Contacts of the helix formed by residues 1016 - 1028 (chain A) in PDB entry 4C3I
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 SER1016 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LEU* 5.3 3.6 - - - -
1015A ARG* 1.3 72.2 - - - +
1017A GLY* 1.3 62.2 + - - +
1018A TYR 3.6 0.4 - - - -
1019A LEU* 4.1 9.9 - - - +
1020A GLN* 3.2 25.7 + - - +
1194A GLY* 2.9 17.3 + - - -
1197A SER* 2.7 35.3 + - - -
1198A THR* 3.8 24.0 - - - +
1219A ILE* 4.7 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1017 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LEU* 6.0 3.1 - - - -
1015A ARG* 3.3 7.8 - - - +
1016A SER* 1.3 78.2 - - - +
1018A TYR* 1.3 55.9 - - - +
1020A GLN* 3.9 3.1 - - - +
1021A ARG* 3.1 28.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
468A ARG* 5.9 1.3 - - - -
1015A ARG* 4.6 5.4 + - + +
1017A GLY* 1.3 71.4 - - - +
1019A LEU* 1.4 64.1 + - - +
1021A ARG* 3.3 35.9 + - - +
1022A CYS* 3.0 56.9 + - - -
1227A MET* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A ARG 4.6 5.4 + - - +
1016A SER* 3.8 14.7 + - - +
1017A GLY 3.4 0.6 - - - -
1018A TYR* 1.4 78.3 - - - +
1020A GLN* 1.3 59.8 + - - +
1022A CYS* 3.6 3.5 + - - +
1023A LEU* 3.4 41.2 + - + +
1193A VAL* 4.2 8.1 - - + -
1194A GLY* 4.9 2.7 - - - -
1197A SER* 4.4 10.5 - - - +
1219A ILE* 4.3 9.0 - - + -
1222A LEU* 3.9 44.0 - - + +
1223A ARG* 3.9 31.6 - - + +
1226A VAL* 4.6 11.0 - - + +
1227A MET* 3.8 17.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A THR 4.5 2.9 - - - +
595A LEU* 3.0 44.7 + - - +
1016A SER 3.2 15.1 + - - +
1017A GLY* 3.9 3.1 - - - +
1019A LEU* 1.3 76.9 - - - +
1021A ARG* 1.4 54.3 + - - +
1023A LEU* 3.3 7.8 + - - +
1024A THR* 2.9 47.7 + - + +
1190A SER 3.5 23.3 - - - +
1191A GLN* 4.0 9.8 + - - +
1194A GLY* 3.4 9.3 - - - -
1195A GLU 3.4 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ARG* 3.4 57.4 - - - +
1017A GLY 3.1 17.8 + - - +
1018A TYR* 3.3 43.5 + - - +
1020A GLN* 1.4 76.0 - - - +
1022A CYS* 1.3 64.8 + - - +
1024A THR* 3.1 16.4 + - - +
1025A LYS* 3.3 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A TYR* 3.0 60.4 + - - +
1019A LEU 3.9 5.4 - - - +
1021A ARG* 1.3 77.8 - - - +
1023A LEU* 1.3 66.1 + - + +
1025A LYS* 3.9 3.4 + - - +
1026A GLN* 3.7 19.9 + - - +
1226A VAL* 5.9 2.0 - - + -
1227A MET* 4.3 17.0 - - + -
----------------------------------------------------------
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 LEU* 3.4 22.1 + - + +
1020A GLN* 3.3 6.4 + - - +
1022A CYS* 1.3 76.5 - - - +
1024A THR* 1.4 59.2 + - - +
1026A GLN* 3.2 5.3 + - - +
1027A LEU* 2.9 50.3 + - + +
1190A SER* 3.3 24.2 - - - +
1193A VAL* 3.9 27.1 - - + -
1226A VAL* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020A GLN* 2.9 34.2 + - + +
1021A ARG* 3.1 17.2 + - - +
1023A LEU* 1.4 73.7 - - - +
1025A LYS* 1.3 55.5 + - - +
1027A LEU* 3.8 1.3 - - - +
1028A GLU* 2.9 33.1 + - - +
1187A ILE* 3.7 25.9 - - + +
1190A SER* 3.3 23.1 - - - +
1191A GLN* 5.1 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1025 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ARG* 6.3 2.5 - - - -
472A MET* 4.3 28.6 - - - -
1021A ARG* 3.3 29.2 + - + +
1022A CYS* 4.4 3.8 - - - +
1023A LEU 3.3 1.0 - - - -
1024A THR* 1.3 81.2 + - - +
1026A GLN* 1.3 56.4 + - - +
1027A LEU 3.5 0.2 - - - -
1028A GLU* 3.4 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A CYS 3.7 14.7 + - - +
1023A LEU* 3.2 5.2 + - - +
1025A LYS* 1.3 77.5 - - - +
1027A LEU* 1.3 66.7 + - + +
1028A GLU* 3.7 0.9 - - - -
1029A GLY 5.2 0.3 + - - -
1030A VAL* 4.7 5.2 - - - +
1040A ASP* 4.7 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A LEU* 2.9 45.3 + - + +
1024A THR 4.7 0.2 - - - +
1026A GLN* 1.3 85.9 - - + +
1028A GLU* 1.3 62.7 + - - +
1029A GLY 3.2 3.1 - - - -
1030A VAL* 3.0 33.9 + - + +
1046A VAL* 6.1 2.9 - - + -
1186A GLY* 3.3 43.9 - - - +
1189A ALA* 4.9 5.4 - - + -
1190A SER* 4.2 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A MET* 5.5 2.8 - - - +
1024A THR 2.9 15.5 + - - +
1025A LYS* 3.4 49.9 + - - +
1026A GLN 4.9 0.4 - - - -
1027A LEU* 1.3 76.2 - - - +
1029A GLY* 1.3 61.9 + - - +
1030A VAL 3.6 4.9 + - - +
1184A ALA* 4.8 6.6 - - - +
1187A ILE* 3.8 25.7 - - + +
----------------------------------------------------------
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