Contacts of the helix formed by residues 1089 - 1096 (chain C) in PDB entry 3DLS
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 ASP1089 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ADP 2.7 37.1 + - - +
1006C GLY* 4.6 0.7 - - - -
1007C SER* 4.6 12.5 + - - -
1087C GLY 3.5 1.7 + - - +
1088C LEU* 1.3 77.1 - - - +
1090C LEU* 1.3 61.4 + - - +
1091C PHE* 3.2 16.1 + - - +
1092C ALA* 3.0 27.5 + - - +
1093C PHE* 2.9 26.8 + - - +
1131C ASP 3.9 0.7 - - - +
1132C GLU* 3.7 20.1 - - - +
1134C ILE 3.2 16.2 - - - +
1135C VAL* 4.2 0.7 - - + +
1136C ILE* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1090 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089C ASP* 1.3 71.3 - - - +
1091C PHE* 1.3 56.7 + - - +
1093C PHE* 3.5 18.0 - - + +
1094C ILE* 2.9 37.7 + - + +
1108C ILE* 4.1 22.0 - - + -
1131C ASP* 3.0 23.4 + - + +
1134C ILE* 2.9 42.2 + - + +
1135C VAL* 4.8 0.2 - - - +
1136C ILE* 3.8 38.4 - - + -
1142C ILE* 4.6 2.5 - - + -
1192C THR* 5.3 5.6 - - + -
1196C LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1091 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007C SER* 5.6 4.3 - - - -
1089C ASP* 3.2 11.8 - - - +
1090C LEU* 1.3 77.2 - - - +
1092C ALA* 1.3 58.2 + - + +
1094C ILE* 3.3 4.7 + - + +
1095C ASP* 2.8 58.2 + - - +
1131C ASP* 3.2 35.8 + - - +
1132C GLU* 3.5 30.3 - - + -
1201C ASN* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1092 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088C LEU* 3.7 18.4 - - + -
1089C ASP* 3.0 24.1 + - - +
1091C PHE* 1.3 80.4 - - + +
1093C PHE* 1.3 65.2 + - - +
1095C ASP* 3.6 7.7 + - - +
1096C ARG* 3.2 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1093 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088C LEU* 4.0 8.4 - - + +
1089C ASP 2.9 13.1 + - - +
1090C LEU* 3.5 28.7 - - + +
1092C ALA* 1.3 75.0 - - - +
1094C ILE* 1.3 64.2 + - + +
1096C ARG* 3.3 15.4 + - - +
1098C PRO* 3.2 42.7 - - + +
1100C LEU* 4.2 19.1 - - + -
1108C ILE* 4.4 10.8 - - + -
1136C ILE* 4.3 13.5 - - + -
1140C PHE* 5.0 1.3 - + - -
1196C LEU* 4.8 1.8 - - + -
1262C TRP* 3.6 33.2 - + - -
1265C VAL* 4.1 13.7 - - + -
1266C PHE* 3.5 38.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1094 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090C LEU* 2.9 27.9 + - + +
1091C PHE* 3.3 5.4 + - + +
1093C PHE* 1.3 79.3 - - + +
1095C ASP* 1.3 65.8 + - - +
1096C ARG 3.2 1.8 - - - -
1097C HIS* 3.0 20.8 + - - -
1098C PRO* 3.6 11.1 - - + +
1131C ASP* 4.3 11.7 - - + +
1192C THR 5.6 0.4 - - - +
1195C THR* 3.6 34.5 - - + +
1196C LEU* 3.8 27.6 - - + +
1199C GLU* 4.1 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1095 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091C PHE* 2.8 43.5 + - + +
1092C ALA* 3.7 11.0 - - - +
1094C ILE* 1.3 73.4 - - - +
1096C ARG* 1.3 59.5 + - + +
1097C HIS* 3.2 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1096 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088C LEU* 5.7 0.7 - - + -
1092C ALA* 3.2 13.9 + - + +
1093C PHE 3.6 1.6 - - - +
1094C ILE 3.2 1.0 - - - -
1095C ASP* 1.3 76.6 - - + +
1097C HIS* 1.3 70.3 + - - +
1266C PHE* 3.2 47.0 - - + -
1267C ARG 3.2 39.8 + - - -
----------------------------------------------------------
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