Contacts of the helix formed by residues 1986 - 1999 (chain A) in PDB entry 6AJ4
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 ASP1986 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1979A ALA* 5.2 1.5 + - - +
1982A GLN* 4.6 16.3 - - - +
1984A PRO 3.6 0.6 + - - -
1985A ALA* 1.3 74.6 - - - +
1987A PRO* 1.3 78.4 - - - +
1988A LYS* 3.5 10.4 + - - +
1989A MET* 3.6 15.1 + - + +
1990A LEU* 3.0 22.9 + - - +
2B GLN* 3.5 20.8 - - - +
3B THR* 2.9 45.6 + - - +
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Residues in contact with PRO1987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1985A ALA* 3.7 8.8 - - - +
1986A ASP* 1.3 92.5 - - - +
1988A LYS* 1.3 59.6 + - + +
1990A LEU* 3.0 5.1 + - + -
1991A GLN* 2.8 56.4 + - + +
2048A ASN* 5.0 0.4 - - - +
2051A LEU* 4.7 28.3 - - + +
2B GLN* 4.1 9.0 - - - +
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Residues in contact with LYS1988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1986A ASP* 4.0 5.8 - - - +
1987A PRO* 1.3 83.2 - - + +
1989A MET* 1.3 62.3 + - - +
1991A GLN* 3.6 9.5 + - - +
1992A MET* 3.0 24.8 + - - +
3B THR* 3.9 29.7 + - + +
5B LYS* 4.1 21.5 - - + +
56B PHE* 3.6 7.9 - - + -
74B GLN* 3.3 41.6 + - + -
76B ASP* 3.5 29.8 + - - +
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Residues in contact with MET1989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975A GLU* 5.8 0.4 - - - +
1979A ALA* 5.0 6.5 - - + -
1982A GLN* 5.0 9.6 - - - +
1986A ASP* 3.5 21.6 + - + +
1987A PRO 3.2 0.6 - - - -
1988A LYS* 1.3 78.6 - - - +
1990A LEU* 1.3 57.5 + - - +
1992A MET* 3.5 19.7 + - - +
1993A VAL* 3.1 39.4 + - + +
3B THR* 3.1 38.1 + - + +
41B ALA* 3.9 21.1 - - + -
52B THR* 3.9 21.1 - - + -
54B GLY* 4.6 6.7 - - - -
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Residues in contact with LEU1990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1976A LEU* 5.2 4.7 - - + -
1979A ALA* 4.2 33.2 - - + +
1980A THR* 4.3 9.4 - - - +
1985A ALA* 5.4 1.8 - - + -
1986A ASP 3.0 16.8 + - - +
1987A PRO 3.0 3.9 + - - +
1989A MET* 1.3 75.2 - - - +
1991A GLN* 1.3 65.7 + - - +
1993A VAL* 3.2 1.9 + - - +
1994A LEU* 2.9 26.3 + - + +
2044A ALA* 4.0 28.3 - - + +
2047A LYS* 3.6 34.3 - - + +
2048A ASN* 4.5 11.7 - - - +
2051A LEU* 4.1 14.4 - - + -
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Residues in contact with GLN1991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1987A PRO* 2.8 41.5 + - - +
1988A LYS* 4.1 9.3 - - - +
1990A LEU* 1.3 73.1 - - - +
1992A MET* 1.3 56.5 + - - +
1994A LEU* 3.1 6.2 + - - -
1995A GLN* 2.6 38.7 + - - +
2048A ASN* 3.2 34.0 + - - +
2052A ILE* 4.1 7.3 - - - +
2056A GLN* 2.9 35.9 + - - +
2059A TYR* 3.1 27.1 + - + +
2063A LEU* 5.5 0.9 - - + -
5B LYS* 4.6 6.6 + - - +
56B PHE* 5.1 2.0 - - + -
74B GLN* 6.2 0.4 - - - +
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Residues in contact with MET1992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972A LYS* 6.1 1.6 - - - +
1975A GLU* 4.6 7.4 - - - +
1988A LYS 3.0 13.8 + - - +
1989A MET* 3.5 16.4 - - - +
1991A GLN* 1.3 77.7 - - - +
1993A VAL* 1.3 84.4 + - + +
1996A GLY* 3.3 4.2 + - - -
38B ASP 4.6 0.6 - - - +
39B ASN* 3.0 46.2 + - + +
40B TYR 3.6 26.9 - - - +
41B ALA* 4.2 12.6 - - + +
54B GLY* 3.6 19.3 - - - -
55B LEU 3.8 3.8 - - - +
56B PHE* 3.3 37.6 - - + -
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Residues in contact with VAL1993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972A LYS* 4.0 14.1 + - + +
1975A GLU* 3.9 40.2 - - + +
1976A LEU* 3.6 29.2 - - + +
1979A ALA* 4.9 4.7 - - + -
1989A MET* 3.1 25.4 + - + +
1990A LEU* 3.7 8.1 - - + +
1991A GLN 3.2 0.2 - - - -
1992A MET* 1.3 92.8 - - + +
1994A LEU* 1.3 62.4 + - - +
1996A GLY* 3.4 3.5 + - - -
1997A SER* 3.1 24.6 + - - -
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Residues in contact with LEU1994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1976A LEU* 4.0 13.2 - - + +
1990A LEU* 2.9 20.6 + - + +
1991A GLN* 3.8 2.0 - - - +
1993A VAL* 1.3 73.3 - - - +
1995A GLN* 1.3 59.7 + - - +
1996A GLY 3.0 2.0 - - - -
1997A SER* 2.8 20.6 + - - +
1998A VAL* 3.1 24.6 + - + +
2041A CYS* 3.9 21.3 - - + +
2044A ALA* 3.7 25.8 - - + +
2045A LEU* 3.9 33.9 - - + +
2048A ASN* 4.3 16.2 - - + +
2063A LEU* 3.9 23.8 - - + -
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Residues in contact with GLN1995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991A GLN 2.6 22.3 + - - +
1992A MET 4.4 1.3 - - - +
1994A LEU* 1.3 73.8 - - - +
1996A GLY* 1.3 55.8 + - - +
1999A GLY* 3.1 38.9 + - - +
2000A THR* 5.2 0.8 - - - +
2001A THR* 4.9 6.7 - - - +
2059A TYR* 3.5 21.2 + - + +
2063A LEU* 3.8 29.1 - - + +
38B ASP* 5.7 2.4 - - - +
39B ASN* 3.6 13.2 + - - +
56B PHE* 3.4 22.5 - - - +
57B ASP 5.6 2.6 + - - -
71B SER* 3.2 21.7 + - - -
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Residues in contact with GLY1996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972A LYS* 4.7 0.9 - - - -
1992A MET 3.3 9.5 + - - -
1993A VAL 3.7 5.2 - - - -
1994A LEU 3.0 1.4 - - - -
1995A GLN* 1.3 77.7 - - - +
1997A SER* 1.3 57.2 + - - +
1999A GLY 5.0 0.2 - - - -
2000A THR* 3.0 20.8 - - - +
37B PHE* 3.3 13.3 - - - -
38B ASP* 3.4 25.7 + - - -
39B ASN* 3.7 14.8 - - - +
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Residues in contact with SER1997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972A LYS* 3.5 24.8 - - - +
1976A LEU* 4.1 11.4 - - - +
1993A VAL 3.1 12.8 + - - -
1994A LEU* 2.8 12.3 + - - -
1996A GLY* 1.3 79.1 - - - +
1998A VAL* 1.3 64.2 + - - +
2000A THR* 3.7 1.8 - - - +
2006A PRO* 3.5 32.1 - - - +
2037A PHE* 3.6 23.2 - - - -
2041A CYS* 4.8 1.1 - - - -
2070A LEU* 4.6 0.3 - - - +
37B PHE* 3.4 6.7 - - - -
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Residues in contact with VAL1998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1994A LEU* 3.1 26.6 + - + +
1995A GLN* 4.7 1.6 - - - -
1997A SER* 1.3 80.7 - - - +
1999A GLY* 1.3 63.1 + - - +
2000A THR* 3.6 4.3 + - - +
2037A PHE* 5.4 0.2 - - + -
2041A CYS* 4.0 26.5 - - + -
2045A LEU* 5.0 0.2 - - + -
2063A LEU* 3.7 29.2 - - + +
2066A ASN* 3.5 15.9 - - + +
2067A TYR* 3.8 34.3 - - + +
2069A ARG* 5.7 1.9 + - - -
2070A LEU* 4.4 15.7 - - + +
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Residues in contact with GLY1999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1995A GLN* 3.1 39.5 + - - +
1997A SER 3.6 0.2 - - - -
1998A VAL* 1.3 82.0 - - - +
2000A THR* 1.3 63.7 + - - +
2001A THR* 3.5 10.2 - - - +
2063A LEU* 5.2 1.3 - - - -
2066A ASN* 3.5 20.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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