Contacts of the helix formed by residues 1308 - 1316 (chain B) in PDB entry 1FP7
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 LEU1308 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276B ALA 4.1 11.7 - - - +
1277B ASN* 5.9 0.2 - - - -
1304B PHE* 4.2 15.0 - - + -
1305B GLY 2.9 4.9 + - - +
1306B ALA 3.2 0.8 - - - -
1307B ASP* 1.3 96.0 - - - +
1309B GLY* 1.3 58.5 + - - +
1310B ALA 3.1 0.7 - - - -
1311B GLU* 3.8 2.9 - - - -
1312B LYS* 2.6 46.9 + - - +
1459B TYR* 3.1 27.4 - - + +
1489B MET* 3.7 26.5 - - + +
1491B LYS* 3.9 14.1 - - + +
1492B THR 3.6 22.2 - - - +
1493B GLN* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276B ALA* 4.9 1.9 + - - -
1280B HIS 3.8 11.5 - - - +
1302B ALA* 3.6 7.5 - - - +
1303B GLY* 2.8 39.3 + - - -
1305B GLY 3.7 0.6 + - - -
1308B LEU* 1.3 76.9 - - - +
1310B ALA* 1.3 51.5 + - - +
1312B LYS* 3.5 1.6 - - - +
1313B PHE* 2.4 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B LEU* 4.7 4.3 - - + -
1063B THR* 3.6 16.4 + - + +
1302B ALA* 4.0 4.6 - - - +
1303B GLY 4.0 2.6 + - - -
1306B ALA* 2.9 38.4 - - + +
1308B LEU 3.1 0.6 - - - +
1309B GLY* 1.3 73.3 - - - +
1311B GLU* 1.3 62.7 + - - +
1312B LYS 2.7 2.3 + - - -
1313B PHE* 2.9 17.2 + - - +
1314B TYR* 2.9 32.7 + - + +
1328B THR* 6.1 0.7 - - + -
1370B ILE* 6.1 2.2 - - + -
1373B PHE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306B ALA 3.3 3.5 + - - +
1307B ASP 3.2 27.8 - - - +
1308B LEU* 3.3 7.3 + - - +
1310B ALA* 1.3 76.9 - - - +
1312B LYS* 1.3 77.2 + - + +
1314B TYR* 3.8 2.7 - - - +
1315B ASP* 2.5 51.7 + - - +
1373B PHE* 3.7 25.1 - - + -
1440B LEU* 5.6 0.7 - - - +
1454B ILE* 4.0 32.3 - - + +
1458B ILE* 4.1 15.1 - - + +
1459B TYR* 4.4 6.3 + - - +
1487B VAL 4.1 8.0 - - - +
1489B MET 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276B ALA 2.8 23.0 + - - +
1277B ASN* 2.8 19.0 + - - +
1279B ALA 4.0 0.4 - - - +
1280B HIS* 3.8 18.4 - - + -
1308B LEU* 2.6 41.8 + - - +
1309B GLY 3.5 1.8 - - - +
1310B ALA 2.7 2.2 + - - -
1311B GLU* 1.3 83.6 - - - +
1313B PHE* 1.3 58.6 + - - +
1314B TYR 2.8 1.9 + - - -
1315B ASP* 3.0 2.0 + - - +
1316B VAL* 2.5 53.0 + - + +
1487B VAL 5.3 0.7 - - - +
1488B VAL* 3.2 25.1 - - + +
1489B MET* 2.6 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B LEU* 4.2 13.9 - - + -
1061B LEU* 3.3 52.9 - - + -
1282B CYS* 3.5 33.1 - - - -
1300B THR* 3.6 19.3 - - + -
1301B GLU 5.1 0.7 - - - -
1302B ALA* 3.9 7.4 - - + -
1309B GLY 2.4 32.6 + - - +
1310B ALA 2.9 4.4 + - - +
1312B LYS* 1.3 65.4 - - - +
1314B TYR* 1.3 65.6 + + - +
1317B LYS* 2.9 45.6 + - + +
1318B CYS* 3.1 31.1 + - - -
1323B PHE* 5.8 0.9 - + - -
1325B PRO* 3.6 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B LEU* 4.3 6.0 - - + +
1310B ALA* 2.9 38.6 + - + +
1311B GLU 3.8 1.3 - - - +
1312B LYS 2.8 0.6 + - - -
1313B PHE* 1.3 89.8 - + - +
1315B ASP* 1.3 64.5 + - - +
1316B VAL 3.0 5.9 + - - -
1318B CYS* 3.3 5.2 - - - +
1319B ARG* 3.2 19.4 + - - -
1325B PRO* 4.1 17.5 - - + -
1328B THR* 3.0 35.1 + - - +
1370B ILE* 4.6 8.7 - - + +
1373B PHE* 3.7 52.7 - + + -
1375B VAL* 3.8 13.2 - - + +
1437B PHE* 3.3 38.2 - + + -
1439B VAL* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311B GLU* 2.5 37.4 + - - +
1312B LYS* 3.0 3.2 + - - +
1314B TYR* 1.3 78.9 - - - +
1316B VAL* 1.3 61.0 + - + +
1319B ARG* 3.0 37.0 + - - +
1320B TYR* 5.5 0.2 - - - -
1373B PHE* 3.7 9.4 - - - -
1439B VAL* 3.7 8.2 - - - +
1440B LEU* 3.6 22.9 + - - +
1441B TYR* 2.9 42.5 - - + +
1486B PRO* 4.6 5.2 - - - +
1487B VAL 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211B LEU* 3.5 20.0 - - + -
1280B HIS* 3.5 37.7 - - + -
1312B LYS* 2.5 45.1 + - + +
1314B TYR 3.0 0.2 + - - -
1315B ASP* 1.3 75.0 - - + +
1317B LYS* 1.3 73.8 + - - +
1319B ARG* 3.5 3.1 + - - +
1320B TYR* 3.4 29.1 + - + -
1441B TYR* 5.8 0.7 - - - +
1486B PRO* 5.7 8.7 - - + -
1487B VAL 5.8 2.2 - - - +
1488B VAL* 4.9 12.1 - - + -
1523B ARG* 5.7 7.2 - - + +
----------------------------------------------------------
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