - + +
982A LEU 3.0 8.4 - - - +
----------------------------------------------------------
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