Contacts of the helix formed by residues 1971 - 1992 (chain L) in PDB entry 6LTJ
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 LEU1971 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1862L LYS* 6.0 0.4 - - + -
1969L THR* 5.3 3.4 - - - +
1970L LEU* 1.3 72.0 - - - +
1972L ASP* 1.3 58.1 + - - +
1973L TRP* 3.4 34.3 - - + +
1974L GLN* 2.6 51.0 + - + +
1975L ASP 3.1 6.8 + - - -
457P GLN* 5.3 5.8 - - - +
461P ARG* 3.3 21.5 - - - +
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Residues in contact with ASP1972 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860L GLU* 3.5 31.7 - - + +
1861L SER 5.3 0.5 - - - +
1970L LEU 3.3 5.7 + - - -
1971L LEU* 1.3 71.1 - - - +
1973L TRP* 1.3 66.1 + - - +
1974L GLN 3.3 0.2 - - - -
1975L ASP* 3.5 14.2 - - + +
1976L SER* 2.9 31.4 + - - -
461P ARG* 4.9 5.1 - - + +
464P LYS* 4.6 15.8 + - - +
471P GLY* 5.7 3.3 + - - -
472P ASN* 4.9 11.4 + - - +
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Residues in contact with TRP1973 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1726L GLU 5.2 5.4 - - - -
1858L HIS* 4.0 25.0 - + + +
1860L GLU* 3.7 20.6 - - + -
1861L SER 3.1 28.0 - - - +
1862L LYS* 3.7 32.9 - - + +
1971L LEU* 3.1 37.4 - - + +
1972L ASP* 1.3 83.2 + - - +
1974L GLN* 1.3 89.6 + - + +
1976L SER* 3.4 2.1 + - - -
1977L LEU* 2.9 51.2 + - + +
2048L TRP* 4.7 8.7 - + - -
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Residues in contact with GLN1974 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1969L THR 4.2 2.3 - - - +
1970L LEU* 3.5 11.2 - - + +
1971L LEU* 2.6 50.6 + - + +
1973L TRP* 1.3 110.0 - - + +
1975L ASP* 1.3 54.0 + - - +
1977L LEU* 3.4 0.8 + - - -
1978L ALA* 2.9 31.2 + - - +
2048L TRP* 3.5 64.3 - - + +
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Residues in contact with ASP1975 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1970L LEU* 4.1 26.8 - - + +
1971L LEU 3.1 5.4 + - - +
1972L ASP* 3.5 18.3 - - + +
1973L TRP 3.2 0.2 - - - -
1974L GLN* 1.3 77.6 - - - +
1976L SER* 1.3 58.1 + - - +
1978L ALA* 3.3 5.3 + - - +
1979L LYS* 2.9 58.7 + - - +
188Q MET* 5.9 2.8 - - - +
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Residues in contact with SER1976 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430I LEU* 5.3 0.7 - - - +
1857L THR 4.5 2.6 - - - +
1858L HIS* 3.9 14.6 - - - -
1859L PHE* 4.8 1.9 + - - +
1860L GLU* 2.6 36.0 + - - -
1972L ASP 2.9 8.5 + - - -
1973L TRP 3.8 3.1 - - - -
1974L GLN 3.4 0.2 - - - -
1975L ASP* 1.3 78.1 + - - +
1977L LEU* 1.3 56.4 + - - +
1979L LYS* 3.3 9.7 + - - +
1980L ARG* 3.0 29.5 + - - +
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Residues in contact with LEU1977 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1723L CYS* 4.4 13.0 - - - -
1726L GLU* 3.5 47.1 - - + +
1727L ILE* 3.6 24.5 - - + -
1857L THR* 3.6 24.7 - - + +
1858L HIS* 4.4 8.0 - - + +
1973L TRP* 2.9 40.9 + - + +
1974L GLN* 3.8 4.7 - - - +
1976L SER* 1.3 77.1 - - - +
1978L ALA* 1.3 57.4 + - - +
1980L ARG* 3.3 1.6 + - + +
1981L CYS* 2.9 26.9 + - - +
2048L TRP* 4.8 1.6 - - + -
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Residues in contact with ALA1978 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1727L ILE* 4.1 10.5 - - - +
1970L LEU* 6.4 0.9 - - + -
1974L GLN 2.9 18.7 + - - +
1975L ASP* 3.8 7.0 - - - +
1977L LEU* 1.3 75.2 - - - +
1979L LYS* 1.3 66.3 + - - +
1981L CYS* 3.3 1.4 + - - +
1982L VAL* 2.9 30.3 + - + +
2048L TRP* 4.2 10.3 - - + -
2051L ASP* 5.8 1.1 - - - +
2052L CYS* 3.9 24.9 - - + -
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Residues in contact with LYS1979 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430I LEU* 4.0 5.5 - - + +
433I ALA* 3.6 41.9 + - + +
434I LEU* 4.5 20.0 + - + +
1975L ASP* 2.9 46.9 + - - +
1976L SER* 3.6 8.1 - - - +
1978L ALA* 1.3 76.1 - - - +
1980L ARG* 1.3 58.9 + - - +
1982L VAL* 3.4 4.9 + - - +
1983L CYS* 2.9 28.1 + - - +
188Q MET* 5.1 15.1 - - - +
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Residues in contact with ARG1980 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I THR 3.6 16.0 + - - -
430I LEU* 3.5 28.6 - - + +
1681L LEU* 3.8 14.6 - - - +
1684L SER* 3.1 28.1 + - - -
1685L THR* 2.6 33.1 + - - +
1688L LEU* 4.2 18.1 - - + +
1719L TYR* 5.4 5.8 - - + -
1723L CYS* 4.1 13.2 - - - -
1856L GLN 4.6 2.4 + - - -
1857L THR* 3.1 34.9 + - - +
1858L HIS* 5.7 0.4 - - - +
1976L SER 3.0 16.6 + - - +
1977L LEU* 3.7 4.7 - - + +
1978L ALA 3.2 0.2 - - - -
1979L LYS* 1.3 74.6 - - - +
1981L CYS* 1.3 64.2 + - - +
1983L CYS* 3.2 1.9 + - - +
1984L VAL* 3.0 29.0 + - + +
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Residues in contact with CYS1981 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1720L PHE* 3.6 17.4 - - - -
1723L CYS* 3.5 30.5 - - + -
1724L LEU* 3.8 9.2 - - - -
1727L ILE* 3.6 15.3 - - + -
1977L LEU 2.9 16.0 + - - +
1978L ALA* 3.3 3.3 + - - +
1980L ARG* 1.3 75.6 - - - +
1982L VAL* 1.3 57.4 + - - +
1984L VAL* 3.3 2.3 + - - +
1985L SER* 3.0 26.5 + - - -
2052L CYS* 4.7 1.1 - - - -
2056L LEU* 3.6 30.5 - - - -
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Residues in contact with VAL1982 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I ALA* 4.9 15.3 - - + +
1978L ALA* 2.9 22.1 + - + +
1979L LYS* 3.9 5.6 - - - +
1981L CYS* 1.3 76.3 - - - +
1983L CYS* 1.3 58.3 + - - +
1985L SER* 2.9 7.8 + - - -
1986L ASN* 2.9 29.0 + - + +
2052L CYS* 4.1 19.3 - - + -
2055L MET* 3.5 44.4 - - + -
2056L LEU* 4.0 4.7 - - + -
2059L ASN* 4.3 10.8 - - - +
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Residues in contact with CYS1983 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430I LEU* 3.9 27.8 - - + -
432I THR* 3.0 31.0 - - - +
433I ALA* 4.7 4.0 - - + -
1688L LEU* 4.4 14.1 - - + -
1692L ASN* 3.1 22.6 - - - +
1979L LYS 2.9 18.3 + - - +
1980L ARG 3.2 5.6 + - - +
1982L VAL* 1.3 77.9 - - - +
1984L VAL* 1.3 58.1 + - + +
1986L ASN* 3.4 3.0 + - - -
1987L THR* 2.9 31.1 + - - -
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Residues in contact with VAL1984 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688L LEU* 3.8 25.8 - - + -
1716L LEU* 3.6 22.2 - - + +
1719L TYR* 4.2 14.4 - - + -
1720L PHE* 3.6 33.9 - - + +
1723L CYS* 4.4 6.1 - - - -
1980L ARG* 3.0 22.9 + - + +
1981L CYS* 3.8 4.0 - - - +
1983L CYS* 1.3 74.2 - - - +
1985L SER* 1.3 64.1 + - - +
1987L THR* 3.1 7.9 + - - -
1988L ILE* 3.0 25.7 + - + +
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Residues in contact with SER1985 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1720L PHE* 3.4 32.7 - - - -
1981L CYS 3.0 11.5 + - - -
1982L VAL* 2.9 8.1 + - - -
1984L VAL* 1.3 76.9 - - - +
1986L ASN* 1.3 57.6 + - - +
1988L ILE* 3.3 5.5 + - - +
1989L ARG* 2.9 27.9 + - - +
2056L LEU* 3.4 15.7 - - - +
2059L ASN* 2.7 37.1 + - - +
2063L THR* 4.8 1.0 + - - -
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Residues in contact with ASN1986 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I ALA 5.5 3.8 + - - +
439I TYR* 2.8 28.7 + - - +
440I LYS* 3.5 24.4 - - - +
1692L ASN* 2.9 24.3 + - - +
1982L VAL* 2.9 21.0 + - + +
1983L CYS* 3.8 4.3 - - - +
1985L SER* 1.3 74.6 + - - +
1987L THR* 1.3 61.3 + - - +
1989L ARG* 4.0 13.0 - - - +
1990L SER* 2.9 42.0 + - - -
2059L ASN* 3.9 11.6 - - - +
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Residues in contact with THR1987 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688L LEU* 4.4 10.5 + - + +
1691L ILE* 3.4 29.9 - - + +
1692L ASN* 2.9 24.3 + - - +
1695L LEU* 3.5 9.3 - - + +
1716L LEU* 3.5 33.0 - - + -
1983L CYS* 2.9 21.0 + - - -
1984L VAL* 3.1 12.4 + - - -
1986L ASN* 1.3 77.9 - - - +
1988L ILE* 1.3 56.1 + - - +
1991L LEU* 3.0 24.3 + - + +
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Residues in contact with ILE1988 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1713L LEU* 5.1 4.0 - - + -
1716L LEU* 4.3 29.6 - - + +
1717L VAL* 4.8 4.0 - - + +
1720L PHE* 3.9 33.7 - - + -
1984L VAL* 3.0 13.2 + - + +
1985L SER* 3.7 7.2 - - - +
1987L THR* 1.3 74.4 - - - +
1989L ARG* 1.3 65.5 + - - +
1991L LEU* 3.1 9.4 + - - +
1992L SER* 3.0 17.8 + - - -
2001L MET* 3.6 22.8 - - + +
2007L LEU* 3.8 31.4 - - + -
2011L LEU* 5.6 2.2 - - + -
2063L THR* 4.0 10.5 - - + +
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Residues in contact with ARG1989 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440I LYS* 3.3 33.9 - - - +
441I ARG 2.5 32.3 + - - +
442I SER* 3.9 8.9 - - - +
443I LYS* 3.9 10.1 - - - +
1985L SER 2.9 17.6 + - - +
1986L ASN* 3.3 13.2 + - - +
1988L ILE* 1.3 76.8 - - - +
1990L SER* 1.3 59.2 + - - +
1992L SER* 2.3 31.3 + - - -
1993L PHE* 3.2 18.6 - - + -
2058L GLU* 3.8 8.1 + - - +
2059L ASN* 3.1 32.8 + - + +
2062L VAL* 3.7 31.9 - - + +
2063L THR* 3.4 19.7 + - - +
2106L LEU* 6.3 0.2 - - - +
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Residues in contact with SER1990 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439I TYR 4.4 1.6 + - - -
441I ARG* 3.8 18.0 + - - +
1692L ASN* 4.2 3.2 + - - -
1695L LEU* 3.6 36.6 - - - +
1696L TYR* 5.5 1.4 + - - -
1701L ILE* 4.1 6.8 - - - +
1986L ASN* 2.9 33.5 + - - -
1989L ARG* 1.3 75.8 - - - +
1991L LEU* 1.3 61.8 + - - +
1993L PHE* 3.2 26.7 + - - +
1994L VAL 4.1 1.9 + - - -
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Residues in contact with LEU1991 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1691L ILE* 5.9 0.9 - - + -
1695L LEU* 3.6 26.9 - - + +
1704L PHE* 3.9 19.1 - - + +
1706L LEU* 4.0 28.7 - - + -
1712L LEU* 4.7 3.8 - - + -
1713L LEU* 4.7 6.7 - - + -
1716L LEU* 3.6 29.8 - - + -
1987L THR* 3.0 16.2 + - + +
1988L ILE* 3.1 10.3 + - - +
1990L SER* 1.3 78.0 - - - +
1992L SER* 1.3 61.5 + - - +
1993L PHE 3.0 1.7 + - - -
1994L VAL* 3.3 4.7 + - - -
1997L ASN* 2.9 42.8 - - - +
2001L MET* 3.8 8.5 - - + -
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Residues in contact with SER1992 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1988L ILE 3.0 11.0 + - - -
1989L ARG* 2.3 28.0 + - - +
1991L LEU* 1.3 76.6 - - - +
1993L PHE* 1.3 59.3 + - - +
1994L VAL 3.6 5.5 + - - +
1997L ASN* 4.9 0.7 - - - -
1998L ASP* 4.9 7.2 + - - +
2001L MET* 3.6 15.9 - - - -
2063L THR* 4.0 21.2 - - - -
2066L ASN* 3.2 43.5 + - - +
2067L ILE* 4.4 3.1 - - - -
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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
------------------------------------------------------------
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