Contacts of the helix formed by residues 2025 - 2046 (chain A) in PDB entry 3PZD
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 GLU2025 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752A ASP 4.8 6.6 - - - +
1753A LYS* 4.4 9.6 - - + +
1958A PHE* 3.9 22.3 - - + -
1959A ASP* 5.0 10.4 + - - +
2023A THR* 2.9 14.4 + - - +
2024A SER* 1.3 88.7 - - - +
2026A VAL* 1.3 64.4 + - - +
2027A VAL* 3.1 3.6 - - - -
2028A ASP* 2.8 43.5 + - + +
2029A VAL* 2.9 18.5 + - + +
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Residues in contact with VAL2026 (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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2004A ALA* 4.0 16.4 - - + -
2008A ASN* 3.5 30.1 - - + -
2009A THR 3.6 9.0 - - - +
2010A TYR* 3.7 20.4 - - + +
2023A THR* 3.3 35.4 - - + +
2024A SER 3.5 2.4 + - - -
2025A GLU* 1.3 76.1 - - - +
2027A VAL* 1.3 63.3 + - + +
2029A VAL* 3.7 1.1 + - - -
2030A ALA* 3.1 22.9 + - - +
1440B ILE* 3.7 21.3 - - + -
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Residues in contact with VAL2027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1756A GLU* 4.8 12.6 - - - +
2025A GLU 2.9 2.2 + - - -
2026A VAL* 1.3 77.5 - - + +
2028A ASP* 1.3 63.3 + - - +
2030A ALA* 3.1 6.4 + - - +
2031A LYS* 2.8 35.1 + - + +
1440B ILE* 4.7 13.9 - - + +
1441B THR* 3.8 27.9 - - + +
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Residues in contact with ASP2028 (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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1753A LYS* 3.3 50.1 + - - +
1754A ALA* 4.7 6.8 - - + +
1789A TYR* 4.4 1.9 + - - -
1958A PHE* 4.5 12.3 - - + -
2025A GLU* 2.8 40.3 + - + +
2027A VAL* 1.3 78.4 - - - +
2029A VAL* 1.3 62.4 + - - +
2031A LYS* 3.2 7.7 + - - +
2032A LEU* 3.0 22.9 + - - +
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Residues in contact with VAL2029 (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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1958A PHE* 3.6 42.2 - - + -
1960A VAL* 6.0 1.1 - - + -
1973A LEU* 4.3 12.8 - - + -
1975A VAL* 4.5 7.1 - - + +
2010A TYR* 3.7 14.8 - - + -
2023A THR* 4.7 11.2 - - + -
2025A GLU* 2.9 22.9 + - + +
2026A VAL 3.8 4.3 - - - +
2028A ASP* 1.3 75.5 - - - +
2030A ALA* 1.3 63.0 + - - +
2032A LEU* 3.2 4.2 + - - +
2033A MET* 3.0 50.0 + - + +
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Residues in contact with ALA2030 (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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2010A TYR* 3.8 20.2 - - + -
2026A VAL 3.1 16.0 + - - +
2027A VAL 3.6 3.4 - - - +
2029A VAL* 1.3 78.7 - - - +
2031A LYS* 1.3 58.3 + - - +
2033A MET 3.3 0.9 + - - -
2034A LYS* 2.9 31.2 + - - +
1437B LEU* 3.6 19.7 - - + +
1440B ILE* 4.1 13.2 - - + -
1441B THR* 3.8 17.0 - - + -
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Residues in contact with LYS2031 (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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1756A GLU* 3.6 31.2 + - + +
1758A ARG* 4.0 13.5 - - - +
1789A TYR* 3.7 12.9 + - + +
2027A VAL* 2.8 18.1 + - + +
2028A ASP* 3.4 12.3 - - - +
2030A ALA* 1.3 72.9 - - - +
2032A LEU* 1.3 56.6 + - - +
2034A LYS* 3.5 17.7 + - - +
2035A ALA* 3.0 28.2 + - - +
1438B ASN* 4.9 4.2 + - - -
1441B THR* 3.8 22.1 + - + +
1443B SER* 2.8 32.3 + - - -
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Residues in contact with LEU2032 (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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1789A TYR* 3.5 55.4 + - + +
1790A CYS* 3.9 4.0 - - - -
1956A THR* 3.3 37.7 - - + +
1958A PHE* 4.0 15.3 - - + -
1975A VAL* 4.0 16.4 - - + -
2028A ASP 3.0 11.6 + - - +
2029A VAL* 3.2 8.3 + - - +
2031A LYS* 1.3 73.4 - - - +
2033A MET* 1.3 65.7 + - - +
2035A ALA* 3.3 1.4 + - - +
2036A TYR* 3.1 36.0 + - + -
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Residues in contact with MET2033 (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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1973A LEU* 4.0 4.9 - - + -
1975A VAL* 3.8 19.5 - - + -
1980A VAL* 3.8 31.6 - - + -
1996A TYR* 4.2 15.7 - - + +
2002A PHE* 3.4 27.1 - - + -
2010A TYR* 3.1 34.1 - - + +
2012A ILE* 5.8 0.4 - - + -
2029A VAL* 3.0 34.4 + - + +
2030A ALA 3.8 4.0 - - - +
2032A LEU* 1.3 75.8 - - - +
2034A LYS* 1.3 58.0 + - - +
2036A TYR* 3.3 2.8 + - - +
2037A ILE* 2.8 33.8 + - + +
1437B LEU* 3.9 11.9 - - + -
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Residues in contact with LYS2034 (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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2030A ALA 2.9 17.9 + - - +
2031A LYS* 3.6 21.9 - - - +
2033A MET* 1.3 74.4 - - - +
2035A ALA* 1.3 57.5 + - - +
2037A ILE* 3.3 3.4 + - - +
2038A SER* 2.8 46.4 + - - -
1434B MET* 3.9 31.9 - - + +
1437B LEU* 3.8 19.7 - - + +
1438B ASN* 3.7 31.9 - - - +
1441B THR* 6.1 0.7 - - + -
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Residues in contact with ALA2035 (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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1741A MET* 4.5 10.8 - - + -
1789A TYR* 4.0 14.8 - - + -
1790A CYS* 3.7 18.4 - - - -
2031A LYS* 3.0 18.9 + - - +
2032A LEU 3.3 6.0 + - - +
2034A LYS* 1.3 77.3 - - - +
2036A TYR* 1.3 61.4 + - - +
2038A SER* 2.5 25.5 + - - -
2039A MET* 3.0 15.8 + - - +
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Residues in contact with TYR2036 (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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1789A TYR 4.0 1.5 + - - -
1790A CYS* 3.4 19.3 - - + -
1791A PHE* 2.7 38.3 + - - -
1792A LEU* 3.9 13.6 - - + +
1954A GLY 3.5 14.4 + - - -
1955A SER* 5.3 0.2 - - - -
1956A THR* 5.3 1.5 + - - -
1975A VAL* 3.7 20.5 + - + -
1976A SER 3.3 22.2 - - - +
1977A ALA* 3.4 26.0 - - - +
1996A TYR* 3.7 13.5 - - + +
2032A LEU* 3.1 42.1 + - + -
2033A MET 3.6 6.5 - - - +
2035A ALA* 1.3 73.4 - - - +
2037A ILE* 1.3 66.2 + - - +
2039A MET* 2.9 15.9 + - - +
2040A ILE* 3.1 18.1 + - - +
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Residues in contact with ILE2037 (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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1996A TYR* 3.6 40.2 - - + -
2002A PHE* 4.0 11.2 - - + -
2033A MET 2.8 25.2 + - - +
2034A LYS 3.9 3.6 - - - +
2036A TYR* 1.3 71.4 - - - +
2038A SER* 1.3 62.3 + - - +
2040A ILE* 3.1 18.3 + - - +
2041A VAL* 3.3 12.7 + - + +
1430B LEU* 3.8 34.3 - - + +
1433B LEU* 4.5 11.0 - - + -
1434B MET* 3.8 19.1 - - + -
1437B LEU* 3.7 23.8 - - + -
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Residues in contact with SER2038 (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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2034A LYS* 2.8 28.8 + - - -
2035A ALA* 2.5 26.2 + - - -
2037A ILE* 1.3 73.1 - - - +
2039A MET* 1.3 71.3 + - - +
2041A VAL* 3.3 6.8 + - - +
2042A LYS* 2.9 27.5 + - - +
1434B MET* 3.9 22.8 - - - -
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Residues in contact with MET2039 (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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1741A MET* 4.9 19.7 - - - +
1790A CYS* 5.2 0.9 - - - -
1792A LEU* 3.7 43.6 - - + +
2035A ALA 3.0 13.2 + - - +
2036A TYR 2.9 10.5 + - - +
2038A SER* 1.3 98.2 + - - +
2040A ILE* 1.3 57.8 + - - +
2042A LYS* 3.9 34.7 - - + +
2043A LYS* 3.2 27.7 + - - +
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Residues in contact with ILE2040 (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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1977A ALA 3.4 24.0 - - - +
1978A ASP* 4.5 5.8 - - + -
1996A TYR* 3.6 28.0 - - + -
2036A TYR 3.1 12.6 + - - +
2037A ILE* 3.1 10.7 + - - +
2039A MET* 1.3 75.9 - - - +
2041A VAL* 1.3 58.8 + - - +
2043A LYS* 3.4 5.8 + - + +
2044A ARG* 3.0 28.4 + - + +
1427B MET* 5.4 5.2 - - + -
1430B LEU* 4.1 20.9 - - + -
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Residues in contact with VAL2041 (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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2037A ILE 3.3 16.1 + - - +
2038A SER* 3.6 10.1 - - - +
2040A ILE* 1.3 74.8 - - - +
2042A LYS* 1.3 63.1 + - - +
2044A ARG* 3.4 2.3 + - - +
2045A TYR* 3.3 48.6 + - + +
1427B MET* 4.2 16.8 - - - +
1430B LEU* 4.3 23.8 - - + -
1431B GLU* 4.2 21.5 - - - +
1434B MET* 4.6 11.0 - - + -
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Residues in contact with LYS2042 (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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2038A SER 2.9 17.5 + - - +
2039A MET* 4.1 34.1 - - + +
2041A VAL* 1.3 76.7 - - - +
2043A LYS* 1.3 62.9 + - - +
2045A TYR* 3.5 5.2 + - - +
2046A SER* 3.2 26.2 + - - -
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Residues in contact with LYS2043 (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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1792A LEU 5.8 3.8 - - - +
2039A MET 3.2 18.0 + - - +
2040A ILE* 3.6 8.3 - - + +
2041A VAL 3.3 0.2 - - - -
2042A LYS* 1.3 80.2 - - - +
2044A ARG* 1.3 60.8 + - - +
2046A SER* 3.0 22.1 + - - +
1408B HIS* 3.2 39.7 + - + +
1409B LYS 5.0 2.0 - - - +
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Residues in contact with ARG2044 (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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2040A ILE* 3.0 17.9 + - + +
2041A VAL 3.8 4.7 - - - +
2042A LYS 3.3 0.2 - - - -
2043A LYS* 1.3 76.6 - - - +
2045A TYR* 1.3 65.5 + - + +
2046A SER 4.2 3.8 - - - +
1408B HIS* 3.8 14.8 - - + +
1427B MET* 4.1 26.7 - - + -
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Residues in contact with TYR2045 (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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2041A VAL* 3.3 44.9 + - + +
2042A LYS* 4.3 4.7 - - - +
2043A LYS 3.3 0.4 - - - -
2044A ARG* 1.3 77.9 - - + +
2046A SER* 1.3 63.4 + - - +
1427B MET* 3.7 28.2 - - + +
1431B GLU* 5.2 4.6 + - - -
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Residues in contact with SER2046 (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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2042A LYS* 3.2 18.7 + - - -
2043A LYS* 3.0 23.8 + - - +
2044A ARG 4.2 3.6 - - - +
2045A TYR* 1.3 80.9 - - - +
2047A THR* 1.3 69.2 + - - +
1408B HIS* 3.9 7.8 + - - +
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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