Contacts of the helix formed by residues 1361 - 1374 (chain A) in PDB entry 1NF1
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 LEU1361 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288A CYS 5.4 0.4 - - - +
1289A PHE* 3.6 40.4 - - + +
1292A TYR* 4.4 14.8 - - + +
1293A GLY* 4.4 13.2 - - - -
1296A TYR* 5.7 0.2 - - + -
1357A PHE* 3.8 26.7 - - + -
1358A PRO* 3.0 25.7 + - + +
1360A GLN* 1.3 77.0 - - - +
1362A ARG* 1.3 57.2 + - - +
1363A SER 3.0 4.7 - - - -
1364A VAL* 2.9 13.6 + - + -
1365A CYS* 2.9 35.5 + - - -
1388A MET* 6.3 0.2 - - - -
1392A PHE* 4.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354A SER* 2.5 37.6 + - - -
1355A SER* 4.6 2.8 - - - +
1357A PHE* 3.2 33.3 + - + -
1358A PRO 3.3 6.3 + - - +
1359A PRO* 3.8 17.7 - - + +
1360A GLN 3.6 0.2 - - - -
1361A LEU* 1.3 77.4 - - - +
1363A SER* 1.3 56.7 - - - +
1365A CYS 4.0 0.2 - - - -
1366A HIS* 2.9 28.7 + - - +
1460A ASP* 2.8 33.9 + - - +
1461A ILE* 3.6 22.2 - - - +
1462A ALA* 4.6 1.7 - - - -
1463A SER 4.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254A TYR* 2.7 40.0 + - - -
1359A PRO 3.1 12.8 + - - -
1360A GLN* 2.9 12.8 + - - -
1362A ARG* 1.3 74.8 - - - +
1364A VAL* 1.3 58.8 + - - +
1365A CYS 3.3 0.2 - - - -
1366A HIS* 3.8 6.7 - - - +
1367A CYS* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254A TYR* 3.9 18.2 - - + +
1257A LEU* 4.4 13.2 - - + -
1261A PHE* 4.5 9.2 - - + -
1285A MET* 5.5 5.6 - - + -
1288A CYS* 4.2 20.6 - - + -
1289A PHE* 4.8 8.7 - - + -
1292A TYR* 4.0 20.9 - - + -
1360A GLN 3.4 17.9 - - - +
1361A LEU* 2.9 21.2 + - + +
1363A SER* 1.3 79.3 + - - +
1365A CYS* 1.3 55.4 + - - +
1367A CYS* 3.4 6.2 - - - +
1368A LEU* 3.2 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1289A PHE* 4.4 13.2 - - - -
1357A PHE* 4.3 10.1 - - - -
1361A LEU* 2.9 34.3 + - - +
1364A VAL* 1.3 74.3 - - - +
1366A HIS* 1.3 61.2 + - - +
1367A CYS 3.1 1.3 - - - -
1368A LEU* 3.9 6.8 - - - +
1369A TYR* 2.9 29.6 + - - +
1384A VAL* 4.1 26.7 - - + +
1388A MET* 5.3 2.9 - - - -
1461A ILE* 3.6 27.8 - - - +
1462A ALA* 4.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1362A ARG 2.9 22.4 + - - +
1363A SER* 3.8 9.2 - - - +
1365A CYS* 1.3 75.1 - - - +
1367A CYS* 1.3 69.5 + - - +
1369A TYR* 3.1 20.1 - + - +
1370A GLN* 2.7 44.5 + - + +
1462A ALA* 3.0 30.9 + - - +
1463A SER* 4.3 8.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254A TYR* 4.4 20.4 - - + -
1257A LEU* 4.1 25.8 - - + -
1258A TRP* 4.3 26.4 - - - -
1261A PHE* 4.7 3.1 - - - -
1363A SER 2.8 19.6 + - - +
1364A VAL* 3.4 8.3 - - - +
1365A CYS 3.1 0.2 - - - -
1366A HIS* 1.3 84.0 - - - +
1368A LEU* 1.3 65.8 + - - +
1370A GLN* 3.1 8.9 + - - +
1371A VAL* 3.1 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261A PHE* 3.6 24.6 - - + -
1275A PHE* 3.6 37.2 - - + -
1285A MET* 3.4 25.6 - - + -
1289A PHE* 5.3 3.1 - - + -
1364A VAL 3.2 12.6 + - - +
1365A CYS* 3.9 5.2 - - - +
1367A CYS* 1.3 77.8 - - - +
1369A TYR* 1.3 64.5 + - - +
1371A VAL* 3.0 5.0 + - + +
1372A VAL* 3.0 38.1 + - + +
1383A ALA* 4.9 2.0 - - + +
1384A VAL* 3.9 35.0 - - + +
1387A ALA* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365A CYS 2.9 20.8 + - - +
1366A HIS* 3.1 13.2 - + - +
1368A LEU* 1.3 76.7 - - - +
1370A GLN* 1.3 74.4 + - + +
1372A VAL* 3.5 6.1 + - - +
1373A SER* 2.9 41.7 + - - -
1379A ASN 5.3 0.7 + - - -
1380A SER* 4.4 6.2 + - - -
1381A ILE* 3.9 40.0 - - + +
1384A VAL* 4.1 11.2 - - + +
1459A LEU* 4.1 17.3 - - + +
1462A ALA* 4.1 26.0 - - + -
1463A SER* 5.0 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258A TRP* 4.1 13.9 - - + -
1366A HIS* 2.7 42.2 + - + +
1367A CYS* 3.1 6.3 + - - +
1369A TYR* 1.3 91.7 - - + +
1371A VAL* 1.3 59.7 + - - +
1373A SER* 3.8 8.2 - - - -
1374A GLN* 2.8 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258A TRP* 3.5 27.1 - - + +
1261A PHE* 3.9 19.1 - - + +
1262A SER* 3.7 42.0 - - - +
1265A VAL* 4.4 13.6 - - + +
1367A CYS* 3.1 23.3 - - - +
1368A LEU* 3.0 8.5 + - + +
1370A GLN* 1.3 76.0 - - - +
1372A VAL* 1.3 67.9 + - + +
1374A GLN* 2.9 27.3 + - + +
1375A ARG 4.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1265A VAL* 4.7 12.8 - - + -
1274A LEU* 4.6 5.4 - - + -
1275A PHE* 4.9 6.7 - - + -
1368A LEU* 3.0 37.6 + - + +
1369A TYR* 3.6 7.0 - - - +
1371A VAL* 1.3 74.4 - - + +
1373A SER* 1.3 53.0 + - - +
1375A ARG* 2.9 10.7 + - - +
1376A PHE* 2.8 45.1 + - + +
1380A SER* 3.7 33.7 - - - +
1383A ALA* 4.2 18.6 - - + -
1384A VAL* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1369A TYR* 2.9 33.0 + - - -
1370A GLN* 3.9 11.4 - - - -
1371A VAL 3.2 0.2 - - - -
1372A VAL* 1.3 70.6 - - - +
1374A GLN* 1.3 64.8 + - - +
1375A ARG 3.0 6.9 + - - -
1376A PHE 4.0 10.3 - - - -
1377A PRO* 3.6 22.0 - - - +
1380A SER* 3.3 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258A TRP* 4.1 21.5 - - + -
1262A SER* 6.0 0.4 - - - +
1265A VAL* 5.9 1.3 - - + -
1370A GLN* 2.8 34.4 + - - +
1371A VAL* 2.9 23.0 + - + +
1373A SER* 1.3 80.9 + - - +
1375A ARG* 1.3 58.0 + - + +
----------------------------------------------------------
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