Contacts of the helix formed by residues 1577 - 1588 (chain C) in PDB entry 3ZQK
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 ASN1577 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542C TYR* 3.7 11.5 - - - +
1543C SER 2.9 16.4 + - - +
1544C TYR* 3.0 39.0 + - - +
1546C VAL* 5.4 0.2 - - - +
1575C ARG* 3.7 13.9 - - - +
1576C THR* 1.3 68.1 - - - +
1578C THR* 1.3 63.1 + - - +
1579C GLY 3.2 3.1 - - - -
1580C LEU* 3.1 15.6 + - + +
1581C ALA 3.1 17.2 + - - -
1613C SER* 3.5 19.2 - - - -
1614C ASP* 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542C TYR* 2.9 25.1 + - - +
1576C THR* 2.9 20.3 + - - +
1577C ASN* 1.3 69.7 - - - +
1579C GLY* 1.3 64.6 + - - +
1581C ALA* 3.3 2.9 + - - +
1582C LEU* 3.0 23.8 + - + +
1606C MET* 3.6 37.9 - - + -
1608C THR* 4.4 5.1 + - + +
1610C ASN 5.1 0.3 + - - -
1612C ALA* 3.9 11.0 - - + +
1614C ASP* 3.3 0.8 + - - -
1616C ILE* 3.5 19.1 - - + -
1642C ILE* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1578C THR* 1.3 75.0 - - - +
1580C LEU* 1.3 62.9 + - - +
1582C LEU* 3.2 6.3 + - - +
1583C ARG* 3.0 34.9 + - - +
1614C ASP* 2.9 10.3 + - - -
1615C GLU 3.5 17.9 - - - -
1616C ILE* 3.1 21.8 - - - +
1617C LYS 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544C TYR 3.5 25.4 - - - +
1545C MET* 4.4 3.8 - - - -
1546C VAL* 4.1 17.7 - - + +
1577C ASN* 3.1 17.5 + - + +
1579C GLY* 1.3 76.0 - - - +
1581C ALA* 1.3 57.4 + - - +
1583C ARG* 3.3 28.6 + - + +
1584C TYR* 2.9 31.5 + - + +
1614C ASP* 2.9 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1581 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502C VAL* 4.0 12.3 - - + -
1540C LEU* 4.1 2.6 - - + +
1542C TYR* 3.7 42.0 - - + -
1546C VAL* 3.8 14.3 - - + +
1577C ASN 3.1 3.7 + - - +
1578C THR* 3.6 8.7 - - - +
1579C GLY 3.2 0.2 - - - -
1580C LEU* 1.3 79.5 - - - +
1582C LEU* 1.3 64.3 + - + +
1584C TYR* 3.3 2.1 + - - +
1585C LEU* 3.1 28.1 + - - +
1606C MET* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1582 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1578C THR* 3.0 21.1 + - + +
1579C GLY* 3.2 5.4 + - - +
1581C ALA* 1.3 74.1 - - - +
1583C ARG* 1.3 65.5 + - + +
1585C LEU* 3.3 18.2 + - + +
1586C SER 3.3 15.8 + - - -
1604C VAL* 5.2 1.3 - - + -
1606C MET* 4.0 23.3 - - + -
1616C ILE* 4.1 27.6 - - + -
1617C LYS 5.0 9.6 - - - +
1618C ARG* 5.7 0.4 - - - -
1619C LEU* 3.4 42.7 - - + +
1625C VAL* 5.0 8.1 - - + -
1642C ILE* 4.1 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1583 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579C GLY* 3.0 27.1 + - - +
1580C LEU* 3.7 32.7 - - + +
1582C LEU* 1.3 78.5 - - + +
1584C TYR* 1.3 57.1 + - - +
1586C SER* 3.1 10.1 + - - +
1587C ASP* 2.9 41.1 + - - +
1614C ASP* 5.0 3.2 + - - +
1615C GLU* 4.0 14.3 + - - +
1617C LYS* 5.7 16.2 - - + +
1619C LEU* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1584 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540C LEU* 4.0 11.7 - - + -
1546C VAL* 3.8 37.4 + - + -
1548C VAL* 3.4 24.3 - - + +
1580C LEU* 2.9 19.5 + - + +
1581C ALA 3.3 4.9 + - - +
1583C ARG* 1.3 72.9 - - - +
1585C LEU* 1.3 62.0 + - - +
1587C ASP* 4.6 3.6 - - + +
1588C HIS* 2.8 78.8 + + + +
1589C SER* 3.2 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1585 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1500C ALA* 3.7 27.6 - - + -
1502C VAL* 3.6 19.3 - - + -
1538C THR* 5.0 0.2 - - + -
1540C LEU* 3.9 20.6 - - + -
1581C ALA 3.1 17.7 + - - +
1582C LEU* 3.3 24.7 - - + +
1584C TYR* 1.3 79.9 - - - +
1586C SER* 1.3 60.1 + - - +
1589C SER* 3.2 16.6 + - - +
1590C PHE* 2.9 46.0 + - + -
1604C VAL* 3.9 22.4 - - + -
1619C LEU* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1582C LEU 3.3 4.9 + - - -
1583C ARG* 3.1 16.2 + - - +
1585C LEU* 1.3 82.2 - - - +
1587C ASP* 1.3 65.8 + - - +
1588C HIS 3.6 0.2 - - - -
1590C PHE* 4.4 15.6 - - - +
1591C LEU* 4.8 6.2 - - - +
1619C LEU* 3.9 21.8 - - - +
1620C PRO* 4.7 8.6 - - - +
1623C ILE* 4.4 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1583C ARG* 2.9 27.1 + - - +
1584C TYR* 4.4 2.9 - - + +
1586C SER* 1.3 87.0 + - - +
1588C HIS* 1.3 60.7 + - + +
1591C LEU* 3.3 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1548C VAL* 4.1 13.1 - - + +
1551C PRO* 6.3 0.8 - - - +
1584C TYR* 2.8 66.2 + + + +
1586C SER 3.6 0.6 - - - -
1587C ASP* 1.3 78.4 - - + +
1589C SER* 1.3 70.4 + - - +
1590C PHE 3.2 1.1 - - - -
1591C LEU* 3.2 17.8 + - - +
1594C GLN* 3.3 53.7 + - + +
----------------------------------------------------------
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