Contacts of the helix formed by residues 975 - 988 (chain A) in PDB entry 3AR2
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 LEU 975 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A CYS* 4.3 20.3 - - - -
971A LEU* 2.9 28.6 + - + +
972A LYS* 5.5 0.7 - - - -
974A SER* 1.3 72.9 - - - +
976A PRO* 1.3 62.9 - - + +
977A VAL 3.1 1.3 + - - -
978A ILE* 3.2 28.4 + - + +
979A GLY 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 976 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A TYR* 2.9 30.8 + - + +
972A LYS* 3.3 27.4 - - - +
973A ILE* 3.5 4.3 - - + +
974A SER 3.1 2.7 - - - -
975A LEU* 1.3 90.7 - - + +
977A VAL* 1.3 61.5 + - - -
978A ILE 3.1 2.2 - - - -
979A GLY* 3.3 12.8 + - - +
980A LEU* 3.3 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A ILE* 4.2 22.2 - - + +
843A TYR* 3.9 24.5 - - + -
844A VAL* 4.0 17.3 - - + -
907A ILE* 3.8 15.5 - - + +
910A CYS* 3.7 25.1 - - + -
911A ASN* 4.2 8.7 - - + +
914A ASN* 3.8 7.5 + - - +
974A SER 2.8 24.9 + - - +
976A PRO* 1.3 71.8 - - - +
978A ILE* 1.3 69.8 + - + +
980A LEU* 3.5 4.7 + - + +
981A ASP* 3.4 18.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
910A CYS* 3.0 43.1 - - + +
913A LEU* 4.6 5.8 - - + -
914A ASN* 3.6 14.5 - - - +
922A LEU* 3.4 31.4 - - + -
975A LEU* 3.2 31.2 - - + +
977A VAL* 1.3 79.7 - - + +
979A GLY* 1.3 59.8 + - - +
982A GLU* 3.0 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 979 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A LEU 4.2 1.0 + - - -
976A PRO* 3.3 10.2 + - - +
978A ILE* 1.3 79.9 - - - +
980A LEU* 1.3 57.0 + - - +
982A GLU* 3.4 7.9 - - - +
983A ILE* 3.1 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 980 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A ALA* 3.4 27.4 - - + +
840A ILE* 3.7 16.6 - - + -
843A TYR* 3.7 31.9 - - + -
976A PRO 3.3 12.0 + - - +
977A VAL* 3.7 8.5 - - + +
978A ILE 3.2 0.4 - - - -
979A GLY* 1.3 74.1 - - - +
981A ASP* 1.3 61.7 + - - +
983A ILE* 3.1 11.8 + - + +
984A LEU* 2.9 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 981 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ARG* 3.4 6.9 + - - -
836A ARG* 2.8 49.2 + - - -
840A ILE* 3.7 21.7 - - + +
911A ASN* 4.8 1.6 - - - +
914A ASN* 3.2 41.2 - - - +
977A VAL 3.4 5.5 + - - +
980A LEU* 1.3 76.7 - - - +
982A GLU* 1.3 55.0 + - - +
984A LEU* 2.9 3.6 + - - -
985A LYS* 2.5 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 982 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A ASN* 4.8 1.4 + - - +
921A SER* 3.1 38.2 + - - -
922A LEU* 3.5 25.8 + - - +
923A MET 5.0 0.2 + - - -
978A ILE* 3.0 26.7 + - + +
979A GLY* 3.4 11.4 - - - +
981A ASP* 1.3 77.7 - - - +
983A ILE* 1.3 59.9 + - + +
985A LYS* 3.5 10.6 + - - +
986A PHE* 2.9 26.7 + - - +
989A ARG* 4.1 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 983 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A GLY 3.1 17.3 + - - +
980A LEU* 3.3 12.1 - - + +
981A ASP 3.1 0.6 - - - -
982A GLU* 1.3 78.2 - - + +
984A LEU* 1.3 60.8 + - + +
986A PHE* 3.0 13.7 + - + +
987A ILE* 2.8 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 984 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A TRP* 3.1 36.2 - - + -
835A PHE* 3.7 30.7 - - + -
836A ARG* 3.5 33.2 + - - -
839A ALA* 3.9 20.2 - - + -
840A ILE* 3.8 24.2 - - + -
980A LEU* 2.9 22.8 + - + +
981A ASP 3.4 6.3 - - - +
983A ILE* 1.3 77.6 - - + +
985A LYS* 1.3 59.9 + - - +
987A ILE* 3.6 7.8 + - + -
988A ALA* 3.3 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 985 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ARG* 3.5 23.8 - - - +
836A ARG* 3.5 19.7 - - - +
913A LEU 4.8 0.2 + - - -
914A ASN* 2.9 36.0 + - - +
916A LEU* 6.2 0.2 - - - +
917A SER* 4.2 4.0 + - - +
918A GLU 3.6 9.0 - - - +
919A ASN* 3.9 12.2 - - - +
920A GLN 3.1 28.8 + - - +
921A SER 4.9 0.2 - - - -
922A LEU* 4.6 10.5 - - - +
981A ASP* 2.5 38.3 + - - +
982A GLU* 3.7 15.2 + - - +
984A LEU* 1.3 71.0 - - - +
986A PHE* 1.3 60.2 + - - +
987A ILE 3.3 0.4 - - - -
988A ALA* 3.7 2.6 + - - +
989A ARG* 3.0 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A GLU 2.9 15.7 + - - +
983A ILE* 3.0 17.9 + - + +
985A LYS* 1.3 74.1 - - - +
987A ILE* 1.3 72.0 + - + +
989A ARG* 3.4 21.4 + - - +
990A ASN* 3.0 57.8 + - + +
991A TYR* 4.7 4.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 987 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A TRP* 3.4 31.4 - - + -
983A ILE* 2.8 40.3 + - + +
984A LEU* 3.7 7.4 - - + +
986A PHE* 1.3 84.2 - - + +
988A ALA* 1.3 56.3 + - - +
989A ARG 3.1 0.4 + - - -
991A TYR* 3.1 55.9 + - + +
992A LEU* 5.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A TRP* 3.3 36.8 - - + +
836A ARG* 5.3 0.2 - - - +
919A ASN* 3.7 23.4 - - - +
984A LEU 3.3 7.7 + - - +
985A LYS 3.9 1.1 - - - +
986A PHE 3.5 0.2 - - - -
987A ILE* 1.3 77.6 - - - +
989A ARG* 1.3 57.2 + - - +
990A ASN 3.5 0.4 - - - -
992A LEU* 2.7 44.8 - - + +
993A GLU* 3.4 6.2 - - - +
----------------------------------------------------------
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