Contacts of the helix formed by residues 1983 - 1992 (chain A) in PDB entry 4M6W
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 SER1983 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860A ARG 5.4 0.7 + - - -
1890A MET* 3.9 25.6 + - - +
1891A PHE* 3.5 34.7 - - - -
1977A LEU* 5.2 0.2 - - - -
1981A ASN 4.1 0.4 + - - -
1982A ILE* 1.3 78.0 - - - +
1984A TYR* 1.3 64.0 + - - +
1985A ILE* 3.3 9.3 - - - +
1986A THR* 2.6 36.0 + - - -
1987A ALA* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1984 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821A LEU* 3.7 12.1 - - + -
1848A CYS* 3.8 19.1 - - + +
1849A PRO* 3.7 42.1 - - + +
1850A LEU* 3.7 25.1 - - + -
1856A ILE* 4.1 5.3 - - + +
1890A MET* 5.5 0.2 - - - +
1891A PHE* 5.2 0.2 - - - -
1963A THR* 6.1 0.7 - - - -
1973A LEU* 3.8 28.7 - - + +
1977A LEU* 4.0 29.8 - - + +
1982A ILE 3.9 0.4 + - - -
1983A SER* 1.3 73.5 - - - +
1985A ILE* 1.3 58.3 + - - +
1987A ALA* 3.6 2.9 + - - +
1988A LEU* 2.9 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1985 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821A LEU* 4.4 4.0 - - + -
1856A ILE* 3.8 28.4 - - + +
1858A SER 3.9 7.2 - - - +
1859A ASN* 3.3 30.7 - - + +
1860A ARG 4.4 4.5 - - - +
1891A PHE* 4.6 1.1 - - + -
1959A ILE* 3.8 33.9 - - + +
1961A VAL* 4.5 7.4 - - + -
1963A THR* 5.2 0.9 - - + -
1983A SER* 3.3 13.7 - - - +
1984A TYR* 1.3 77.4 - - - +
1986A THR* 1.3 69.4 + - - +
1988A LEU* 3.9 24.5 - - + -
1989A ASN* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860A ARG 5.7 1.6 + - - -
1890A MET 4.9 3.1 + - - -
1982A ILE* 3.9 25.2 - - + +
1983A SER* 2.6 32.2 + - - -
1985A ILE* 1.3 77.0 - - - +
1987A ALA* 1.3 64.0 + - - +
1989A ASN* 3.0 11.8 - - - +
1990A MET* 2.9 34.7 + - + +
2012A ALA* 3.8 6.6 + - + +
2013A GLN 5.3 1.4 + - - -
2014A VAL* 3.6 32.2 - - + +
2018A LYS* 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1987 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1973A LEU* 3.7 19.5 - - + -
1976A TYR* 3.9 22.7 - - + -
1977A LEU* 4.2 13.7 - - + -
1982A ILE* 3.7 11.5 - - + +
1983A SER 3.1 8.9 + - - +
1984A TYR 3.7 8.1 - - - +
1986A THR* 1.3 78.5 - - - +
1988A LEU* 1.3 61.8 + - - +
1990A MET* 3.2 6.6 + - - +
1991A CYS* 3.2 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821A LEU* 4.2 5.8 - - + -
1848A CYS* 5.7 0.2 - - - -
1961A VAL* 4.6 6.9 - - + +
1963A THR* 3.8 49.1 - - + -
1964A VAL 4.4 8.1 - - - +
1973A LEU* 4.3 20.6 - - + +
1984A TYR* 2.9 52.8 + - + +
1985A ILE* 3.4 22.4 - - + +
1986A THR 3.1 0.4 - - - -
1987A ALA* 1.3 74.6 - - - +
1989A ASN* 1.3 57.5 + - - +
1990A MET 3.1 0.2 - - - -
1991A CYS* 3.1 23.0 + - + +
1992A HIS* 3.2 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1859A ASN* 3.2 35.0 + - - +
1959A ILE 5.4 0.6 + - - -
1961A VAL* 4.1 16.0 - - + +
1985A ILE* 3.0 16.5 + - - +
1986A THR* 3.0 17.1 - - - +
1988A LEU* 1.3 75.8 - - - +
1990A MET* 1.3 57.9 + - - +
1992A HIS* 2.9 18.4 - - - +
1993A GLN* 3.6 21.9 - - - +
1994A PHE* 4.7 0.2 - - - -
2011A TYR 3.0 21.0 - - - +
2012A ALA 3.0 20.1 - - - +
2013A GLN* 4.0 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1976A TYR* 3.7 41.5 + - + -
1979A ILE* 4.5 8.1 - - + -
1982A ILE* 4.7 10.8 - - + -
1986A THR* 2.9 29.9 + - - +
1987A ALA* 3.4 13.2 - - - +
1988A LEU 3.1 0.6 - - - -
1989A ASN* 1.3 74.4 - - - +
1991A CYS* 1.3 61.9 + - - +
1992A HIS 3.0 9.7 - - - +
1994A PHE* 3.2 30.3 - - + +
2000A MET* 3.8 25.6 - - + -
2008A ILE* 5.3 1.1 - - + -
2012A ALA* 3.7 26.2 - - + -
2022A ILE* 4.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964A VAL 5.7 3.8 - - - +
1970A SER* 4.5 17.7 + - - +
1972A ALA* 4.0 4.7 - - + -
1973A LEU* 3.6 34.1 - - - -
1976A TYR* 3.5 25.1 - - - -
1987A ALA 3.2 17.8 + - - -
1988A LEU* 3.1 9.5 + - + +
1990A MET* 1.3 75.6 - - - +
1992A HIS* 1.3 56.6 + - - +
1994A PHE 3.2 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1992 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1961A VAL* 4.2 20.0 - - + -
1962A PRO* 3.5 38.8 - - + +
1964A VAL* 6.2 0.2 - - - +
1988A LEU 3.2 10.4 + - - +
1989A ASN* 2.9 18.8 - - - +
1990A MET* 3.0 6.1 - - - +
1991A CYS* 1.3 74.2 - - - +
1993A GLN* 1.3 72.1 - - + +
1994A PHE 2.9 13.2 + - - -
----------------------------------------------------------
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