Contacts of the helix formed by residues 970 - 985 (chain A) in PDB entry 4UHW
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 ALA 970 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A TYR* 4.0 18.4 - - + +
957A LYS 3.5 17.9 - - - +
958A GLU* 2.6 13.2 + - - -
968A ILE* 3.7 9.8 - - + -
969A ASN* 1.3 71.4 - - - +
971A LYS* 1.3 62.8 + - - +
972A ASN 3.4 2.2 - - - -
973A LEU* 3.4 25.7 + - + +
974A ILE* 3.4 16.8 + - - +
1164A TYR* 4.1 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 971 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A GLU* 3.1 37.2 + - + +
969A ASN* 3.3 21.0 + - - +
970A ALA* 1.3 75.8 - - - +
972A ASN* 1.3 67.3 + - - +
974A ILE* 3.0 25.5 + - + +
975A GLN* 2.8 43.2 + - + +
1256A SER* 5.3 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 972 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A ASN 4.9 1.4 + - - -
970A ALA 3.4 0.4 - - - -
971A LYS* 1.3 87.1 + - - +
973A LEU* 1.3 60.1 + - - +
975A GLN* 2.9 24.6 - - - +
976A CYS* 3.0 34.3 + - - +
1164A TYR* 4.0 11.8 - - + -
1190A ASP* 2.8 40.4 + - - +
1253A LEU* 3.6 13.1 - - + +
1254A PRO 5.5 0.4 + - - -
1256A SER* 3.9 19.9 + - - +
1266A LYS* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 973 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A ALA* 3.6 44.9 - - + +
955A MET* 3.7 16.6 - - + -
956A TYR* 4.5 8.5 - - + +
970A ALA* 3.4 28.0 + - + +
972A ASN* 1.3 75.2 - - - +
974A ILE* 1.3 64.5 + - - +
976A CYS* 3.5 3.3 + - - +
977A TRP* 3.2 22.2 + - - +
1011A PRO* 4.3 10.7 - - + +
1012A LEU 3.5 28.0 - - - +
1013A LYS* 4.6 1.1 - - + +
1164A TYR* 3.8 25.9 - - + -
1165A GLY 4.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 974 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A MET* 3.4 26.7 - - + -
956A TYR 3.6 19.3 - - - +
957A LYS* 4.8 4.9 - - + -
958A GLU* 4.9 7.9 - - + +
970A ALA 3.4 16.2 - - - +
971A LYS* 3.0 10.5 + - + +
973A LEU* 1.3 77.2 - - + +
975A GLN* 1.3 51.8 + - + +
977A TRP* 3.1 6.6 + - + +
978A ARG* 2.8 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 975 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A LYS* 2.8 49.3 + - + +
972A ASN* 2.9 18.6 - - - +
973A LEU 3.4 0.2 - - - -
974A ILE* 1.3 78.3 - - + +
976A CYS* 1.3 53.9 + - - +
978A ARG* 3.2 8.8 + - - +
979A GLU* 2.8 39.2 + - + +
1253A LEU* 3.8 30.7 - - + +
1254A PRO* 5.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 976 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A ASN 3.0 24.1 + - - +
973A LEU 3.7 5.4 - - - +
975A GLN* 1.3 75.9 - - - +
977A TRP* 1.3 56.4 + - - +
980A CYS* 3.2 29.3 + - - +
1164A TYR 3.6 25.8 - - - -
1165A GLY* 3.6 24.5 - - - +
1166A ALA* 3.5 4.9 - - - +
1188A VAL* 4.0 16.9 - - - +
1189A MET 4.3 3.4 - - - -
1190A ASP* 3.8 9.4 - - - -
1253A LEU* 3.4 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A GLU* 3.9 28.5 - - + -
951A ARG* 4.1 16.4 - - + -
952A ILE* 3.4 35.9 - - + +
955A MET* 4.4 16.4 - - + -
973A LEU 3.2 12.3 + - - +
974A ILE* 3.1 9.9 + - + +
976A CYS* 1.3 75.4 - - - +
978A ARG* 1.3 71.5 + - - +
980A CYS* 3.5 1.6 + - - +
981A MET* 3.1 39.7 + - + +
1009A MET* 3.6 44.6 - - + -
1010A VAL 3.9 2.9 - - - -
1011A PRO* 3.7 45.3 - - + -
1166A ALA* 4.1 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 978 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A ILE* 4.0 25.0 - - - +
974A ILE* 2.8 44.3 + - + +
975A GLN* 3.2 9.4 + - - +
977A TRP* 1.3 77.4 - - - +
979A GLU* 1.3 64.3 + - - +
981A MET* 3.2 7.8 + - - +
982A ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 979 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LYS* 5.9 1.2 - - - +
975A GLN* 2.8 20.6 + - - +
978A ARG* 1.3 72.7 - - - +
980A CYS* 1.3 53.9 + - - +
982A ALA* 3.2 6.2 + - + +
983A MET* 2.7 43.7 + - + +
1188A VAL* 3.6 21.8 - - + +
1251A ALA* 3.5 25.5 - - - +
1252A LEU 5.2 0.9 - - - -
1253A LEU* 4.9 8.8 - - + +
1254A PRO* 4.6 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 980 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A CYS 3.2 21.9 + - - +
977A TRP 4.0 2.5 - - - +
979A GLU* 1.3 74.1 - - - +
981A MET* 1.3 62.8 + - - +
983A MET* 4.4 1.8 - - - -
984A SER* 2.9 32.1 + - - -
1009A MET* 3.9 7.4 - - - -
1166A ALA* 4.0 11.2 - - + -
1167A ALA* 3.9 11.0 - - - -
1168A CYS* 3.7 22.7 - - - -
1186A ASP* 3.6 30.3 - - - -
1188A VAL* 3.8 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 981 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A GLU* 5.7 2.0 - - - -
952A ILE* 5.9 3.8 - - + -
977A TRP* 3.1 39.8 + - + +
978A ARG* 3.2 9.8 + - - +
980A CYS* 1.3 76.6 - - - +
982A ALA* 1.3 59.3 + - - +
985A SER* 3.3 2.3 + - - -
986A TYR* 3.2 64.3 + - + +
987A SER* 4.3 14.1 + - - +
1009A MET* 3.8 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 982 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A ARG 3.0 12.8 + - - +
979A GLU* 3.6 10.1 - - + +
981A MET* 1.3 75.2 - - - +
983A MET* 1.3 67.8 + - - +
985A SER* 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 983 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LYS* 5.5 11.4 - - - +
979A GLU* 2.7 26.2 + - + +
980A CYS* 4.2 1.8 - - - +
982A ALA* 1.3 74.6 - - - +
984A SER* 1.3 61.0 + - - +
985A SER* 3.4 4.5 + - - -
1184A ARG* 3.8 10.9 + - - -
1186A ASP* 3.7 20.6 - - + +
1187A ILE 3.6 38.8 - - - +
1188A VAL* 3.8 12.3 - - + -
1249A HIS* 3.8 19.5 - - + +
1250A ILE 5.2 0.7 - - - -
1251A ALA* 3.9 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 984 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980A CYS 2.9 20.8 + - - -
983A MET* 1.3 78.6 - - - +
985A SER* 1.3 65.4 + - - +
986A TYR* 3.2 24.4 + - - +
989A ARG* 3.0 31.2 + - - -
1009A MET* 3.8 4.0 - - - +
1168A CYS* 3.8 10.4 - - - -
1184A ARG* 3.3 6.0 + - - +
1186A ASP* 3.5 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 985 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A MET 3.3 2.6 + - - -
982A ALA 3.1 17.5 + - - -
983A MET 4.1 3.5 + - - -
984A SER* 1.3 81.1 + - - +
986A TYR* 1.3 64.2 + - - +
987A SER 3.4 2.2 + - - -
988A LEU* 3.6 21.0 + - - +
989A ARG* 3.2 26.0 + - - +
1184A ARG* 5.2 2.4 + - - -
----------------------------------------------------------
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