Contacts of the helix formed by residues 1960 - 1981 (chain C) in PDB entry 6AJL
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 THR1960 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1930C PHE* 3.6 13.5 - - + -
1958C ILE* 5.1 5.6 - - + +
1959C LEU* 1.3 73.7 - - - +
1961C PRO* 1.3 77.4 - - - +
1962C ILE* 3.5 20.9 - - - +
1963C GLU* 2.5 29.9 + - - +
1964C VAL 2.9 17.5 + - - -
2026C HIS* 4.4 5.0 - - + -
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Residues in contact with PRO1961 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926C LEU 3.4 20.9 - - - +
1927C HIS 3.2 22.7 - - - +
1929C GLN 2.9 26.2 - - - +
1930C PHE* 3.4 30.5 - - + -
1960C THR* 1.3 87.2 - - - +
1962C ILE* 1.3 57.4 + - - +
1964C VAL* 3.0 4.6 + - + +
1965C ALA* 2.9 23.6 + - - +
2013C PHE* 3.8 14.0 - - + -
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Residues in contact with ILE1962 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1960C THR* 3.5 13.7 - - - +
1961C PRO* 1.3 73.5 - - - +
1963C GLU* 1.3 60.6 + - - +
1965C ALA* 3.0 2.3 + - - +
1966C ILE* 2.7 48.3 + - + +
2013C PHE* 3.6 37.9 - - + +
2026C HIS* 3.3 49.4 - - + +
2027C HIS* 3.8 10.1 - - + +
2030C LEU* 4.1 13.9 - - + -
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Residues in contact with GLU1963 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1958C ILE 3.7 6.8 - - - +
1959C LEU* 3.3 28.1 - - + +
1960C THR* 2.5 48.3 + - - +
1962C ILE* 1.3 82.6 - - - +
1964C VAL* 1.3 63.0 + - - +
1966C ILE* 3.1 19.8 + - + +
1967C GLU* 3.2 17.7 + - - +
2026C HIS* 3.5 35.6 + - + +
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Residues in contact with VAL1964 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926C LEU* 6.3 2.9 - - + -
1929C GLN* 3.1 40.4 - - + +
1930C PHE 3.9 0.4 - - - -
1931C LYS* 3.7 47.5 + - + +
1959C LEU* 3.8 9.2 - - + +
1960C THR 2.9 14.6 + - - +
1961C PRO 3.2 7.6 - - - +
1963C GLU* 1.3 76.3 - - - +
1965C ALA* 1.3 62.9 + - - +
1967C GLU* 3.5 5.6 + - - +
1968C ASP* 3.4 16.7 + - + +
33D VAL* 5.1 7.9 - - + -
34D PRO* 5.3 5.6 - - + +
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Residues in contact with ALA1965 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926C LEU* 5.5 7.0 - - + -
1961C PRO 2.9 11.8 + - - +
1962C ILE 3.6 6.5 - - - +
1964C VAL* 1.3 74.9 - - - +
1966C ILE* 1.3 66.1 + - - +
1967C GLU 3.1 2.2 - - - -
1968C ASP* 2.8 20.7 + - + +
1969C MET* 3.0 17.2 + - - +
2009C VAL* 4.3 21.5 - - + -
2013C PHE* 3.8 24.0 - - + -
2030C LEU* 4.6 3.1 - - + -
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Residues in contact with ILE1966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1962C ILE* 2.7 30.3 + - + +
1963C GLU* 3.1 10.1 + - + +
1965C ALA* 1.3 71.8 - - - +
1967C GLU* 1.3 62.1 + - + +
1969C MET* 3.6 3.0 + - - +
1970C GLN* 3.2 30.1 + - - +
2026C HIS* 3.4 36.6 - - + +
2029C LYS* 4.2 22.7 - - + +
2030C LEU* 3.6 32.8 - - + +
2033C CYS* 3.9 19.9 - - - -
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Residues in contact with GLU1967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1931C LYS* 2.7 36.3 + - - +
1933C LYS* 4.2 18.2 + - - +
1959C LEU* 3.8 20.3 - - + +
1963C GLU 3.2 11.1 + - - +
1964C VAL 3.7 8.1 - - - +
1965C ALA 3.1 0.8 - - - -
1966C ILE* 1.3 77.3 - - + +
1968C ASP* 1.3 64.3 + - - +
1970C GLN* 3.2 14.8 + - - +
1971C LYS* 2.9 28.0 + - - +
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Residues in contact with ASP1968 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964C VAL* 3.4 10.5 + - + +
1965C ALA* 2.8 13.1 + - + +
1967C GLU* 1.3 77.3 - - - +
1969C MET* 1.3 66.7 + - + +
1971C LYS* 4.1 11.4 - - - +
1972C LYS* 3.3 15.1 + - - +
2009C VAL* 6.3 1.8 - - + -
34D PRO 4.3 4.5 - - - +
35D THR* 2.9 37.0 + - - -
36D VAL* 3.2 25.9 + - + +
37D PHE* 3.5 18.4 - - + -
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Residues in contact with MET1969 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1965C ALA 3.0 12.1 + - - +
1966C ILE 3.8 5.8 - - - +
1968C ASP* 1.3 77.9 - - - +
1970C GLN* 1.3 58.3 + - - +
1972C LYS* 3.1 2.9 + - - +
1973C THR* 2.8 35.8 + - - +
2006C PRO* 4.5 2.7 - - + -
2009C VAL* 4.8 11.4 - - + -
2030C LEU* 4.1 19.5 - - + -
2033C CYS* 4.2 16.2 - - + +
2034C PHE* 3.6 36.8 - - + -
2037C PHE* 3.6 40.4 - - + -
37D PHE* 3.5 23.3 - - + -
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Residues in contact with GLN1970 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966C ILE* 3.2 21.7 + - - +
1967C GLU* 3.2 16.1 + - - +
1969C MET* 1.3 79.6 - - - +
1971C LYS* 1.3 63.1 + - - +
1973C THR* 3.8 5.7 - - - +
1974C GLN* 3.1 24.3 + - - +
2029C LYS* 3.5 33.1 - - - +
2033C CYS* 4.2 17.0 - - - -
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Residues in contact with LYS1971 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967C GLU 2.9 16.5 + - - +
1968C ASP* 4.1 11.2 - - - +
1970C GLN* 1.3 77.0 - - - +
1972C LYS* 1.3 53.9 + - + +
1974C GLN* 3.0 7.0 + - - +
1975C GLU* 2.7 49.3 + - - +
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Residues in contact with LYS1972 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968C ASP 3.3 4.3 + - - +
1969C MET 3.1 3.1 + - - +
1971C LYS* 1.3 76.7 - - - +
1973C THR* 1.3 67.3 + - - +
1975C GLU* 3.3 29.7 + - - +
1976C LEU* 2.8 23.1 + - - +
1992C MET* 6.0 0.8 - - - +
1993C VAL* 3.6 22.7 + - + +
1996C GLY 5.0 0.2 + - - -
1997C SER* 3.5 24.2 - - - +
2037C PHE* 4.2 6.5 - - + -
35D THR* 5.7 0.4 - - - -
37D PHE* 3.5 55.8 - - + +
38D ASP 3.9 18.4 + - - -
39D ASN* 4.7 4.8 + - - +
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Residues in contact with THR1973 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1969C MET 2.8 24.3 + - - -
1970C GLN* 3.8 6.5 - - - -
1972C LYS* 1.3 71.6 - - - +
1974C GLN* 1.3 58.3 + - + +
1976C LEU* 3.1 9.0 + - - +
1977C ALA* 2.8 26.0 + - + +
2033C CYS 4.2 2.9 + - - -
2036C ASP* 3.3 33.4 - - + +
2037C PHE* 3.3 35.9 + - - +
2040C ARG* 3.6 15.7 - - + +
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Residues in contact with GLN1974 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1970C GLN 3.1 15.6 + - - +
1971C LYS* 3.0 6.5 + - - +
1973C THR* 1.3 74.5 - - + +
1975C GLU* 1.3 57.7 + - - +
1977C ALA* 3.9 18.0 - - + +
1978C PHE* 2.7 49.1 + - - +
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Residues in contact with GLU1975 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1971C LYS* 2.7 35.5 + - + +
1972C LYS* 3.3 37.2 + - - +
1974C GLN* 1.3 72.3 - - - +
1976C LEU* 1.3 58.9 + - - +
1978C PHE* 3.6 5.7 + - - +
1979C ALA* 3.2 25.3 + - - +
1989C MET* 6.4 0.2 - - - -
1992C MET* 4.5 11.3 - - - +
1993C VAL* 3.5 25.5 - - + +
39D ASN 5.4 2.1 - - - +
41D ALA* 5.4 4.9 + - - +
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Residues in contact with LEU1976 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972C LYS 2.8 16.9 + - - +
1973C THR 3.4 6.7 - - - +
1975C GLU* 1.3 69.8 - - - +
1977C ALA* 1.3 57.9 + - - +
1979C ALA* 4.4 1.2 - - - +
1980C THR* 2.5 40.4 + - - -
1990C LEU* 4.7 2.0 - - + +
1993C VAL* 3.8 15.0 - - + -
1994C LEU* 3.8 22.2 - - + +
1997C SER* 3.7 22.0 - - - +
2037C PHE* 3.9 13.5 - - + -
2040C ARG* 4.1 11.9 - - + +
2041C CYS* 3.4 40.6 - - - +
2044C ALA* 4.0 16.6 - - + +
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Residues in contact with ALA1977 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1973C THR* 2.8 20.1 + - + +
1974C GLN* 3.7 21.5 - - + +
1976C LEU* 1.3 73.5 - - - +
1978C PHE* 1.3 61.2 + - - +
1980C THR* 4.3 4.5 - - - -
1981C HIS* 3.2 36.5 + - + +
2040C ARG* 4.0 22.8 - - - +
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Residues in contact with PHE1978 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974C GLN* 2.7 34.7 + - - +
1975C GLU* 3.9 5.4 - - - +
1976C LEU 3.1 0.2 - - - -
1977C ALA* 1.3 78.3 - - - +
1979C ALA* 1.3 69.8 + - + +
1980C THR 3.2 0.9 + - - -
1981C HIS* 3.3 10.1 + - - -
1982C GLN* 3.5 44.7 + - + +
1989C MET* 6.2 2.5 - - + -
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Residues in contact with ALA1979 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1975C GLU 3.2 15.6 + - - +
1976C LEU 4.4 0.2 - - - +
1978C PHE* 1.3 82.4 - - + +
1980C THR* 1.3 64.9 + - - +
1982C GLN* 3.9 26.0 + - - +
1985C ALA* 5.3 2.9 - - - +
1986C ASP 5.1 2.8 + - - -
1989C MET* 4.5 6.5 - - + -
1990C LEU* 3.7 44.0 - - + +
1993C VAL* 4.3 10.3 - - + -
2047C LYS* 5.6 0.2 - - - +
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Residues in contact with THR1980 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1976C LEU 2.5 23.6 + - - -
1977C ALA* 3.8 5.1 - - - -
1979C ALA* 1.3 78.7 - - - +
1981C HIS* 1.3 66.1 + - + +
1982C GLN 2.7 20.5 + - - +
1985C ALA* 5.2 0.3 - - - +
1990C LEU* 3.7 6.0 - - - +
2040C ARG 4.5 1.4 + - - -
2043C ASP* 3.8 31.2 - - + +
2044C ALA* 3.2 21.7 + - - +
2047C LYS* 3.9 33.4 - - + -
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Residues in contact with HIS1981 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977C ALA* 3.2 27.8 + - + +
1978C PHE* 3.7 2.9 - - - +
1980C THR* 1.3 86.5 - - + +
1982C GLN* 1.3 58.2 + - - +
1983C ASP* 4.4 1.1 + - - +
2040C ARG* 5.5 4.7 + - - -
2043C ASP* 5.0 10.3 + - + +
2047C LYS* 5.5 2.7 - - - +
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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) + - + + + + + -
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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