Contacts of the helix formed by residues 1446 - 1457 (chain H) in PDB entry 6C3P
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 SER1446 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1445H CYS* 1.3 76.8 - - - +
1447H ASP* 1.3 66.8 + - - +
1448H SER* 3.3 17.3 + - - -
1449H THR* 2.5 38.7 + - - +
1450H LEU* 3.0 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1447 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436H ARG* 2.7 49.0 + - - -
1445H CYS 4.4 0.2 + - - -
1446H SER* 1.3 71.3 + - - +
1448H SER* 1.3 65.1 + - - +
1450H LEU* 3.4 14.6 - - + +
1451H TRP* 2.8 46.8 + - + +
1470H LEU* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1448 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1446H SER* 3.1 13.5 + - - -
1447H ASP* 1.3 78.6 - - - +
1449H THR* 1.3 60.5 + - - +
1451H TRP* 3.4 7.4 + - - +
1452H GLU* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1449 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1445H CYS* 4.2 8.1 - - - +
1446H SER* 2.5 38.7 + - - +
1448H SER* 1.3 78.2 - - - +
1450H LEU* 1.3 58.8 + - - +
1452H GLU* 3.2 20.1 + - - +
1453H ALA* 2.9 29.3 + - - +
1496H VAL* 5.7 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1450 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435H ILE 5.8 0.2 - - - -
1436H ARG* 3.8 22.2 - - - +
1439H LEU* 3.9 25.6 - - + +
1440H ASP* 3.2 37.2 - - - +
1445H CYS* 4.5 5.4 - - + -
1446H SER 3.0 16.8 + - - +
1447H ASP* 3.4 32.3 - - - +
1449H THR* 1.3 78.4 - - - +
1451H TRP* 1.3 58.4 + - - +
1453H ALA* 3.2 6.6 + - - +
1454H LEU* 2.9 33.4 + - - +
1470H LEU* 4.5 15.0 - - + -
1496H VAL* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1451 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447H ASP* 2.8 46.5 + - + +
1448H SER* 3.7 5.8 - - - +
1450H LEU* 1.3 71.8 - - - +
1452H GLU* 1.3 56.8 + - - +
1454H LEU* 3.5 13.1 - - + +
1455H GLU* 2.8 30.9 + - - +
1460H LYS* 3.3 55.2 - - + +
1463H VAL* 3.8 33.4 - - + -
1464H LYS* 4.8 8.1 - - + -
1469H GLY* 4.6 10.3 - - - -
1470H LEU* 3.3 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1452 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1448H SER* 2.9 16.1 + - - +
1449H THR* 3.3 26.3 + - - +
1450H LEU 3.1 0.2 - - - -
1451H TRP* 1.3 76.6 - - - +
1453H ALA* 1.3 57.9 + - - +
1455H GLU* 3.2 6.2 + - - +
1456H ILE* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1453 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439H LEU* 5.5 2.0 - - + -
1449H THR 2.9 16.9 + - - +
1450H LEU* 3.2 4.9 + - - +
1452H GLU* 1.3 75.8 - - - +
1454H LEU* 1.3 61.8 + - - +
1456H ILE* 3.3 12.2 - - - +
1457H ALA* 3.2 26.0 + - - +
1492H ALA* 3.9 26.8 - - + +
1495H PHE* 4.4 5.8 - - + +
1496H VAL* 4.2 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1454 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435H ILE* 4.7 14.1 - - + -
1439H LEU* 4.7 10.1 - - + -
1450H LEU 2.9 18.7 + - - +
1451H TRP* 3.5 22.4 - - + +
1453H ALA* 1.3 76.1 - - - +
1455H GLU* 1.3 54.5 + - - +
1457H ALA* 3.3 2.3 + - - -
1458H GLN 2.9 6.8 + - - -
1459H LEU* 2.5 52.2 + - + +
1460H LYS* 3.4 13.0 - - - +
1463H VAL* 4.1 21.5 - - + -
1470H LEU* 3.7 32.5 - - + -
1489H PHE* 5.3 7.9 - - + -
1492H ALA* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1455 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451H TRP 2.8 17.7 + - - +
1452H GLU* 3.2 6.5 + - - +
1454H LEU* 1.3 72.5 - - - +
1456H ILE* 1.3 59.9 + - + +
1457H ALA 3.0 4.0 - - - -
1458H GLN* 2.5 33.4 + - - +
1460H LYS* 3.2 27.5 - - + +
1461H LEU* 3.2 33.5 - - - +
1464H LYS* 4.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1456 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1452H GLU* 2.9 38.2 + - + +
1453H ALA* 3.3 17.7 - - - +
1455H GLU* 1.3 74.8 - - + +
1457H ALA* 1.3 56.4 + - - +
1458H GLN* 3.1 14.0 + - - +
1495H PHE* 3.4 38.7 - - + -
1519H LEU* 4.7 5.0 - - - +
1522H VAL* 3.4 32.0 - - + +
1523H VAL* 5.1 7.0 + - + +
1526H ALA* 4.6 17.0 - - + -
1527H PHE* 5.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1457 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453H ALA 3.2 19.2 + - - +
1454H LEU 3.8 0.2 - - - +
1455H GLU 3.0 1.2 - - - -
1456H ILE* 1.3 74.8 - - - +
1458H GLN* 1.3 75.6 + - - +
1459H LEU* 3.2 16.3 - - + +
1488H LEU* 2.9 30.6 - - + +
1492H ALA* 3.9 15.5 - - + +
1495H PHE* 4.2 15.7 - - + -
1519H LEU* 4.6 3.6 - - - -
----------------------------------------------------------
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