Contacts of the helix formed by residues 1969 - 1981 (chain X) in PDB entry 3HM6
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 ASP1969 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1673X LYS* 2.7 19.7 + - - -
1967X ILE* 3.4 5.4 - - + +
1968X SER* 1.3 76.1 - - - +
1970X GLN* 1.3 64.5 + - - +
1971X ASP* 3.6 14.9 + - - +
1972X THR* 2.7 35.4 + - - +
1973X ILE* 3.4 25.2 + - - +
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Residues in contact with GLN1970 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968X SER* 3.3 19.3 + - - +
1969X ASP* 1.3 73.2 + - - +
1971X ASP* 1.3 58.3 + - - +
1973X ILE* 3.8 14.4 - - - +
1974X HIS* 2.7 36.9 + - - +
2057X ARG* 3.2 37.9 + - - +
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Residues in contact with ASP1971 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1673X LYS* 4.4 10.9 - - - +
1969X ASP* 3.3 16.9 + - - +
1970X GLN* 1.3 79.6 - - - +
1972X THR* 1.3 56.8 + - - +
1974X HIS* 3.5 2.7 - - - +
1975X ILE* 2.8 37.2 + - + +
2022X LEU* 3.7 30.2 - - + +
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Residues in contact with THR1972 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1672X PRO* 3.9 30.7 - - + +
1673X LYS* 3.1 21.6 + - - +
1967X ILE* 4.1 15.2 - - + +
1969X ASP* 2.7 31.9 + - - +
1970X GLN 3.3 0.4 - - - -
1971X ASP* 1.3 76.4 - - - +
1973X ILE* 1.3 58.0 + - - +
1975X ILE* 3.4 4.2 + - - +
1976X TRP* 2.9 58.4 + - + +
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Residues in contact with ILE1973 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1958X LEU* 5.2 2.9 - - + +
1959X ASP* 3.5 26.5 - - - +
1962X ALA* 3.6 31.0 - - + -
1967X ILE* 4.0 15.7 - - + +
1969X ASP 3.4 15.7 + - - +
1970X GLN* 3.4 29.1 + - - +
1971X ASP 3.4 0.2 - - - -
1972X THR* 1.3 73.6 - - - +
1974X HIS* 1.3 65.4 + - - +
1976X TRP* 3.2 12.6 + - + +
1977X LYS* 3.0 37.7 + - + +
2057X ARG* 3.8 11.2 - - - +
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Residues in contact with HIS1974 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1970X GLN 2.7 22.3 + - - +
1971X ASP* 3.5 8.1 - - - +
1973X ILE* 1.3 71.3 - - - +
1975X ILE* 1.3 66.8 + - + +
1977X LYS* 3.1 6.1 + - - +
1978X THR* 3.0 28.1 + - - -
2019X ALA 5.4 1.1 - - - -
2020X CYS* 2.9 32.4 + - - -
2021X THR 4.9 0.2 - - - -
2022X LEU* 3.8 33.3 - - + +
2046X LYS 5.5 1.6 - - - -
2049X VAL* 3.9 13.7 - - + -
2050X GLU* 5.0 11.4 - - + +
2053X TYR* 3.4 33.8 - + + -
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Residues in contact with ILE1975 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1673X LYS* 3.4 59.9 - - + +
1675X MET 4.7 0.2 - - - +
1971X ASP* 2.8 26.6 + - + +
1972X THR* 3.4 6.1 - - - +
1974X HIS* 1.3 76.7 - - + +
1976X TRP* 1.3 67.4 + - + +
1978X THR* 3.2 5.8 + - - -
1979X ASN* 3.0 45.9 + - - +
2022X LEU* 4.2 15.3 - - + -
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Residues in contact with TRP1976 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664X VAL* 3.6 28.0 - - + -
1668X VAL* 5.0 0.4 - - + -
1672X PRO* 2.8 44.7 + - + -
1675X MET* 3.6 36.5 - - + +
1676X LEU* 4.4 1.3 - - - +
1958X LEU* 3.7 46.9 - - + -
1961X GLN* 4.3 7.4 - - + -
1962X ALA* 3.8 26.2 - - + -
1967X ILE* 4.4 10.3 - - + -
1972X THR* 2.9 34.9 + - + +
1973X ILE* 3.2 14.8 + - + +
1975X ILE* 1.3 78.4 - - + +
1977X LYS* 1.3 53.8 + - - +
1979X ASN* 3.4 5.7 + - - +
1980X SER* 2.7 37.9 + - - -
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Residues in contact with LYS1977 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1955X PHE* 3.8 53.4 + - + +
1958X LEU* 3.7 20.9 - - + -
1959X ASP* 3.0 36.0 + - - -
1973X ILE* 3.0 26.9 + - + +
1974X HIS* 3.5 6.3 - - - +
1976X TRP* 1.3 73.7 - - - +
1978X THR* 1.3 64.2 + - - +
1980X SER* 3.2 2.6 + - - -
1981X LEU 3.1 18.9 + - - -
1982X PRO* 3.4 6.2 - - - +
2053X TYR* 3.9 37.9 + - + +
2057X ARG* 3.9 15.2 - - - +
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Residues in contact with THR1978 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974X HIS* 3.0 15.7 + - - -
1975X ILE* 3.5 10.8 - - - -
1977X LYS* 1.3 75.8 - - - +
1979X ASN* 1.3 63.2 + - - +
1982X PRO* 3.4 6.7 - - + +
1983X LEU* 2.8 57.1 + - + +
2020X CYS* 3.2 44.6 + - + +
2053X TYR* 2.8 21.8 + - - -
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Residues in contact with ASN1979 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1673X LYS 4.8 1.8 + - - -
1675X MET 3.0 21.5 + - - +
1676X LEU* 3.2 27.4 + - + +
1677X ARG* 3.8 12.1 - - - +
1975X ILE* 3.0 32.0 + - - +
1976X TRP 3.7 4.5 - - - +
1977X LYS 3.2 0.2 - - - -
1978X THR* 1.3 84.9 - - - +
1980X SER* 1.3 53.6 + - - +
1981X LEU 3.6 0.2 - - - -
1983X LEU* 4.6 13.2 - - - +
1984X ARG* 2.7 40.3 + - - +
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Residues in contact with SER1980 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1676X LEU* 3.5 17.0 - - - +
1687X LEU* 3.8 9.4 - - - +
1691X MET* 3.4 24.3 - - - +
1954X PHE* 3.5 25.5 - - - -
1955X PHE* 4.6 2.2 - - - -
1958X LEU* 3.5 15.6 - - - +
1976X TRP 2.7 20.8 + - - -
1977X LYS* 3.2 5.6 + - - -
1979X ASN* 1.3 79.6 - - - +
1981X LEU* 1.3 57.6 + - - +
1984X ARG* 3.5 14.5 - - - +
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Residues in contact with LEU1981 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1691X MET* 4.0 11.0 - - + -
1695X LEU* 3.5 30.7 - - + -
1951X VAL* 3.8 29.2 - - + -
1955X PHE* 3.7 27.1 - - + -
1977X LYS 3.1 8.4 + - - +
1979X ASN 3.6 1.4 - - - -
1980X SER* 1.3 80.3 - - - +
1982X PRO* 1.3 69.1 - - + +
1983X LEU 3.4 0.4 - - - -
1984X ARG* 3.9 0.4 - - - -
1985X PHE* 2.7 39.8 + - + +
1986X TRP* 3.3 24.1 + - + +
2052X TYR* 3.9 15.3 - - + +
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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