Contacts of the helix formed by residues 1005 - 1022 (chain A) in PDB entry 3LXK
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 SER1005 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A VAL* 3.7 21.3 - - - +
979A ASP 3.6 20.2 - - - -
980A TYR* 4.1 6.3 - - - -
997A GLU* 4.8 3.3 + - - -
1003A ILE* 5.3 3.0 - - - +
1004A PHE* 1.3 77.2 - - - +
1006A ARG* 1.3 63.6 + - - +
1007A GLN* 3.1 20.3 + - - +
1008A SER* 2.8 27.7 + - - -
1009A ASP 3.1 5.7 + - - -
1082A PRO* 4.9 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1006 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A GLY* 2.9 42.6 + - - -
944A ARG* 3.7 32.0 - - - +
945A CYS 4.1 16.4 - - - +
946A VAL* 3.9 9.0 - - + +
974A LEU* 3.7 18.9 - - - +
979A ASP* 3.8 27.3 + - - +
1005A SER* 1.3 75.3 - - - +
1007A GLN* 1.3 64.6 + - + +
1009A ASP* 3.3 14.0 - - - +
1010A VAL* 3.2 27.0 + - - +
1088A PHE* 3.9 8.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1007 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A SER* 3.1 10.7 + - - +
1006A ARG* 1.3 83.2 - - + +
1008A SER* 1.3 62.2 + - - +
1009A ASP 3.3 0.2 - - - -
1010A VAL* 3.3 13.4 + - - +
1011A TRP 3.3 12.1 + - - -
1082A PRO* 3.4 33.8 + - + +
1083A GLN* 5.3 2.6 + - - -
1085A ARG* 3.0 52.5 + - - +
1086A PRO 3.3 13.6 + - - +
1087A SER* 4.4 9.6 - - - +
1088A PHE* 5.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1008 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A VAL* 4.9 0.2 - - - +
995A ALA* 3.8 14.3 + - - +
997A GLU* 3.7 15.0 - - - -
998A SER* 3.9 11.7 - - - -
1004A PHE* 3.4 15.1 - - - +
1005A SER* 2.8 38.2 + - - -
1007A GLN* 1.3 73.5 - - - +
1009A ASP* 1.3 65.7 + - - +
1011A TRP* 3.2 4.7 + - - +
1012A SER* 3.1 23.8 + - - -
1085A ARG* 3.8 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1009 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A MET* 3.5 28.1 - - + +
945A CYS 4.4 1.4 - - - +
946A VAL* 3.6 9.8 - - - +
947A HIS* 2.8 26.1 + - - +
948A ARG* 3.0 27.9 + - - -
949A ASP 4.8 0.2 + - - -
950A LEU* 3.8 6.0 + - + +
1005A SER 3.1 12.9 + - - +
1006A ARG* 3.3 14.9 - - - +
1007A GLN 3.3 0.2 - - - -
1008A SER* 1.3 79.0 + - - +
1010A VAL* 1.3 56.5 + - - +
1012A SER* 3.2 9.4 + - - -
1013A PHE* 2.9 27.9 + - - +
1088A PHE* 3.7 5.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1010 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A ARG 3.2 16.1 + - - +
1007A GLN* 3.6 21.5 - - - +
1008A SER 3.2 0.6 - - - -
1009A ASP* 1.3 71.8 - - - +
1011A TRP* 1.3 66.8 + - - +
1013A PHE* 3.1 4.4 + - - +
1014A GLY 3.1 17.5 + - - -
1077A CYS* 3.5 31.7 - - - +
1085A ARG* 4.0 7.2 - - + -
1086A PRO* 3.4 28.7 - - + +
1088A PHE* 3.6 32.8 - - + +
1091A LEU* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1011 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992A PHE 5.1 1.8 + - - -
993A TRP 3.4 21.9 + - - -
994A TYR 3.3 10.7 + - - -
995A ALA* 3.5 24.2 - - + -
996A PRO* 3.5 32.1 - - + -
1007A GLN 3.3 3.4 + - - -
1008A SER 3.2 10.6 + - - +
1010A VAL* 1.3 77.6 - - - +
1012A SER* 1.3 61.8 + - - +
1014A GLY 3.0 11.1 + - - -
1015A VAL* 3.4 9.7 + - + +
1034A PHE* 5.8 2.9 - + - -
1054A LEU* 3.9 26.0 - - + -
1059A ARG* 3.9 24.9 - - - -
1077A CYS 3.4 12.1 + - - +
1078A TRP* 3.2 66.9 + + + -
1079A ALA 3.8 4.9 - - - -
1085A ARG* 3.8 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1012 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A ARG 5.7 3.0 + - - -
950A LEU* 3.7 28.6 + - - +
993A TRP* 2.8 29.5 + - - +
994A TYR* 4.9 0.7 - - - -
995A ALA 5.0 0.7 + - - -
1008A SER 3.1 11.5 + - - -
1009A ASP* 3.2 11.3 + - - -
1011A TRP* 1.3 77.6 - - - +
1013A PHE* 1.3 57.6 + - - +
1015A VAL* 3.0 10.4 + - - +
1016A VAL* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1013 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A SER* 3.7 24.7 - - - -
933A ILE* 3.8 28.3 - - + -
934A CYS* 3.9 9.9 - - + -
950A LEU* 3.7 11.8 - - + +
1009A ASP 2.9 13.6 + - - +
1010A VAL 3.1 7.8 + - - +
1012A SER* 1.3 77.7 - - - +
1014A GLY* 1.3 57.6 + - - +
1016A VAL* 3.0 11.2 + - + +
1017A LEU* 2.8 61.3 + - + +
1077A CYS* 4.0 13.5 - - - -
1088A PHE* 3.6 24.2 - + + -
1091A LEU* 4.1 13.9 - - + -
1095A LEU* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1014 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A VAL 3.1 6.7 + - - -
1011A TRP 3.0 9.9 + - - -
1013A PHE* 1.3 78.2 - - - +
1015A VAL* 1.3 54.9 + - - +
1017A LEU* 3.3 10.6 + - - +
1018A TYR* 3.0 21.7 + - - +
1074A MET* 3.9 4.7 - - - +
1077A CYS* 3.7 18.8 - - - -
1078A TRP* 3.3 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1015 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992A PHE 3.9 15.3 - - - +
993A TRP* 3.3 38.8 - - + +
1011A TRP* 3.4 17.8 + - + +
1012A SER* 3.0 8.4 + - - +
1014A GLY* 1.3 73.5 - - - +
1016A VAL* 1.3 59.6 + - - +
1018A TYR* 3.2 3.9 + - - +
1019A GLU* 2.8 26.8 + - - +
1030A PRO* 3.7 26.7 - - + -
1034A PHE* 5.8 1.6 - - + -
1060A LEU* 4.8 6.7 - - + -
1078A TRP* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1016 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A LEU* 5.7 0.7 - - + -
933A ILE* 3.9 34.1 - - + -
950A LEU* 3.8 14.8 - - + +
951A ALA* 3.7 36.8 - - - +
952A ALA* 5.0 8.3 - - + +
955A ILE* 5.2 1.6 - - + -
993A TRP* 4.8 0.2 - - - +
1012A SER 2.9 17.1 + - - +
1013A PHE* 3.0 14.8 + - + +
1015A VAL* 1.3 72.9 - - - +
1017A LEU* 1.3 64.1 + - - +
1019A GLU* 3.2 12.1 + - + +
1020A LEU* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1017 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A SER* 3.3 35.9 - - - +
1013A PHE* 2.8 49.7 + - + +
1014A GLY* 3.3 11.9 + - - +
1016A VAL* 1.3 72.9 - - - +
1018A TYR* 1.3 62.2 + - - +
1020A LEU* 3.3 5.8 + - + -
1021A PHE* 3.0 37.7 + - + +
1070A VAL* 4.9 5.6 - - + +
1073A LEU* 4.6 10.5 - - + -
1074A MET* 3.9 34.3 - - + +
1077A CYS* 4.5 5.2 - - - -
1091A LEU* 5.8 0.9 - - + -
1095A LEU* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1018 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A GLY 3.0 12.5 + - - +
1015A VAL* 3.3 12.8 - - - +
1017A LEU* 1.3 77.5 - - - +
1019A GLU* 1.3 61.0 + - - +
1021A PHE 3.4 1.0 + - - -
1022A THR* 2.9 45.9 + - + +
1028A CYS* 2.6 36.5 + - - +
1030A PRO* 4.0 25.6 - - + -
1033A GLU* 3.9 16.6 - - - +
1060A LEU* 3.6 36.1 - - + -
1061A PRO* 3.2 29.3 + - - +
1063A PRO* 4.0 16.8 - - + +
1074A MET* 3.9 12.1 - - - +
1078A TRP* 4.3 8.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A ARG* 5.1 5.7 - - - -
951A ALA* 3.6 1.9 - - - -
952A ALA* 2.8 41.4 + - + +
953A ARG 4.7 1.7 + - - -
993A TRP* 3.0 36.1 + - - -
1015A VAL 2.8 18.1 + - - +
1016A VAL* 3.2 13.8 + - - +
1018A TYR* 1.3 75.6 - - - +
1020A LEU* 1.3 59.5 - - + +
1022A THR* 3.1 9.0 + - - -
1024A CYS* 2.8 49.3 + - - +
1030A PRO* 4.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A LEU* 3.7 26.9 - - + -
914A LEU* 3.8 15.4 - - + +
926A LEU* 3.4 27.6 - - + +
929A TYR* 3.9 23.8 - - + -
930A SER* 3.4 35.0 - - - +
933A ILE* 4.1 16.4 - - + -
952A ALA* 6.3 0.7 - - + -
1013A PHE* 6.0 0.2 - - + -
1016A VAL* 2.9 23.2 + - + +
1017A LEU* 3.3 9.6 + - + +
1019A GLU* 1.3 74.7 - - + +
1021A PHE* 1.3 68.7 + - + +
1023A TYR* 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A ALA* 4.5 10.3 - - + -
926A LEU* 3.7 35.2 - - + +
927A LEU* 4.0 15.9 - - + -
930A SER* 3.9 20.2 - - - -
1017A LEU* 3.0 24.9 + - + +
1018A TYR 3.8 0.7 - - - -
1020A LEU* 1.3 80.3 - - + +
1022A THR* 1.3 56.9 + - - +
1023A TYR* 3.4 10.1 - - - -
1063A PRO* 3.5 29.9 - - + +
1064A PRO* 4.3 8.7 - - - +
1066A CYS* 4.4 6.4 - - + +
1067A PRO* 3.8 34.3 - - + -
1070A VAL* 3.7 32.5 - - + -
1074A MET* 4.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ARG* 3.6 3.8 + - - -
1018A TYR* 2.9 49.9 + - + +
1019A GLU* 3.1 12.6 + - - -
1021A PHE* 1.3 74.8 - - - +
1023A TYR* 1.3 62.8 + - - +
1024A CYS* 3.6 6.4 + - - -
1025A ASP* 2.9 33.0 + - - +
1028A CYS* 3.7 26.6 + - - -
1029A SER* 5.4 1.6 - - - -
1030A PRO* 5.7 0.5 - - - +
1063A PRO* 3.7 23.1 - - + -
1064A PRO* 4.8 2.7 - - + -
----------------------------------------------------------
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