Contacts of the helix formed by residues 1564 - 1580 (chain A) in PDB entry 3PZD
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 THR1564 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549A TYR* 3.7 14.8 - - - +
1557A LEU* 5.2 4.5 - - - -
1558A LYS* 5.1 1.8 - - - +
1563A THR* 1.3 90.8 + - - +
1565A LEU* 1.3 66.1 + - - +
1566A GLN* 4.0 5.6 + - - +
1567A ASP* 2.9 27.2 + - - +
1568A GLU* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547A LEU* 3.6 35.2 - - + +
1548A PRO 4.2 1.1 - - - +
1549A TYR* 3.4 42.3 + - + +
1552A ILE* 3.9 22.7 - - + -
1557A LEU* 4.4 4.2 - - + +
1564A THR* 1.3 73.6 - - - +
1566A GLN* 1.3 57.2 + - - +
1568A GLU* 3.3 1.5 + - - +
1569A ALA* 2.9 30.7 + - - +
1599A LEU* 4.1 25.1 - - + -
1601A PRO* 3.7 29.2 - - + -
1602A LEU* 3.5 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542A SER* 4.6 7.1 - - - -
1543A PRO* 3.7 27.6 - - + +
1547A LEU* 3.7 14.6 - - + -
1564A THR* 3.3 5.3 + - - +
1565A LEU* 1.3 77.2 - - + +
1567A ASP* 1.3 64.9 + - - +
1569A ALA* 3.2 3.5 + - - +
1570A ILE* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563A THR* 2.9 26.9 + - - +
1564A THR* 2.9 20.8 + - + +
1566A GLN* 1.3 79.9 - - - +
1568A GLU* 1.3 58.7 + - - +
1570A ILE* 3.3 13.4 + - - +
1571A LYS* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561A GLY 4.9 1.1 - - - +
1562A TYR* 3.5 22.0 - - + -
1563A THR* 2.7 40.7 + - - +
1564A THR 2.9 22.5 + - - +
1567A ASP* 1.3 75.2 - - - +
1569A ALA* 1.3 60.8 + - - +
1571A LYS* 3.7 18.3 + - - +
1572A ILE* 2.8 35.3 + - - +
1595A THR* 4.5 6.6 + - + +
1599A LEU* 4.0 16.6 - - + -
1602A LEU* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543A PRO* 4.0 8.7 - - + -
1547A LEU* 4.0 9.4 - - + -
1565A LEU 2.9 11.8 + - - +
1566A GLN 3.5 4.7 - - - +
1568A GLU* 1.3 78.1 - - - +
1570A ILE* 1.3 60.9 + - - +
1572A ILE* 3.4 5.3 + - - +
1573A PHE* 3.2 12.3 + - - +
1602A LEU* 3.4 27.0 - - + +
1605A GLU* 3.8 17.7 - - + -
1609A GLN* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540A LEU* 3.5 23.3 + - - +
1541A HIS* 3.4 24.9 - - - +
1542A SER* 3.8 26.2 - - - +
1543A PRO* 4.4 1.6 - - + -
1566A GLN* 3.0 28.5 + - + +
1567A ASP* 3.6 11.9 - - - +
1569A ALA* 1.3 74.5 - - - +
1571A LYS* 1.3 62.9 + - - +
1573A PHE* 3.5 9.5 + - - +
1574A ASN* 3.2 18.6 + - + +
1609A GLN* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1567A ASP* 2.9 19.0 + - - +
1568A GLU* 3.9 19.1 + - - +
1570A ILE* 1.3 76.1 - - - +
1572A ILE* 1.3 61.2 + - + +
1573A PHE 3.2 0.2 - - - -
1574A ASN* 3.0 20.6 + - - +
1575A SER* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1568A GLU 2.8 26.6 + - - +
1569A ALA* 3.8 7.4 - - - +
1571A LYS* 1.3 73.8 - - + +
1573A PHE* 1.3 53.5 + - - +
1575A SER* 2.8 8.9 + - - +
1576A LEU* 2.7 43.4 + - + +
1592A ILE* 4.2 19.3 - - + +
1595A THR* 3.7 35.9 - - + +
1596A GLY 5.0 0.9 - - - +
1602A LEU* 4.6 11.2 - - + -
1606A LEU* 3.4 42.4 - - + -
1609A GLN* 4.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536A THR* 3.9 11.7 - - + -
1538A HIS 3.8 11.2 - - - -
1539A PRO* 4.7 0.2 - - + -
1540A LEU* 3.6 33.9 - - + -
1569A ALA 3.2 6.0 + - - +
1570A ILE 3.6 9.4 - - - +
1571A LYS 3.2 0.4 - - - -
1572A ILE* 1.3 77.8 - - - +
1574A ASN* 1.3 58.3 + - - +
1576A LEU* 3.4 9.1 + - + +
1577A GLN* 3.0 51.8 + - + +
1609A GLN* 3.4 37.6 + - + +
1612A LYS* 3.7 20.9 - - + -
1613A GLN* 3.6 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570A ILE* 3.2 12.8 + - + +
1571A LYS* 3.0 27.0 + - - +
1573A PHE* 1.3 74.3 - - - +
1575A SER* 1.3 54.7 + - - +
1577A GLN* 3.1 13.0 + - - +
1578A GLN* 2.8 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1571A LYS* 2.8 31.5 + - - +
1572A ILE* 2.8 14.9 + - - +
1574A ASN* 1.3 72.1 + - - +
1576A LEU* 1.3 61.3 + - - +
1578A GLN* 3.3 6.4 + - - +
1579A LEU* 2.9 30.7 + - - +
1588A ILE* 3.8 18.4 - - - +
1592A ILE* 4.0 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1572A ILE* 2.7 23.7 + - + +
1573A PHE* 3.5 12.8 - - + +
1575A SER* 1.3 72.4 - - - +
1577A GLN* 1.3 63.4 + - + +
1579A LEU* 3.8 11.2 + - - +
1580A GLU* 3.9 13.0 + - - +
1592A ILE* 3.8 13.5 - - + -
1606A LEU* 4.9 2.7 - - + -
1609A GLN* 3.6 41.1 - - + +
1610A LEU* 3.9 26.2 - - + -
1613A GLN* 5.1 10.7 + - + -
1628A SER* 5.5 2.6 + - - +
1631A ILE* 3.4 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535A TYR* 6.0 0.7 - - - +
1536A THR 3.0 21.2 + - - -
1537A HIS* 2.9 31.4 + - - +
1538A HIS 3.3 10.5 + - - +
1539A PRO* 4.1 9.9 - - - +
1573A PHE* 3.0 37.7 + - + +
1574A ASN* 3.1 13.1 + - - +
1576A LEU* 1.3 79.8 - - + +
1578A GLN* 1.3 59.0 + - + +
1580A GLU* 3.1 30.3 - - - +
1613A GLN* 4.2 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1574A ASN* 2.8 45.3 + - - +
1575A SER* 3.3 7.8 + - - +
1577A GLN* 1.3 76.9 - - + +
1579A LEU* 1.3 62.1 + - - +
1580A GLU 3.1 2.1 + - - -
1581A SER* 3.5 9.4 + - - +
1582A MET* 3.3 18.3 - - - +
1588A ILE* 5.4 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1575A SER 2.9 18.1 + - - +
1576A LEU 3.9 6.7 - - - +
1577A GLN 3.4 0.2 - - - -
1578A GLN* 1.3 74.6 - - - +
1580A GLU* 1.3 65.9 + - - +
1581A SER 3.0 1.6 + - - -
1582A MET* 3.2 21.5 + - + +
1585A PRO* 3.7 32.1 - - + +
1588A ILE* 3.8 30.0 - - + +
1589A ILE* 4.0 11.9 - - + +
1592A ILE* 5.2 0.7 - - + -
1627A TYR* 3.1 36.7 - - + -
1631A ILE* 3.2 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535A TYR* 3.0 37.9 + - - -
1576A LEU 3.9 13.2 + - - +
1577A GLN* 3.1 29.7 + - - +
1579A LEU* 1.3 78.1 - - - +
1581A SER* 1.3 60.6 + - - +
1582A MET 3.6 2.3 + - - -
1613A GLN* 4.8 1.9 + - - -
1623A VAL* 4.9 2.9 - - - +
1624A GLY* 4.1 36.9 + - - +
1625A ASN 4.7 0.5 + - - -
1627A TYR* 4.0 16.0 - - - +
1628A SER* 5.5 1.9 + - - -
----------------------------------------------------------
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