Contacts of the helix formed by residues 1513 - 1529 (chain H) in PDB entry 6BAA
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 ASP1513 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1511H SER* 5.0 2.3 - - - -
1512H ILE* 1.3 80.3 + - - +
1514H MET* 1.3 62.2 + - - +
1515H ALA* 4.2 2.7 - - + +
1516H THR* 3.6 22.9 - - - +
1517H GLU* 3.2 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1514 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513H ASP* 1.3 74.7 - - - +
1515H ALA* 1.3 60.5 + - - +
1516H THR 3.2 0.2 - - - -
1517H GLU* 4.4 0.6 - - - +
1518H ASN* 3.0 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1515 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513H ASP* 4.2 2.6 - - + +
1514H MET* 1.3 78.6 - - - +
1516H THR* 1.3 58.3 + - - +
1518H ASN* 3.9 4.7 - - - +
1519H ILE* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1516 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485H GLY* 5.6 8.7 - - - -
1512H ILE* 4.2 13.0 - - - -
1513H ASP* 3.6 20.9 - - - +
1514H MET 3.2 0.4 - - - -
1515H ALA* 1.3 79.0 - - - +
1517H GLU* 1.3 62.0 + - - +
1519H ILE* 3.7 5.3 - - - +
1520H LEU* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1517 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512H ILE* 4.5 9.1 - - + +
1513H ASP 3.2 24.0 + - - +
1514H MET* 4.4 1.3 - - - +
1516H THR* 1.3 78.7 - - - +
1518H ASN* 1.3 58.1 + - - +
1520H LEU* 3.6 6.1 - - - +
1521H GLN* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1518 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514H MET 3.0 21.6 + - - +
1515H ALA* 3.9 5.4 - - - +
1517H GLU* 1.3 74.0 - - - +
1519H ILE* 1.3 59.7 + - - +
1521H GLN* 3.5 5.8 + - - +
1522H LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1519 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459H GLN* 6.5 1.1 - - + -
1515H ALA 2.9 20.9 + - - +
1516H THR* 3.7 6.5 - - - +
1517H GLU 3.3 0.2 - - - -
1518H ASN* 1.3 72.6 - - - +
1520H LEU* 1.3 57.2 + - - +
1522H LYS* 3.2 7.9 + - - +
1523H VAL* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1520 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516H THR 2.8 21.6 + - - +
1517H GLU* 3.6 7.6 - - - +
1519H ILE* 1.3 71.7 - - - +
1521H GLN* 1.3 53.1 + - - +
1523H VAL* 3.4 7.5 + - - +
1524H VAL* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1521 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517H GLU 2.9 18.1 + - - +
1518H ASN* 3.7 7.2 - - - +
1520H LEU* 1.3 74.6 - - - +
1522H LYS* 1.3 59.4 + - - +
1524H VAL* 3.3 7.8 + - - +
1525H MET* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1522 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518H ASN 2.9 17.8 + - - +
1519H ILE* 3.2 8.9 + - - +
1521H GLN* 1.3 75.7 - - - +
1523H VAL* 1.3 57.9 + - - +
1525H MET* 3.3 7.4 + - - +
1526H THR* 2.9 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1523 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1458H ALA* 6.1 4.7 - - - -
1492H LEU* 5.7 9.4 - - + -
1519H ILE 2.8 19.3 + - - +
1520H LEU* 3.6 8.5 - - - +
1522H LYS* 1.3 70.2 - - - +
1524H VAL* 1.3 56.3 + - - +
1526H THR* 3.9 4.8 - - - +
1527H ALA* 2.8 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1524 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1520H LEU 2.8 21.0 + - - +
1521H GLN* 3.5 10.1 - - - +
1523H VAL* 1.3 73.6 - - - +
1525H MET* 1.3 56.6 + - - +
1527H ALA* 3.8 5.7 - - - +
1528H PHE* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1525 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521H GLN 2.8 20.7 + - - +
1522H LYS* 3.3 8.0 + - - +
1524H VAL* 1.3 73.8 - - - +
1526H THR* 1.3 61.0 + - - +
1528H PHE* 3.6 3.5 + - - +
1529H ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1526 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1522H LYS 2.9 16.7 + - - -
1523H VAL* 3.9 6.1 - - - -
1525H MET* 1.3 73.4 - - - +
1527H ALA* 1.3 65.5 + - - +
1529H ALA* 3.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1527 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1523H VAL 2.8 23.5 + - - +
1524H VAL* 3.8 7.0 - - - +
1526H THR* 1.3 73.8 - - - +
1528H PHE* 1.3 61.4 + - - +
1529H ALA 3.3 3.5 + - - +
1531H ARG* 3.2 38.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1528 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372H GLY 2.9 18.4 - - - +
1374H LYS* 3.8 29.6 - - + +
1524H VAL 2.8 22.2 + - - +
1525H MET* 3.9 3.8 - - - +
1527H ALA* 1.3 70.6 - - - +
1529H ALA* 1.3 62.8 + - - +
1530H ASP 3.1 0.2 + - - -
1531H ARG* 2.8 25.7 - - - +
1532H THR 5.5 0.2 - - - -
1533H VAL* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1529 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372H GLY 4.6 2.0 - - - -
1525H MET 3.1 14.4 + - - +
1526H THR* 3.4 17.8 - - - +
1527H ALA 3.2 8.4 - - - +
1528H PHE* 1.3 74.9 - - - +
1530H ASP* 1.3 62.8 + - - +
1531H ARG* 3.2 7.7 + - - +
----------------------------------------------------------
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