Contacts of the helix formed by residues 1258 - 1267 (chain A) 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 SER1258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195A VAL* 4.7 3.4 - - - -
1256A ARG 3.8 0.8 + - - -
1257A PRO* 1.3 74.8 - - - +
1259A PHE* 1.3 65.3 + - - +
1260A LEU* 3.1 11.8 + - - +
1261A GLU* 2.8 38.0 + - - +
1262A ILE* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120A ALA* 3.7 14.0 - - + +
1123A MET* 3.5 53.8 - - + -
1124A ALA* 3.7 19.5 - - + -
1127A ASN* 3.5 28.9 - - + -
1194A ASP* 3.8 9.6 - - + -
1195A VAL* 3.6 30.5 - - + +
1198A PHE* 3.7 28.5 - + + -
1257A PRO 4.2 0.2 + - - -
1258A SER* 1.3 73.1 - - - +
1260A LEU* 1.3 61.7 + - - +
1262A ILE* 3.5 14.3 + - + +
1263A ILE* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124A ALA* 4.1 19.7 - - + +
1258A SER* 3.1 8.1 + - - +
1259A PHE* 1.3 75.7 - - - +
1261A GLU* 1.3 66.3 + - + +
1263A ILE* 3.2 6.3 + - + +
1264A SER* 3.0 21.9 + - - -
1279A PHE* 4.5 7.6 - - + -
1280A TYR* 3.6 32.6 - - + -
1285A ASN* 3.7 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256A ARG 4.5 1.4 - - - +
1257A PRO* 3.3 10.9 - - - +
1258A SER* 2.8 41.3 + - - +
1260A LEU* 1.3 70.7 - - + +
1262A ILE* 1.3 63.9 + - - +
1264A SER* 2.9 19.4 + - - -
1265A SER* 3.1 14.0 + - - -
986B VAL* 3.8 28.2 - - + +
987B TYR* 4.2 21.7 - - - +
1049B ASN* 5.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120A ALA* 4.2 7.6 - - + -
1195A VAL* 4.3 7.4 - - + -
1198A PHE* 3.7 44.6 - - + -
1244A LEU* 4.3 22.7 - - + -
1248A CYS* 4.0 13.9 - - - -
1257A PRO* 3.7 18.8 - - + -
1258A SER 3.0 18.4 + - - +
1259A PHE* 3.6 20.4 - - + +
1261A GLU* 1.3 76.0 - - - +
1263A ILE* 1.3 65.0 + - - +
1265A SER* 2.8 24.9 + - - -
1266A ILE* 3.6 13.5 + - + +
986B VAL* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117A GLY* 4.3 5.6 - - - +
1120A ALA* 3.5 20.4 - - + +
1121A ASP* 3.5 39.3 - - + +
1124A ALA* 4.1 9.0 - - + -
1259A PHE 3.1 16.6 + - - +
1260A LEU* 3.2 6.5 + - - +
1262A ILE* 1.3 77.6 - - - +
1264A SER* 1.3 58.8 + - - +
1266A ILE* 3.2 10.0 + - + +
1267A LYS* 2.8 32.4 + - + +
1270A MET* 6.0 0.4 - - + -
1274A PHE* 4.2 16.4 - - + -
1280A TYR* 3.4 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260A LEU 3.0 9.1 + - - -
1261A GLU* 2.9 15.1 + - - -
1263A ILE* 1.3 78.8 - - - +
1265A SER* 1.3 60.7 + - - +
1266A ILE 3.1 1.2 + - - -
1267A LYS* 3.4 29.2 + - - +
1268A GLU* 5.9 0.3 - - - +
1280A TYR* 2.5 29.3 + - - -
985B ASP 6.0 0.2 - - - -
986B VAL* 5.7 2.2 - - - -
989B PRO* 6.5 1.3 - - - -
990B ASP* 4.5 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244A LEU* 5.2 2.8 - - - +
1261A GLU 3.1 1.7 + - - -
1262A ILE* 2.8 24.0 + - - +
1264A SER* 1.3 79.1 - - - +
1266A ILE* 1.3 68.5 + - - +
1268A GLU* 6.5 0.2 - - - -
1269A GLU* 4.5 5.4 - - - +
981B PHE* 3.8 25.9 - - - -
985B ASP* 3.7 25.5 - - - +
986B VAL* 3.7 20.8 - - - +
990B ASP* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113A ILE* 3.6 39.8 - - + +
1116A ALA* 4.5 7.9 - - + -
1117A GLY* 3.9 18.4 - - - +
1240A MET* 3.8 27.8 - - + -
1244A LEU* 4.8 6.1 - - + -
1262A ILE* 3.7 16.2 - - + +
1263A ILE* 3.7 11.2 - - + +
1264A SER 3.1 0.2 - - - -
1265A SER* 1.3 93.6 - - - +
1267A LYS* 1.3 59.5 + - - +
1268A GLU 3.0 6.3 - - - +
1269A GLU* 2.9 30.2 + - - +
1270A MET* 3.5 11.8 - - - +
981B PHE* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263A ILE* 2.8 24.3 + - + +
1264A SER* 3.4 20.5 + - - +
1266A ILE* 1.3 77.8 - - - +
1268A GLU* 1.3 74.7 + - + +
1269A GLU 3.2 1.4 + - - -
1270A MET* 3.6 25.2 + - - +
1274A PHE* 5.3 1.2 - - + -
1280A TYR* 3.6 28.3 + - + +
1281A TYR* 3.2 33.7 + - + +
990B ASP* 4.8 14.6 + - - +
1024R ASP* 3.4 30.4 + - - +
----------------------------------------------------------
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