Contacts of the helix formed by residues 1457 - 1472 (chain A) in PDB entry 5DKD
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 ASN1457 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1458A LEU* 1.3 67.1 + - - +
1459A THR* 3.8 6.7 - - - +
1460A LYS* 3.7 35.5 - - - +
1461A LYS* 3.1 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457A ASN* 1.3 81.1 - - - +
1459A THR* 1.3 66.7 + - - +
1460A LYS 3.2 0.3 + - - -
1461A LYS* 3.2 7.2 + - + +
1462A MET* 2.9 47.6 + - + +
1519A TYR 4.7 2.5 - - - +
1520A ARG 3.5 26.2 - - - +
1521A SER* 4.2 5.2 - - - -
1522A LEU* 4.5 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457A ASN 3.3 6.8 - - - +
1458A LEU* 1.3 78.3 - - - +
1460A LYS* 1.3 56.3 + - - +
1462A MET* 3.3 10.0 + - - +
1463A LYS* 2.9 52.8 + - - +
1514A ILE* 3.7 24.1 + - + +
1515A ARG* 4.8 3.8 - - - +
1517A HIS* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457A ASN* 3.7 24.4 - - - +
1458A LEU 3.2 0.6 - - - -
1459A THR* 1.3 76.6 - - - +
1461A LYS* 1.3 68.6 + - + +
1463A LYS* 3.4 25.3 - - + +
1464A LYS* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457A ASN* 3.1 25.7 + - - +
1458A LEU* 3.2 10.4 + - + +
1460A LYS* 1.3 84.6 - - + +
1462A MET* 1.3 63.6 + - - +
1464A LYS* 3.6 24.5 - - + +
1465A ILE* 3.2 31.1 + - + +
1522A LEU* 5.0 11.2 - - + -
1564A ILE* 3.9 35.9 + - + +
1565A GLU* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1458A LEU* 2.9 37.5 + - + +
1459A THR* 3.5 11.7 - - - +
1461A LYS* 1.3 75.6 - - - +
1463A LYS* 1.3 62.7 + - - +
1465A ILE* 3.4 3.7 + - - +
1466A VAL* 3.0 26.5 + - - +
1514A ILE* 3.9 17.7 - - + +
1519A TYR* 3.4 40.4 - - + +
1521A SER 3.2 35.7 - - - +
1522A LEU* 3.6 18.1 - - + +
1525A LEU* 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459A THR* 2.9 40.5 + - - +
1460A LYS* 3.4 25.2 - - + +
1462A MET* 1.3 77.0 - - - +
1464A LYS* 1.3 58.3 + - + +
1466A VAL* 4.1 1.2 - - - +
1467A ASP* 2.9 43.8 + - - +
1514A ILE* 4.0 18.1 - - + +
1515A ARG* 5.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1460A LYS* 3.1 26.2 + - + +
1461A LYS* 3.6 30.9 - - + +
1462A MET 3.3 0.6 - - - -
1463A LYS* 1.3 81.1 - - + +
1465A ILE* 1.3 61.9 - - - +
1467A ASP* 3.9 7.9 - - - +
1468A ALA* 3.1 24.8 + - - +
1560A VAL* 4.8 0.2 - - - +
1564A ILE* 3.8 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1461A LYS* 3.2 17.9 + - + +
1462A MET* 3.7 4.3 - - - +
1464A LYS* 1.3 77.0 - - - +
1466A VAL* 1.3 60.2 + - - +
1468A ALA 3.2 1.6 + - - -
1469A VAL* 2.9 28.6 + - - +
1522A LEU* 4.0 26.9 - - + -
1525A LEU* 4.7 4.5 - - + -
1557A PHE* 3.7 34.3 - - + -
1560A VAL* 3.6 19.3 - - + +
1561A ARG* 3.9 29.4 - - + +
1564A ILE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462A MET 3.0 17.0 + - - +
1463A LYS* 4.1 2.7 - - - +
1465A ILE* 1.3 76.6 - - + +
1467A ASP* 1.3 63.6 + - - +
1469A VAL* 3.3 6.3 + - - +
1470A ILE* 2.9 42.7 + - + +
1507A PHE* 4.3 14.6 - - + -
1510A ILE* 4.2 7.0 - - + -
1511A LYS* 4.2 18.6 - - + -
1514A ILE* 3.7 20.0 - - + -
1525A LEU* 4.0 21.5 - - + -
1529A VAL* 5.3 3.4 - - + -
1557A PHE* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463A LYS* 2.9 33.1 + - - +
1464A LYS* 3.9 7.9 - - - +
1466A VAL* 1.3 74.8 - - - +
1468A ALA* 1.3 57.9 + - - +
1470A ILE* 3.3 7.5 + - - +
1471A LYS* 2.9 34.9 + - + +
1511A LYS* 3.7 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1464A LYS 3.1 18.2 + - - +
1465A ILE 3.7 3.4 - - - +
1466A VAL 3.2 0.4 - - - -
1467A ASP* 1.3 77.4 - - - +
1469A VAL* 1.3 64.6 + - - +
1471A LYS* 3.4 8.3 + - - +
1472A TYR* 3.1 23.0 + - - +
1560A VAL* 3.8 22.8 - - + +
1564A ILE* 5.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1465A ILE 2.9 20.8 + - - +
1466A VAL* 3.8 6.1 - - - +
1468A ALA* 1.3 75.9 - - - +
1470A ILE* 1.3 62.4 + - - +
1472A TYR* 3.4 14.0 + - - +
1482A SER* 4.1 6.2 + - - -
1507A PHE* 4.1 24.0 - - + -
1529A VAL* 5.7 1.1 - - + -
1553A LEU* 3.9 26.4 - - + +
1556A VAL* 4.2 9.6 - - + +
1557A PHE* 3.7 43.1 - - + +
1560A VAL* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1466A VAL* 2.9 31.4 + - + +
1467A ASP* 3.6 5.8 - - - +
1469A VAL* 1.3 75.9 - - - +
1471A LYS* 1.3 58.4 + - + +
1472A TYR 3.3 1.2 + - - +
1480A GLN* 2.5 34.6 + - - +
1482A SER* 2.6 22.0 + - - +
1486A ILE* 3.9 27.8 - - + -
1507A PHE* 4.0 22.7 - - + -
1511A LYS* 3.5 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467A ASP* 2.9 20.6 + - + +
1468A ALA* 3.8 8.1 - - - +
1469A VAL 3.3 0.2 - - - -
1470A ILE* 1.3 77.6 - - + +
1472A TYR* 1.3 66.0 + - - +
1473A LYS* 3.2 28.6 - - - +
1480A GLN* 3.7 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1468A ALA 3.1 12.2 + - - +
1469A VAL 3.6 14.9 - - - +
1470A ILE 3.3 2.6 - - - +
1471A LYS* 1.3 80.6 - - - +
1473A LYS* 1.3 82.8 + - - +
1474A ASP* 3.9 9.5 - - - -
1475A SER* 4.4 9.8 + - - -
1480A GLN* 3.4 6.6 - - - +
1481A LEU* 3.4 44.6 + - + -
1482A SER 4.8 0.2 + - - -
1552A VAL* 4.9 3.3 - - + +
1553A LEU* 5.0 1.3 - - + -
1556A VAL* 3.8 40.5 - - + +
1560A VAL* 6.0 2.0 - - + -
----------------------------------------------------------
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