Contacts of the helix formed by residues 1561 - 1569 (chain G) 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 LYS1561 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1546G ASP 3.5 12.3 - - - +
1547G LEU* 3.6 6.8 - - + +
1560G ASP* 1.3 96.6 + - - +
1562G PRO* 1.3 75.9 - - + +
1563G GLU* 3.4 6.7 + - + +
1564G LYS* 3.6 13.6 + - + -
1565G LEU* 3.4 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1562 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542G ILE 4.3 2.0 - - - +
1543G LEU* 4.2 33.9 - - + +
1544G SER 5.0 0.2 - - - -
1545G ALA 3.2 19.3 - - - +
1546G ASP 3.4 15.5 - - - +
1548G VAL* 3.6 26.5 - - + -
1561G LYS* 1.3 86.0 - - + +
1563G GLU* 1.3 64.0 + - - +
1565G LEU* 3.2 5.4 + - + +
1566G LEU* 2.9 28.7 + - + +
1573G PHE* 5.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1563 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561G LYS* 3.4 3.7 - - + +
1562G PRO* 1.3 80.1 - - - +
1564G LYS* 1.3 60.1 + - + +
1566G LEU* 3.3 16.5 - - + +
1567G SER* 2.9 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1564 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560G ASP* 3.1 38.9 + - - +
1561G LYS* 3.6 12.2 + - + +
1562G PRO 3.3 0.2 - - - -
1563G GLU* 1.3 80.7 - - + +
1565G LEU* 1.3 57.7 + - - +
1567G SER* 3.8 3.0 - - - -
1568G ARG* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1565 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1548G VAL* 3.9 23.8 - - + +
1550G VAL* 5.0 4.3 - - + -
1558G GLU 3.3 24.7 - - - +
1560G ASP* 3.6 37.5 - - + +
1561G LYS 3.4 8.0 + - - +
1562G PRO* 3.2 7.2 + - + +
1564G LYS* 1.3 76.3 - - - +
1566G LEU* 1.3 61.8 + - - +
1568G ARG* 3.3 34.5 - - - +
1569G LYS* 3.3 18.7 + - - -
1571G SER* 4.1 20.4 - - - +
1573G PHE* 4.8 12.1 - - + -
1574G ALA* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1566 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543G LEU* 3.8 25.1 - - + -
1562G PRO* 2.9 25.3 + - + +
1563G GLU* 3.3 18.6 - - + +
1565G LEU* 1.3 79.0 - - - +
1567G SER* 1.3 68.3 + - - +
1568G ARG 3.4 0.2 - - - -
1569G LYS* 3.7 12.1 + - - +
1573G PHE* 5.3 6.2 - - + -
1574G ALA* 4.7 11.0 - - - +
1577G VAL* 5.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1567 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563G GLU 2.9 17.8 + - - -
1564G LYS* 4.3 2.9 - - - -
1566G LEU* 1.3 83.3 - - - +
1568G ARG* 1.3 64.5 + - - +
1569G LYS* 4.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1568 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1558G GLU* 3.6 22.4 - - - +
1560G ASP* 5.0 5.9 + - - -
1564G LYS 2.9 19.5 + - - +
1565G LEU* 3.3 32.3 - - - +
1567G SER* 1.3 78.1 - - - +
1569G LYS* 1.3 61.5 + - - +
1570G ASP* 2.8 54.1 + - - +
1571G SER* 3.5 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1569 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1565G LEU 3.3 7.4 + - - -
1566G LEU 3.7 7.6 + - - +
1567G SER 3.4 3.9 - - - +
1568G ARG* 1.3 79.7 - - - +
1570G ASP* 1.3 72.4 + - - +
1571G SER 3.1 12.5 - - - +
1574G ALA* 3.4 22.4 - - + +
1575G SER* 5.5 1.2 + - - -
1578G ARG* 6.3 2.2 - - + -
----------------------------------------------------------
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