Contacts of the helix formed by residues 1249 - 1262 (chain A) in PDB entry 3PT6
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 SER1249 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195A ASN* 6.1 0.2 - - - -
1232A PHE* 3.2 33.0 - - - -
1245A LYS 3.5 7.1 + - - -
1246A PHE* 2.6 29.8 + - - -
1247A LYS 3.5 0.2 - - - -
1248A ASN* 1.3 77.9 - - - +
1250A LEU* 1.3 63.1 + - - +
1251A VAL* 3.3 11.1 - - - +
1252A VAL* 3.1 18.2 + - - +
1253A SER* 3.2 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1148A PHE* 3.7 27.0 - - + -
1193A ASP* 4.6 0.2 - - - +
1194A CYS* 3.9 15.0 - - - -
1195A ASN* 4.2 11.0 - - - +
1227A PRO* 4.2 2.0 - - - -
1228A PRO* 3.4 47.0 + - + +
1249A SER* 1.3 72.0 - - - +
1251A VAL* 1.3 62.1 + - - +
1252A VAL 3.1 2.0 - - - -
1253A SER* 2.9 6.4 + - - -
1254A PHE* 2.9 26.9 + - - +
1603A SAH 3.9 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227A PRO* 3.8 18.7 - - + +
1228A PRO 4.8 3.1 - - - +
1229A CYS* 3.7 16.2 - - - -
1232A PHE* 3.6 23.6 - - + -
1246A PHE* 4.5 9.2 - - + -
1249A SER* 3.3 19.1 - - - +
1250A LEU* 1.3 74.9 - - - +
1252A VAL* 1.3 62.5 + - + +
1254A PHE* 3.2 6.1 + - - +
1255A LEU* 3.1 29.1 + - + +
1268A LEU* 4.7 10.3 - - + -
1274A PHE* 4.8 5.8 - - + -
1286A THR* 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246A PHE* 3.1 38.6 - - + +
1247A LYS* 3.6 20.9 - - - +
1249A SER* 3.1 25.3 + - - +
1250A LEU 3.1 0.8 - - - -
1251A VAL* 1.3 74.9 - - + +
1253A SER* 1.3 63.3 + - - +
1255A LEU* 3.5 12.3 + - + +
1256A SER* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194A CYS* 3.8 25.1 - - - -
1195A ASN* 3.2 30.9 + - - -
1198A LEU* 5.6 2.2 - - - -
1249A SER 3.2 13.8 + - - -
1250A LEU* 2.9 10.8 + - - -
1252A VAL* 1.3 77.4 - - - +
1254A PHE* 1.3 64.4 + - - +
1256A SER* 3.0 9.2 + - - -
1257A TYR* 3.0 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A VAL* 3.7 25.4 - - + -
1148A PHE* 3.9 15.8 - + + -
1223A LEU* 3.9 15.7 - - + +
1224A CYS* 3.4 6.1 - - - -
1225A GLY* 3.0 40.2 - - - -
1227A PRO* 3.7 20.6 - - + -
1250A LEU 2.9 11.1 + - - +
1251A VAL* 3.3 10.3 - - - +
1253A SER* 1.3 76.2 - - - +
1255A LEU* 1.3 56.3 - - - +
1257A TYR* 3.1 10.9 + - + +
1258A CYS* 3.0 24.3 + - - +
1266A PHE* 3.7 23.6 - + - -
1267A LEU 3.5 15.5 - - - -
1268A LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246A PHE* 6.1 1.6 - - + -
1251A VAL* 3.1 21.9 + - + +
1252A VAL* 3.8 14.8 - - + +
1253A SER 3.2 0.2 - - - -
1254A PHE* 1.3 73.3 - - - +
1256A SER* 1.3 55.3 + - - +
1258A CYS* 3.5 6.0 - - + +
1259A ASP* 2.6 35.6 + - - +
1266A PHE* 3.8 27.6 - - + -
1268A LEU* 4.7 10.3 - - + -
1285A LEU 5.1 0.4 - - - +
1286A THR* 4.1 24.0 - - + -
1289A CYS* 3.8 38.1 - - + -
1290A LEU* 5.0 10.3 - - + -
1293A MET* 3.5 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198A LEU* 3.7 22.7 - - - +
1202A MET* 6.1 0.2 - - - +
1252A VAL* 3.2 17.8 + - - +
1253A SER* 3.0 12.4 + - - -
1255A LEU* 1.3 75.2 - - - +
1257A TYR* 1.3 57.8 + - - +
1259A ASP* 3.7 8.8 - - - +
1260A TYR* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145A LEU* 4.0 14.6 - - + -
1147A VAL* 4.5 11.7 - - + -
1170A ILE* 3.5 31.5 - - + +
1194A CYS* 2.6 46.7 + - + -
1197A LEU* 3.7 4.2 - - + +
1198A LEU* 3.6 33.0 + - + -
1223A LEU* 3.7 12.8 - - + -
1253A SER* 3.0 25.5 + - - -
1254A PHE* 3.1 12.8 - - + +
1256A SER* 1.3 74.7 - - - +
1258A CYS* 1.3 60.1 + - - +
1260A TYR* 4.6 1.6 - - - -
1261A TYR* 2.8 64.5 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223A LEU* 3.4 8.4 - - - +
1254A PHE 3.0 7.3 + - - +
1255A LEU* 3.2 10.1 + - + +
1257A TYR* 1.3 76.7 - - - +
1259A ASP* 1.3 63.6 + - - +
1262A ARG* 3.0 27.5 + - - -
1263A PRO* 4.3 4.7 - - - -
1266A PHE* 3.1 47.8 - - + -
1290A LEU* 4.2 8.1 - - - -
1293A MET* 4.3 4.7 - - + +
1295A TYR* 3.6 31.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A GLY* 2.8 31.2 - - - +
851A GLY* 4.9 1.0 - - - -
1255A LEU 2.6 20.6 + - - +
1256A SER* 3.7 9.9 - - - +
1258A CYS* 1.3 74.6 - - - +
1260A TYR* 1.3 60.1 + - - +
1262A ARG* 3.0 44.5 + - - +
1293A MET* 3.7 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ALA 4.3 0.7 - - - +
850A GLY* 4.1 9.0 - - - -
851A GLY 5.1 2.0 - - - -
1198A LEU* 4.4 12.3 - - + -
1201A VAL* 3.5 37.4 + - + +
1202A MET* 4.1 37.7 - - + -
1216A GLN* 4.1 7.6 + - - -
1217A LYS* 3.4 63.2 - - + +
1256A SER 3.0 19.3 + - - +
1257A TYR* 3.2 2.9 + - - +
1259A ASP* 1.3 78.1 - - - +
1261A TYR* 1.3 90.2 + + - +
1262A ARG* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ALA* 4.4 4.6 - - - +
1145A LEU* 4.1 12.3 - - + +
1198A LEU* 5.0 4.0 - - + -
1201A VAL* 3.8 17.6 - - + +
1215A PRO* 2.8 49.4 + - + +
1216A GLN 3.9 6.1 - - - -
1217A LYS* 4.0 14.7 - - - +
1218A GLY 4.7 9.9 + - - -
1220A VAL* 3.6 34.6 - - + +
1223A LEU* 5.3 2.5 - - + -
1257A TYR* 2.8 58.8 + + - +
1260A TYR* 1.3 96.3 - + - +
1262A ARG* 1.3 73.1 + - - +
1263A PRO* 4.2 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A TRP* 2.8 71.0 + - + +
847A ALA* 3.2 40.7 - - - +
849A GLU* 3.0 32.2 + - - +
850A GLY 4.3 0.9 + - - +
1220A VAL 4.8 1.0 - - - +
1258A CYS 3.0 13.4 + - - -
1259A ASP* 3.0 40.3 + - - +
1260A TYR 4.2 0.9 - - - +
1261A TYR* 1.3 80.3 - - - +
1263A PRO* 1.3 70.9 - - - +
1264A ARG* 3.9 0.5 + - - +
1293A MET* 4.4 17.1 + - - +
1295A TYR* 3.3 7.0 - - - -
----------------------------------------------------------
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