Contacts of the helix formed by residues 1223 - 1227 (chain A) in PDB entry 3LQ8
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 PHE1223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 88Z 3.3 67.0 - + - +
1092A VAL* 4.9 4.3 - - + -
1110A LYS* 3.1 21.2 + - - -
1164A ASP* 4.5 8.1 - - + -
1208A ARG 3.4 19.7 - - - -
1209A ASN* 3.0 26.7 + - - +
1211A MET* 3.7 24.9 - - + -
1221A ALA* 6.2 0.2 - - + -
1222A ASP* 1.3 72.7 + - - +
1224A GLY* 1.3 63.7 + - - +
1226A ALA* 3.1 31.8 + - + +
1227A ARG* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 88Z 4.6 1.6 - - - -
1110A LYS* 4.4 0.2 - - - -
1127A GLU* 3.5 17.3 - - - -
1222A ASP* 3.0 19.8 + - - -
1223A PHE* 1.3 74.9 - - - +
1225A LEU* 1.3 63.1 + - - -
1226A ALA 3.2 1.2 + - - -
1227A ARG* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087A GLY 5.5 0.3 - - - -
1088A HIS 5.4 0.2 + - - -
1089A PHE* 3.6 26.9 + - + +
1090A GLY* 3.4 19.1 + - - +
1110A LYS* 4.5 5.8 - - - -
1112A LEU* 3.9 18.4 - - + -
1120A GLU* 3.9 23.6 - - - +
1123A GLN* 4.4 12.3 - - + -
1124A PHE* 3.6 44.2 - - + +
1127A GLU* 3.2 19.6 + - - +
1223A PHE 3.3 1.4 + - - -
1224A GLY* 1.3 71.0 - - - -
1226A ALA* 1.3 56.6 + - - +
1227A ARG 3.3 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085A GLY 6.1 1.0 - - - -
1087A GLY* 4.9 4.4 + - - -
1090A GLY* 4.5 17.3 - - - -
1092A VAL* 4.1 25.1 - - + +
1110A LYS* 3.5 25.2 - - + +
1223A PHE* 3.1 27.3 + - + +
1225A LEU* 1.3 76.7 - - - +
1227A ARG* 1.3 63.4 + - - +
1228A ASP* 3.3 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087A GLY* 3.9 9.9 - - - -
1088A HIS* 4.4 4.3 + - - +
1208A ARG* 3.5 23.1 + - - +
1209A ASN* 2.5 40.2 + - - +
1222A ASP* 5.3 0.2 + - - -
1223A PHE* 3.7 31.9 - - + +
1224A GLY 3.3 15.1 + - - +
1225A LEU 3.3 5.8 - - - +
1226A ALA* 1.3 76.6 - - - +
1228A ASP* 1.3 78.6 + - - +
1231A ASP* 2.4 43.5 + - - +
1232A LYS* 4.6 8.3 - - + +
1235A TYR* 3.8 24.2 + - + -
----------------------------------------------------------
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