Contacts of the helix formed by residues 1262 - 1276 (chain B) in PDB entry 3FK2
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 PRO1262 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246B TYR* 3.6 13.0 - - + +
1251B LEU* 4.1 7.0 - - + -
1254B VAL* 3.7 12.8 - - + +
1255B VAL* 3.4 21.5 - - + -
1260B PRO 3.5 2.0 - - - +
1261B ILE* 1.3 91.1 - - + +
1263B ILE* 1.3 66.0 + - - +
1264B PHE 4.5 0.2 - - - +
1265B ILE* 2.9 30.8 + - + +
1266B GLU* 3.1 10.2 + - - +
1324B PHE* 4.0 30.3 - - + -
1371B VAL* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246B TYR* 3.1 10.9 + - + +
1254B VAL 5.2 4.5 - - - +
1259B LYS* 5.2 15.0 - - + +
1261B ILE 3.9 10.5 - - - +
1262B PRO* 1.3 71.3 - - + +
1264B PHE* 1.3 65.0 + - - +
1266B GLU* 3.2 18.8 + - + +
1267B ARG* 2.9 52.6 + - - +
1299B PHE* 3.9 15.3 - - + -
1303B HIS* 4.0 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246B TYR* 3.3 25.8 + - + -
1247B PHE* 3.7 29.4 - + - -
1262B PRO* 3.2 1.2 - - + -
1263B ILE* 1.3 78.6 - - - +
1265B ILE* 1.3 64.7 + - + +
1267B ARG* 3.3 4.7 + - + +
1268B CYS* 3.1 48.3 + - - -
1295B LEU* 4.4 14.8 - - + -
1296B GLN* 4.2 4.7 - - + -
1299B PHE* 3.7 41.6 - + + -
1307B LEU* 6.1 0.7 - - + -
1320B ALA* 3.2 40.2 - - + -
1321B MET* 4.2 1.8 - - - -
1324B PHE* 4.0 16.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261B ILE* 4.1 6.7 - - + -
1262B PRO* 2.9 26.5 + - + +
1264B PHE* 1.3 79.2 - - + +
1266B GLU* 1.3 64.5 + - - +
1268B CYS* 3.5 1.9 + - - +
1269B ILE* 3.0 34.9 + - + +
1321B MET* 3.9 24.9 - - + +
1324B PHE* 3.7 23.6 - - + -
1325B PHE* 3.6 35.7 - - + -
1371B VAL* 5.4 1.1 - - + -
1374B TYR* 3.8 26.0 - - + -
1375B VAL* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261B ILE* 4.1 28.3 - - + +
1262B PRO 3.1 6.6 + - - +
1263B ILE* 3.5 21.1 - - + +
1265B ILE* 1.3 73.0 - - - +
1267B ARG* 1.3 69.3 + - + +
1270B GLU* 2.9 46.1 + - - +
1374B TYR* 3.4 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263B ILE* 2.9 34.4 + - - +
1264B PHE* 3.3 10.1 + - + +
1266B GLU* 1.3 74.7 - - - +
1268B CYS* 1.3 59.4 + - - +
1270B GLU* 3.9 4.4 - - - +
1271B TYR* 3.0 31.7 + - - +
1299B PHE* 4.2 11.4 - - + -
1303B HIS 2.6 29.6 + - - -
1304B ASN* 3.7 19.8 - - - +
1305B LEU 3.2 26.9 + - - +
1306B ASP* 6.0 0.2 - - - +
1307B LEU* 3.9 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264B PHE* 3.1 53.7 + - - +
1265B ILE 4.1 0.2 - - - +
1267B ARG* 1.3 77.6 - - - +
1269B ILE* 1.3 62.6 + - - +
1271B TYR* 3.7 1.0 - - - +
1272B ILE* 2.8 37.0 + - + +
1295B LEU* 5.1 2.5 - - - -
1307B LEU* 4.2 6.3 - - - -
1317B VAL* 3.6 31.6 - - + -
1321B MET* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1265B ILE* 3.0 19.5 + - + +
1268B CYS* 1.3 77.3 - - - +
1270B GLU* 1.3 59.9 + - + +
1272B ILE* 3.3 5.3 + - - +
1273B GLU* 2.8 39.6 + - - +
1283B TYR* 4.7 0.2 - - - +
1321B MET* 3.5 36.8 - - + -
1374B TYR* 3.4 40.8 - - + +
1375B VAL* 4.3 4.3 - - - -
1378B HIS* 3.4 46.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B GLU* 2.9 46.4 + - - +
1267B ARG* 4.1 5.1 - - - +
1269B ILE* 1.3 77.2 - - + +
1271B TYR* 1.3 58.1 + - - +
1273B GLU* 3.6 9.2 + - - +
1274B ALA* 3.2 27.4 + - - +
1374B TYR* 3.9 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267B ARG 3.0 20.9 + - - +
1268B CYS 3.7 2.2 - - - +
1269B ILE 3.2 0.2 - - - -
1270B GLU* 1.3 74.1 - - - +
1272B ILE* 1.3 59.7 + - + +
1274B ALA* 3.2 5.3 + - + +
1275B THR* 2.8 60.3 + - - -
1307B LEU* 3.7 43.0 + - + -
1308B ALA* 3.9 12.8 + - + -
1311B ASP* 5.4 1.0 - - - -
1312B PHE 3.4 20.7 + - - -
1314B VAL* 4.8 8.7 + - + -
1317B VAL* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268B CYS* 2.8 25.1 + - + +
1269B ILE* 3.8 3.8 - - - +
1271B TYR* 1.3 77.3 - - + +
1273B GLU* 1.3 60.7 + - - +
1276B GLY* 2.7 30.2 + - - +
1277B LEU* 3.4 6.9 + - + +
1282B ILE* 3.5 24.9 - - + -
1283B TYR* 3.5 24.5 - - + +
1314B VAL* 4.4 11.7 - - + +
1317B VAL* 3.8 18.6 - - + +
1318B ALA* 3.5 35.4 - - + +
1321B MET* 4.6 2.5 - - + -
1378B HIS* 4.0 11.2 - - + -
1382B VAL* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269B ILE* 2.8 27.7 + - - +
1270B GLU* 3.9 9.0 - - - +
1272B ILE* 1.3 77.6 - - - +
1274B ALA* 1.3 59.8 + - - +
1275B THR 3.8 0.2 + - - -
1277B LEU* 3.5 30.0 + - + +
1378B HIS* 2.8 40.1 + - + +
1381B LYS* 3.2 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270B GLU 3.2 17.8 + - - +
1271B TYR* 3.2 6.7 + - + +
1273B GLU* 1.3 77.9 - - - +
1275B THR* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271B TYR* 2.8 45.8 + - - -
1272B ILE* 5.0 0.4 - - - -
1274B ALA* 1.3 80.9 - - - +
1276B GLY* 1.3 56.5 + - - +
1277B LEU 3.9 1.3 - - - -
1278B SER 5.4 0.5 + - - -
1279B THR* 4.2 5.5 - - - +
1314B VAL* 4.4 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272B ILE 2.7 19.7 + - - -
1275B THR* 1.3 75.3 - - - +
1277B LEU* 1.3 60.0 + - - +
1278B SER 3.1 7.2 + - - -
1279B THR* 3.2 28.5 + - - +
1282B ILE* 3.3 19.9 - - - +
1314B VAL* 3.4 14.3 - - - +
----------------------------------------------------------
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