Contacts of the helix formed by residues 1308 - 1316 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276A ALA 4.0 11.0 - - - +
1277A ASN* 5.7 0.4 - - + -
1304A PHE* 3.8 32.8 - - + -
1305A GLY 3.8 2.1 + - - +
1307A ASP* 1.3 91.5 - - - +
1309A GLY* 1.3 68.1 + - - +
1310A ALA 3.2 0.7 - - - -
1311A GLU* 3.4 1.4 + - - +
1312A LYS* 2.9 39.2 + - - +
1459A TYR* 3.8 22.4 - - - +
1489A MET 4.0 15.3 - - - +
1491A LYS* 4.0 22.2 - - + +
1492A THR 4.4 4.9 - - - +
1493A GLN* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276A ALA* 5.0 3.1 - - - +
1280A HIS 4.2 13.2 - - - +
1302A ALA* 3.8 15.7 - - - +
1303A GLY* 3.2 28.1 + - - -
1305A GLY 3.4 1.4 + - - -
1308A LEU* 1.3 78.7 - - - +
1310A ALA* 1.3 66.6 + - - +
1312A LYS* 4.0 0.2 - - - +
1313A PHE* 2.7 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A LEU* 4.2 15.9 - - + -
1063A THR* 4.1 13.0 + - + +
1302A ALA* 4.3 0.2 - - - +
1305A GLY 3.8 4.6 + - - -
1306A ALA* 2.7 41.5 - - + +
1308A LEU 3.2 0.4 - - - -
1309A GLY* 1.3 79.4 - - - +
1311A GLU* 1.3 62.2 + - - +
1313A PHE* 2.8 14.9 + - - +
1314A TYR* 3.2 23.2 + - + +
1370A ILE* 5.4 3.8 - - + -
1373A PHE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306A ALA 3.6 2.7 + - - +
1307A ASP* 3.4 25.6 - - - +
1308A LEU 3.5 1.8 - - - +
1310A ALA* 1.3 81.2 - - - +
1312A LYS* 1.3 74.9 + - + +
1314A TYR* 3.0 12.0 + - - +
1315A ASP* 2.4 70.9 + - - +
1316A VAL* 5.7 0.2 - - - +
1373A PHE* 4.0 9.7 - - + -
1440A LEU* 3.8 16.8 - - - +
1441A TYR* 3.9 5.7 - - - -
1454A ILE* 4.0 23.7 - - + +
1458A ILE* 4.6 5.9 - - + +
1459A TYR* 5.3 0.7 - - - +
1487A VAL 4.5 5.7 - - - +
1489A MET* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276A ALA 3.3 22.2 + - - +
1277A ASN* 3.5 7.7 - - - +
1279A ALA 3.8 11.0 - - - +
1280A HIS* 3.8 24.2 - - + +
1308A LEU* 2.9 33.9 + - - +
1311A GLU* 1.3 87.3 - - + +
1313A PHE* 1.3 57.0 + - - +
1315A ASP 4.4 0.7 - - - +
1316A VAL* 2.9 42.3 + - + +
1317A LYS 3.4 1.2 + - - -
1487A VAL 5.5 1.8 - - - +
1488A VAL* 3.6 28.1 - - + +
1489A MET* 2.4 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A LEU* 4.3 13.9 - - + -
1061A LEU* 3.6 47.3 - - + -
1282A CYS* 3.6 27.1 - - + -
1288A THR* 6.1 0.4 - - + -
1300A THR* 3.9 22.0 - - + -
1301A GLU 5.2 0.7 - - - -
1302A ALA* 4.5 0.9 - - + -
1309A GLY 2.7 17.7 + - - +
1310A ALA* 2.8 16.4 + - - +
1312A LYS* 1.3 71.4 - - - +
1314A TYR* 1.3 60.8 + + - +
1317A LYS* 3.2 32.7 - - + +
1318A CYS* 2.7 56.1 + - - -
1323A PHE* 5.5 0.7 - + - -
1325A PRO* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A LEU* 3.8 12.0 - - + +
1310A ALA* 3.3 30.1 - - + +
1311A GLU 3.0 1.8 + - - +
1313A PHE* 1.3 97.1 - + - +
1315A ASP* 1.3 66.8 + - - +
1316A VAL 3.2 1.6 - - - -
1318A CYS* 3.7 3.7 - - - +
1319A ARG* 3.2 26.0 + - - +
1325A PRO* 3.9 19.1 - - + -
1328A THR* 3.2 25.4 + - - +
1370A ILE* 4.2 7.2 - - + +
1373A PHE* 3.3 45.3 - + + -
1375A VAL* 3.8 11.8 - - + +
1437A PHE* 3.3 39.0 - + + -
1439A VAL* 4.3 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311A GLU* 2.4 55.1 + - - +
1312A LYS* 4.7 0.9 - - - -
1314A TYR* 1.3 73.7 - - - +
1316A VAL* 1.3 63.1 + - + +
1319A ARG* 2.7 37.9 + - - +
1373A PHE* 3.6 7.5 - - - -
1439A VAL* 3.6 3.2 - - - -
1440A LEU* 2.9 34.9 + - - +
1441A TYR* 3.3 21.3 - - + +
1486A PRO* 3.9 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211A LEU* 3.6 31.2 - - + -
1280A HIS* 4.1 12.3 - - + -
1311A GLU* 5.7 0.2 - - - +
1312A LYS* 2.9 26.2 + - + +
1315A ASP* 1.3 84.4 - - + +
1317A LYS* 1.3 61.3 + - - +
1318A CYS 3.5 0.4 - - - -
1319A ARG* 2.7 25.0 + - - +
1320A TYR* 2.8 31.8 + - + +
1441A TYR* 5.2 1.1 - - - +
1486A PRO* 4.3 15.7 - - + -
1487A VAL 5.4 2.0 - - - +
1488A VAL* 4.6 17.7 - - + -
1523A ARG* 5.1 5.6 - - + +
----------------------------------------------------------
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