Contacts of the helix formed by residues 1086 - 1094 (chain R) in PDB entry 3F5P
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 ASP1086 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R 741 5.3 0.7 + - - -
1085R GLY* 1.3 74.1 - - - -
1087R LEU* 1.3 67.6 + - - +
1088R LYS* 2.9 19.3 + - - +
1089R SER* 2.7 44.9 + - - -
1090R TYR* 2.9 18.6 + - - +
1139R ARG* 3.6 24.5 - - - +
1141R CYS 3.2 8.5 - - - +
1142R MET* 4.3 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1087 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085R GLY 3.6 1.8 + - - -
1086R ASP* 1.3 70.9 - - - +
1088R LYS* 1.3 58.1 + - - +
1090R TYR* 3.6 3.9 - - + +
1091R LEU* 2.8 48.9 + - + +
1115R MET* 4.0 29.2 - - + -
1119R ILE* 3.8 28.9 - - + -
1138R ALA* 3.3 24.2 - - + +
1141R CYS* 2.7 26.1 + - + +
1143R VAL* 3.8 16.1 - - + +
1149R VAL* 4.1 15.5 - - + -
1201R VAL* 4.8 1.1 - - + -
1205R ILE* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1088 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086R ASP* 2.9 12.4 + - - +
1087R LEU* 1.3 77.1 - - - +
1089R SER* 1.3 67.4 + - - +
1091R LEU* 3.4 0.4 + - - -
1092R ARG* 3.2 61.0 + - + +
1138R ALA* 3.4 8.0 + - + -
1139R ARG* 3.7 32.0 - - + +
1178R TRP* 5.0 13.1 - - - -
1204R GLU* 4.3 16.2 + - - +
1209R ALA* 3.6 18.2 - - + +
1210R GLU 6.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1089 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R 741 4.3 16.6 - - - -
1084R ARG 5.7 0.7 - - - -
1085R GLY 5.6 0.2 - - - -
1086R ASP* 2.7 32.9 + - - -
1088R LYS* 1.3 77.4 - - - +
1090R TYR* 1.3 63.2 + - - +
1092R ARG* 3.1 10.8 + - - +
1093R SER* 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1090 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084R ARG* 4.3 29.3 + - + +
1086R ASP 2.9 12.2 + - - +
1087R LEU* 3.6 18.4 - - + +
1089R SER* 1.3 77.1 - - - +
1091R LEU* 1.3 66.1 + - - +
1093R SER* 2.4 32.4 + - - -
1094R LEU* 3.4 37.9 - - + +
1111R LYS* 6.1 0.5 - - - +
1115R MET* 3.6 31.3 - - + +
1143R VAL* 4.0 14.1 - - + -
1147R PHE* 3.2 40.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1091 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087R LEU* 2.8 52.6 + - + +
1088R LYS 3.8 3.6 - - - +
1090R TYR* 1.3 73.6 - - + +
1092R ARG* 1.3 61.6 + - - +
1094R LEU* 3.2 27.8 + - + +
1115R MET* 4.4 7.4 - - + -
1138R ALA* 4.4 10.8 - - + -
1204R GLU 3.8 10.8 - - - +
1205R ILE* 3.7 48.7 - - + +
1208R LEU* 3.6 28.6 - - + +
1209R ALA* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1092 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088R LYS* 3.2 40.7 + - + +
1089R SER* 3.1 11.8 + - - +
1091R LEU* 1.3 76.9 - - - +
1093R SER* 1.3 59.6 + - - +
1095R ARG* 2.9 58.3 + - - +
1208R LEU 3.9 1.1 - - - -
1209R ALA* 2.6 31.4 + - + -
1210R GLU* 4.9 5.1 - - - +
1211R GLN* 5.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1093 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089R SER 3.0 12.0 + - - -
1090R TYR* 2.4 36.5 + - - -
1092R ARG* 1.3 76.4 - - - +
1094R LEU* 1.3 61.7 + - - +
1095R ARG 3.2 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1094 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090R TYR* 3.4 49.6 - - + +
1091R LEU* 3.5 14.6 - - + +
1092R ARG 3.1 0.8 - - - -
1093R SER* 1.3 83.9 - - - +
1095R ARG* 1.3 60.0 + - - +
1096R PRO* 4.1 1.9 - - - +
1106R PRO* 5.8 1.9 - - - +
1107R PRO* 4.7 20.8 - - + +
1115R MET* 5.5 2.2 - - + -
1208R LEU* 3.7 30.3 - - + +
----------------------------------------------------------
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