Contacts of the helix formed by residues 1412 - 1421 (chain A) in PDB entry 4Z4Q
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 THR1412 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373A HIS* 2.8 39.0 + - + +
1406A LYS* 4.4 0.9 - - - -
1410A ASP 5.0 2.9 - - - +
1411A PHE* 1.3 76.1 - - - +
1413A GLU* 1.3 54.6 + - - +
1414A GLU* 3.6 11.3 - - - +
1415A GLN* 2.9 25.9 + - - +
1416A ALA* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402A LYS* 2.8 33.0 - - - +
1406A LYS* 2.9 42.3 + - - +
1412A THR* 1.3 71.7 - - - +
1414A GLU* 1.3 73.6 + - - +
1416A ALA* 2.9 3.5 + - - +
1417A GLU* 2.7 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370A LYS* 5.9 6.7 - - + +
1373A HIS* 4.0 15.7 - - + +
1374A ILE* 4.3 14.0 - - + +
1412A THR* 3.6 19.3 + - - +
1413A GLU* 1.3 91.8 + - - +
1415A GLN* 1.3 59.3 + - - +
1417A GLU* 3.6 6.4 + - - +
1418A ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373A HIS* 3.0 47.1 + - + +
1374A ILE* 4.5 5.2 - - - +
1376A GLU* 4.3 5.5 + - - +
1377A GLY* 3.4 24.2 - - - +
1380A ARG* 5.5 0.3 + - - -
1410A ASP 4.5 1.7 - - - +
1411A PHE* 3.7 20.8 - - + -
1412A THR* 2.9 45.4 + - - +
1414A GLU* 1.3 76.8 - - - +
1416A ALA* 1.3 60.5 + - - +
1418A ALA* 3.2 7.2 + - - +
1419A ILE* 2.8 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402A LYS* 3.9 38.1 - - + +
1405A LEU* 4.2 16.6 - - + +
1406A LYS* 4.6 3.6 - - + -
1411A PHE* 4.5 2.9 - - + +
1412A THR 2.7 18.1 + - - +
1413A GLU* 3.3 10.8 - - - +
1415A GLN* 1.3 71.1 - - - +
1417A GLU* 1.3 63.7 + - - +
1419A ILE* 3.1 5.7 + - - +
1420A VAL* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1398A LYS* 3.0 29.4 + - - -
1402A LYS* 3.2 35.7 + - + +
1413A GLU* 2.7 24.7 + - + +
1414A GLU* 3.7 8.1 - - - +
1416A ALA* 1.3 74.7 - - - +
1418A ALA* 1.3 66.5 + - - +
1420A VAL* 3.0 7.0 + - - -
1421A THR* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374A ILE* 3.9 33.7 - - + -
1378A LEU* 5.1 6.3 - - + -
1414A GLU 3.1 11.5 + - - +
1415A GLN 3.5 7.4 - - - +
1417A GLU* 1.3 82.2 - - - +
1419A ILE* 1.3 64.7 + - - +
1421A THR* 3.2 15.9 + - - -
1422A LEU* 3.4 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377A GLY* 4.9 1.6 - - - +
1378A LEU* 4.5 12.3 - - + -
1381A VAL* 3.4 31.9 - - + -
1388A VAL* 4.3 18.6 - - + -
1392A ILE* 4.6 7.0 - - + +
1405A LEU* 3.9 21.5 - - + -
1411A PHE* 3.8 34.3 - - + -
1415A GLN* 2.8 23.0 + - + +
1416A ALA 3.4 6.3 - - - +
1418A ALA* 1.3 74.5 - - - +
1420A VAL* 1.3 64.0 + - - +
1422A LEU* 3.3 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392A ILE* 4.0 23.2 - - + +
1398A LYS* 3.9 28.2 - - + +
1401A ALA* 3.8 28.3 - - + -
1402A LYS* 4.3 9.4 - - + +
1405A LEU* 4.1 11.2 - - + -
1416A ALA 2.9 12.8 + - - +
1417A GLU* 3.0 6.9 + - - +
1419A ILE* 1.3 77.7 - - - +
1421A THR* 1.3 68.7 + - + +
1422A LEU 3.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1398A LYS* 3.8 16.4 - - + +
1417A GLU* 3.0 39.7 + - - +
1418A ALA* 3.2 10.7 + - - -
1419A ILE 3.2 0.2 - - - -
1420A VAL* 1.3 84.9 - - + +
1422A LEU* 1.3 62.3 + - - +
1423A GLN* 3.7 5.9 + - - +
----------------------------------------------------------
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