Contacts of the helix formed by residues 1433 - 1445 (chain A) in PDB entry 6J8H
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 MET1433 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342A LEU* 3.9 35.7 - - + +
1343A PHE* 4.1 28.0 - - + -
1346A LYS* 6.2 0.9 - - - +
1415A ALA* 4.3 12.3 - - + +
1416A VAL* 4.6 2.9 - - + -
1418A SER* 5.9 1.3 - - - +
1430A SER* 3.3 34.3 - - - +
1431A LEU 3.3 1.0 - - - -
1432A TYR* 1.3 74.9 - - - +
1434A TYR* 1.3 64.9 + - - +
1435A ILE 3.0 2.0 - - - -
1436A TYR* 2.9 24.9 + - - +
1437A PHE* 3.5 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A ARG* 4.8 11.1 + - - -
908A TRP* 4.5 13.5 - + - -
914A PHE* 4.1 12.1 - + + -
915A HIS* 5.0 4.0 - + - -
918A LEU* 4.0 30.1 - - + -
1412A MET* 2.6 46.4 - - + -
1413A TYR* 4.2 21.1 - - - -
1416A VAL* 3.7 29.9 - - + +
1428A GLU* 4.8 10.0 + - - -
1431A LEU* 3.4 33.1 + - + +
1433A MET* 1.3 78.6 - - - +
1435A ILE* 1.3 64.8 + - - +
1437A PHE* 2.9 20.3 + + - +
1438A VAL* 3.1 15.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A PHE* 3.7 30.3 - - + -
917A PHE* 5.7 3.6 - - + -
1432A TYR* 3.0 29.4 - - + +
1434A TYR* 1.3 78.9 - - - +
1436A TYR* 1.3 62.3 + - - +
1438A VAL* 3.2 11.8 + - + +
1439A VAL* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335A PHE* 2.5 54.4 + + + +
1338A MET* 4.3 15.0 - - + -
1339A GLY* 3.4 18.3 - - - -
1342A LEU* 4.5 13.5 - - + -
1343A PHE* 3.9 31.4 - + + -
1389A PHE* 4.4 6.0 - + - -
1399A LEU* 4.2 12.1 - - + +
1432A TYR 4.3 0.4 + - - -
1433A MET* 2.9 16.9 + - - +
1435A ILE* 1.3 77.7 - - - +
1437A PHE* 1.3 83.9 + + - +
1439A VAL* 3.3 5.8 + - + +
1440A PHE* 3.0 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343A PHE* 4.3 7.9 - + - -
1389A PHE* 4.6 8.1 - + - -
1399A LEU* 6.0 0.9 - - + -
1402A VAL* 4.1 29.6 - - + -
1408A TRP* 6.0 0.2 - - + -
1411A ILE* 4.3 20.2 - - + -
1412A MET* 4.0 41.5 - - + -
1415A ALA* 3.3 34.8 - - + -
1416A VAL* 5.4 0.4 - - + -
1433A MET 3.5 17.5 - - - -
1434A TYR* 2.9 13.2 + - - +
1436A TYR* 1.3 97.4 - + - +
1438A VAL* 1.3 64.1 + - + +
1440A PHE* 3.3 5.8 + + + +
1441A ILE* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A PHE* 6.2 0.2 - - + -
917A PHE* 4.9 14.6 - - + -
918A LEU* 4.3 22.2 - - + -
921A PHE* 4.1 39.7 - - + -
1412A MET* 6.3 1.1 - - + -
1434A TYR* 3.1 18.6 + - + +
1435A ILE* 3.6 15.0 - - + +
1437A PHE* 1.3 75.7 - - + +
1439A VAL* 1.3 66.4 + - + +
1441A ILE* 3.4 2.9 + - - +
1442A ILE* 3.2 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335A PHE* 4.3 14.8 - - + -
1435A ILE* 2.9 33.8 + - + +
1436A TYR* 3.7 6.5 - - + +
1438A VAL* 1.3 79.6 - - + +
1440A PHE* 1.3 62.4 + - - +
1442A ILE* 3.4 5.4 + - + +
1443A PHE* 3.0 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A TRP* 4.1 26.5 - + - -
1335A PHE* 3.5 45.5 - + + -
1399A LEU* 3.6 55.0 - - + -
1402A VAL* 3.8 22.2 - - + -
1403A ALA* 4.1 9.9 - - + -
1436A TYR* 3.0 22.3 + - + +
1437A PHE* 3.8 7.0 - + + +
1438A VAL 3.3 0.2 - - - -
1439A VAL* 1.3 74.1 - - - +
1441A ILE* 1.3 63.6 + - - +
1444A GLY* 2.3 53.9 + - - -
1445A SER 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921A PHE* 4.0 26.2 - - + -
925A CYS* 4.9 2.0 - - - -
1402A VAL* 3.9 18.4 - - + +
1405A PHE* 3.6 30.3 - - + -
1408A TRP* 3.1 39.7 - - + -
1437A PHE* 3.0 20.2 + - + +
1438A VAL* 3.7 4.7 - - + +
1440A PHE* 1.3 78.7 - - + +
1442A ILE* 1.3 60.0 + - - +
1445A SER* 3.1 12.2 + - - +
1446A PHE* 2.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921A PHE* 4.4 18.6 - - + -
1438A VAL* 3.2 29.2 + - + +
1439A VAL* 3.8 6.1 - - + +
1441A ILE* 1.3 78.6 - - - +
1443A PHE* 1.3 67.2 + - + +
1446A PHE* 3.1 31.3 - - + +
1447A PHE* 3.2 29.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A ILE* 3.8 35.9 - - + -
1331A PHE* 4.0 16.4 - + + -
1335A PHE* 3.9 18.8 - + + -
1439A VAL* 3.0 42.7 + - + +
1442A ILE* 1.3 89.1 - - + +
1444A GLY* 1.3 65.7 + - - +
1447A PHE* 3.5 42.0 - + - +
1448A THR* 3.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331A PHE* 5.4 0.7 - - - -
1332A TRP* 3.4 20.8 + - - -
1335A PHE* 4.4 2.9 - - - -
1440A PHE* 2.3 47.4 + - - +
1443A PHE* 1.3 72.2 - - - +
1445A SER* 1.3 52.4 + - - -
1448A THR* 2.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A TRP* 5.6 0.2 - - - -
1403A ALA* 3.9 33.4 + - - -
1405A PHE* 4.1 13.7 - - - -
1440A PHE* 3.4 1.6 + - - -
1441A ILE* 3.1 22.1 + - - +
1444A GLY* 1.3 77.6 - - - +
1446A PHE* 1.3 65.5 + - - +
1447A PHE 3.5 0.4 - - - -
1448A THR* 3.9 0.7 - - - -
1449A LEU* 2.9 34.7 + - - +
----------------------------------------------------------
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