Contacts of the helix formed by residues 1288 - 1302 (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 ASN1288 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1287B GLY* 1.3 68.0 - - - -
1289B LYS* 1.3 66.4 + - - +
1290B SER* 2.9 20.4 + - - -
1291B GLU* 2.9 54.4 + - + +
1292B MET* 3.1 16.3 + - - +
1316B THR* 4.4 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1287B GLY 3.1 7.9 + - - +
1288B ASN* 1.3 71.6 + - - +
1290B SER* 1.3 62.1 + - - +
1292B MET* 3.6 10.8 + - + +
1293B GLU* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288B ASN* 2.9 14.2 + - - -
1289B LYS* 1.3 77.6 - - - +
1291B GLU* 1.3 62.9 + - - +
1293B GLU* 3.4 5.9 + - - +
1294B SER* 2.9 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288B ASN* 2.9 35.0 + - + +
1290B SER* 1.3 81.4 - - - +
1292B MET* 1.3 57.1 + - - +
1294B SER* 3.4 9.2 + - - -
1295B LEU* 3.0 27.2 + - - +
1312B PHE* 3.6 24.4 - - + -
1313B THR* 5.5 3.1 - - - +
1316B THR* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286B SER* 4.5 4.7 - - - +
1287B GLY* 3.3 47.8 - - - +
1288B ASN 3.1 10.0 + - - +
1289B LYS* 3.9 8.7 - - - +
1291B GLU* 1.3 74.3 - - - +
1293B GLU* 1.3 57.4 + - - +
1294B SER 3.0 1.1 - - - -
1295B LEU* 3.0 6.3 + - - +
1296B GLN* 2.7 42.1 + - - +
1315B ASN 4.6 1.6 - - - +
1316B THR* 3.6 22.2 - - + +
1319B GLY* 3.5 35.4 - - - +
1320B ALA* 4.0 10.6 - - + +
1323B SER* 5.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242B TRP* 4.3 14.2 - - - +
1289B LYS 3.2 16.2 + - - +
1290B SER* 3.7 6.3 - - - +
1292B MET* 1.3 78.2 - - - +
1294B SER* 1.3 57.4 + - - +
1296B GLN* 3.7 11.2 + - - +
1297B ARG* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1290B SER 2.9 19.1 + - - -
1291B GLU* 3.4 15.8 + - - -
1293B GLU* 1.3 75.4 - - - +
1295B LEU* 1.3 53.8 + - - +
1297B ARG* 3.1 7.7 + - - +
1298B GLN* 2.8 60.0 + - - +
1312B PHE* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264B PHE* 4.4 14.8 - - + -
1291B GLU 3.0 16.1 + - - +
1292B MET* 3.5 7.9 - - - +
1294B SER* 1.3 74.8 - - - +
1296B GLN* 1.3 57.4 + - - +
1298B GLN* 3.9 1.9 - - - +
1299B PHE* 2.9 26.7 + - - +
1305B LEU* 3.5 25.6 - - + -
1307B LEU* 3.5 16.6 - - + -
1312B PHE* 3.5 26.7 - - + -
1316B THR* 4.4 2.7 - - + +
1317B VAL* 3.9 34.5 - - + +
1320B ALA* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242B TRP* 3.8 18.7 - - + -
1247B PHE* 3.3 38.5 - - + -
1264B PHE* 4.2 8.7 - - + -
1292B MET* 2.7 25.0 + - - +
1293B GLU* 3.7 10.6 - - - +
1295B LEU* 1.3 74.0 - - - +
1297B ARG* 1.3 57.7 + - - +
1299B PHE* 3.2 1.1 + - - +
1300B ASP* 2.8 29.5 + - - +
1320B ALA* 3.6 12.5 + - + -
1323B SER* 3.3 26.2 + - - -
1324B PHE 3.8 1.6 - - - +
1327B GLU* 3.2 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242B TRP* 3.9 54.9 - - + +
1293B GLU* 2.8 26.5 + - - +
1294B SER* 3.5 6.7 - - - +
1296B GLN* 1.3 73.4 - - - +
1298B GLN* 1.3 66.5 + - + +
1300B ASP* 3.1 10.4 + - - +
1301B GLN* 3.1 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1294B SER* 2.8 42.1 + - - +
1295B LEU* 3.9 4.3 - - - +
1297B ARG* 1.3 73.0 - - + +
1299B PHE* 1.3 61.9 + - - +
1301B GLN* 3.3 22.1 + - - +
1302B ASP* 3.4 13.9 + - - +
1305B LEU* 4.3 25.8 - - + +
1310B LYS* 5.5 3.7 - - - +
1312B PHE* 3.8 19.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246B TYR* 3.7 27.8 - + - -
1247B PHE* 4.1 11.2 - + - -
1263B ILE* 3.9 13.7 - - + -
1264B PHE* 3.7 52.3 - + + -
1267B ARG* 4.2 10.5 - - + -
1295B LEU 2.9 18.5 + - - +
1296B GLN* 3.6 3.6 - - - +
1298B GLN* 1.3 74.4 - - - +
1300B ASP* 1.3 68.9 + - - +
1302B ASP 3.0 19.2 - - - +
1303B HIS* 3.1 59.3 + + - -
1305B LEU* 4.0 21.5 - - + +
1307B LEU* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242B TRP* 3.1 11.8 - - + -
1243B GLU 4.4 1.7 - - - +
1244B SER* 3.1 33.3 - - - -
1245B ASN* 4.2 5.5 + - - +
1246B TYR* 3.8 22.0 + - - +
1247B PHE* 4.5 5.6 - - + -
1296B GLN 2.8 13.1 + - - +
1297B ARG* 3.1 16.6 + - - +
1299B PHE* 1.3 81.2 - - - +
1301B GLN* 1.3 60.9 + - + +
1303B HIS* 3.7 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1297B ARG* 3.1 21.1 + - - +
1298B GLN* 3.6 16.5 - - - +
1299B PHE 3.0 1.0 - - - -
1300B ASP* 1.3 80.4 - - + +
1302B ASP* 1.3 63.8 + - + +
1303B HIS* 5.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298B GLN 3.4 7.8 + - - +
1299B PHE 3.0 11.5 + - - +
1301B GLN* 1.3 83.4 - - + +
1303B HIS* 1.3 61.8 + - - +
1304B ASN* 3.2 31.2 + - - +
1305B LEU* 3.3 26.9 + - - +
----------------------------------------------------------
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