Contacts of the helix formed by residues 1015 - 1028 (chain A) in PDB entry 5WS3
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 SER1015 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A GLY* 1.3 76.9 - - - -
1016A ARG* 1.3 65.5 + - - +
1017A ASP* 4.0 8.1 + - - +
1018A GLU* 3.2 34.8 + - - +
1019A ARG* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1016 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A SER* 1.3 73.1 - - - +
1017A ASP* 1.3 58.1 + - - +
1019A ARG* 3.2 23.8 + - - +
1020A LYS* 2.9 29.7 + - + +
1109A TYR 2.8 27.7 + - - -
1110A GLY 3.3 21.8 + - - +
1111A SER* 4.2 7.8 + - - +
1112A VAL 2.9 21.4 + - - -
1113A ASP* 5.6 0.7 - - - -
1134A LEU 2.8 21.2 + - - -
1135A GLY* 3.5 13.7 + - - -
1136A ALA 3.5 13.7 - - - +
1185A ARG* 3.5 36.3 - - - +
1189A LYS* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1017 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A SER* 3.3 8.4 + - - +
1016A ARG* 1.3 77.5 - - - +
1018A GLU* 1.3 64.1 + - + +
1020A LYS* 3.3 13.0 + - - +
1021A LYS* 2.9 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1018 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A GLY* 3.5 11.3 - - - -
1015A SER* 3.2 36.5 + - - +
1017A ASP* 1.3 77.4 - - + +
1019A ARG* 1.3 59.9 + - + +
1021A LYS* 3.4 9.3 + - + +
1022A SER* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A GLU* 5.9 1.8 - - - +
1012A LEU* 3.8 37.7 + - - +
1013A THR 3.3 24.1 + - - +
1014A GLY* 2.6 31.1 + - - -
1015A SER 3.0 9.3 + - - +
1016A ARG* 3.7 31.2 - - - +
1018A GLU* 1.3 76.9 - - + +
1020A LYS* 1.3 57.2 + - - +
1022A SER* 3.3 5.6 + - - -
1023A LEU* 2.8 30.0 + - - +
1107A GLU* 4.3 15.5 - - - +
1110A GLY 2.9 26.6 + - - -
1111A SER* 3.8 13.4 - - - -
2006A 1PE 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A ARG* 2.9 15.3 + - + +
1017A ASP* 3.8 12.9 + - - +
1019A ARG* 1.3 77.5 - - - +
1021A LYS* 1.3 59.9 + - - +
1023A LEU* 3.2 4.8 + - + +
1024A LEU* 2.9 43.4 + - + +
1031A GLU* 4.9 10.2 - - - +
1032A GLY 3.2 25.5 + - - +
1033A VAL* 4.3 2.8 - - - +
1034A THR* 4.0 8.7 - - - +
1111A SER* 3.4 30.6 - - - +
1112A VAL* 5.1 0.2 - - - -
1113A ASP* 2.8 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A ASP* 2.9 39.6 + - - +
1018A GLU* 3.9 7.9 - - + +
1020A LYS* 1.3 77.5 - - + +
1022A SER* 1.3 57.9 + - - +
1024A LEU* 3.4 6.8 + - - +
1025A SER* 2.9 31.8 + - - -
1031A GLU* 3.6 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A GLU 2.9 17.9 + - - -
1019A ARG* 3.7 6.1 - - - -
1021A LYS* 1.3 76.5 - - - +
1023A LEU* 1.3 61.8 + - - +
1025A SER* 3.3 6.6 + - - -
1026A LYS* 2.9 40.1 + - - +
2006A 1PE 3.1 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A ARG 2.8 17.4 + - - +
1020A LYS* 3.5 5.6 - - + +
1022A SER* 1.3 75.9 + - - +
1024A LEU* 1.3 69.3 + - + +
1026A LYS* 3.1 9.2 + - + +
1027A PHE* 3.0 50.9 + - + -
1034A THR* 4.8 2.5 - - + -
1070A ILE* 4.0 15.9 - - + -
1104A PHE* 4.9 4.0 - - + -
1107A GLU* 5.8 2.5 - - + -
1108A LEU* 3.6 24.5 - - + +
1111A SER* 3.4 25.1 - - - +
1112A VAL* 4.0 22.2 - - + +
2006A 1PE 5.3 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020A LYS* 2.9 33.4 + - + +
1021A LYS* 4.0 4.7 - - - +
1023A LEU* 1.3 76.7 - - + +
1025A SER* 1.3 62.8 + - - +
1027A PHE* 3.1 8.7 + - + +
1029A MET* 3.0 61.9 + - + +
1030A ASP 3.6 16.6 - - - +
1031A GLU* 3.8 6.5 - - + -
1032A GLY 3.7 19.1 - - - +
1034A THR* 3.4 35.7 - - + +
1068A ARG* 4.6 4.0 - - + -
1070A ILE* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1025 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A LYS 2.9 18.1 + - - -
1022A SER* 3.5 7.6 - - - -
1024A LEU* 1.3 76.3 - - - +
1026A LYS* 1.3 63.2 + - - +
1028A GLY* 3.1 14.0 + - - -
1029A MET 4.2 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A SER* 2.9 35.1 + - - +
1023A LEU* 3.1 8.3 + - + +
1025A SER* 1.3 77.3 - - - +
1027A PHE* 1.3 68.5 + - + +
1028A GLY 3.5 0.5 + - - -
2006A 1PE 2.5 99.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A LEU* 3.0 40.9 + - + +
1024A LEU* 3.1 6.4 + - + +
1026A LYS* 1.3 84.2 - - + +
1028A GLY* 1.3 63.8 + - - +
1029A MET* 3.5 18.0 - - + +
1070A ILE* 3.7 35.9 - - + -
1094A LYS* 3.4 36.1 - - + +
1096A ILE* 3.5 31.6 - - + -
1104A PHE* 3.6 30.1 - + - -
1108A LEU* 4.1 2.7 - - + -
2006A 1PE 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A SER* 3.1 14.5 + - - -
1026A LYS 3.2 1.6 + - - -
1027A PHE* 1.3 79.3 - - - +
1029A MET* 1.3 59.9 + - - +
1091A GLY 4.8 4.3 - - - +
----------------------------------------------------------
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