Contacts of the helix formed by residues 2041 - 2059 (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 ASP2041 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926X LYS* 2.6 37.0 + - - -
1930X GLN* 3.2 22.7 + - - +
2038X TYR* 3.2 14.6 + - + +
2040X ARG* 1.3 88.2 + - - +
2042X ILE* 1.3 61.0 + - - +
2044X ARG* 2.9 38.2 + - - +
2045X TYR* 3.0 37.4 + - + -
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Residues in contact with ILE2042 (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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2015X THR* 4.0 23.1 - - + +
2018X ASP* 3.8 43.1 - - + +
2019X ALA* 4.2 1.0 - - - +
2034X ASN* 4.3 3.8 - - - +
2035X LYS* 4.2 22.2 - - + +
2038X TYR* 3.0 32.5 + - + +
2039X ALA* 4.5 2.0 - - - +
2041X ASP* 1.3 74.9 - - - +
2043X PRO* 1.3 70.6 - - + +
2045X TYR* 3.3 8.8 + - - +
2046X LYS* 3.0 32.7 + - - +
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Residues in contact with PRO2043 (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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2039X ALA 3.2 21.5 - - - +
2040X ARG 3.4 10.3 - - - +
2042X ILE* 1.3 94.7 - - + +
2044X ARG* 1.3 58.7 + - - +
2046X LYS* 3.6 19.5 - - + +
2047X ARG* 3.4 19.4 - - - +
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Residues in contact with ARG2044 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934X ASP* 3.3 37.9 + - - +
1938X GLN* 3.9 17.0 - - - +
2040X ARG 4.6 4.7 - - - +
2041X ASP* 2.9 31.7 + - - +
2043X PRO* 1.3 79.5 - - - +
2045X TYR* 1.3 83.5 + - + +
2047X ARG* 3.2 19.4 + - - +
2048X MET* 3.3 25.6 + - + +
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Residues in contact with TYR2045 (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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1930X GLN* 2.8 16.0 + - - -
1933X VAL* 3.7 9.4 - - - +
1934X ASP* 2.7 25.3 + - - -
1937X PHE* 3.5 45.8 - + + -
1941X LEU* 4.3 2.9 - - + +
2015X THR* 4.1 16.2 - - + -
2019X ALA* 3.4 21.5 - - + -
2038X TYR* 4.8 1.8 - + - -
2041X ASP* 3.0 36.0 + - + -
2042X ILE* 3.3 4.7 + - - +
2044X ARG* 1.3 100.4 - - - +
2046X LYS* 1.3 56.2 + - - +
2048X MET* 3.2 24.2 + - + +
2049X VAL* 2.9 30.5 + - - +
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Residues in contact with LYS2046 (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* 5.5 1.7 - - - -
2018X ASP 3.6 10.5 - - - -
2019X ALA* 3.4 24.8 + - - +
2021X THR 3.2 23.8 + - - +
2022X LEU* 3.8 13.1 + - + +
2023X ALA 3.7 22.4 + - - -
2024X ASP* 4.1 10.9 - - - +
2042X ILE* 3.0 26.8 + - - +
2043X PRO* 3.6 16.6 - - + +
2044X ARG 3.2 0.2 - - - -
2045X TYR* 1.3 74.5 - - - +
2047X ARG* 1.3 59.7 + - + +
2049X VAL* 3.3 3.2 + - - +
2050X GLU* 3.0 28.1 + - - +
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Residues in contact with ARG2047 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2043X PRO 3.4 16.6 - - - +
2044X ARG* 3.4 11.0 - - - +
2046X LYS* 1.3 75.5 - - - +
2048X MET* 1.3 61.8 + - + +
2050X GLU* 3.5 20.7 + - - +
2051X ARG* 3.0 35.9 + - + +
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Residues in contact with MET2048 (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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1937X PHE* 4.0 7.6 - - + +
1938X GLN* 3.7 42.2 - - + +
1941X LEU* 4.0 24.3 - - + +
2044X ARG* 3.3 27.1 + - + +
2045X TYR* 3.2 34.0 + - + +
2047X ARG* 1.3 77.4 - - + +
2049X VAL* 1.3 56.2 + - - +
2051X ARG* 3.4 8.7 + - - +
2052X TYR* 3.0 29.7 + - - +
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Residues in contact with VAL2049 (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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1941X LEU* 4.0 17.3 - - + -
1974X HIS* 3.9 11.2 - - + -
2019X ALA* 3.3 28.3 - - + +
2020X CYS* 4.0 18.6 - - - -
2045X TYR 2.9 21.2 + - - +
2046X LYS 3.6 6.1 - - - +
2047X ARG 3.3 0.2 - - - -
2048X MET* 1.3 74.6 - - - +
2050X GLU* 1.3 62.2 + - - +
2052X TYR* 3.2 8.2 + - - +
2053X TYR* 3.1 59.8 + - + +
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Residues in contact with GLU2050 (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* 5.0 12.5 - - + +
2046X LYS 3.0 16.8 + - - +
2047X ARG* 3.6 24.6 - - - +
2048X MET 3.4 0.2 - - - -
2049X VAL* 1.3 76.6 - - - +
2051X ARG* 1.3 62.7 + - - +
2053X TYR* 3.7 5.6 + - - +
2054X ALA* 3.2 22.4 + - - +
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Residues in contact with ARG2051 (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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1943X THR* 3.3 38.6 + - - +
2047X ARG* 3.0 23.3 + - + +
2048X MET* 3.6 9.2 - - - +
2050X GLU* 1.3 75.4 - - - +
2052X TYR* 1.3 54.0 + - - +
2054X ALA* 3.2 8.5 + - - +
2055X ASP* 2.7 36.4 + - - +
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Residues in contact with TYR2052 (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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1698X PHE* 6.0 1.7 - - - -
1940X ILE 3.7 19.2 + - - -
1941X LEU* 3.4 42.6 - - + +
1942X SER 4.0 12.3 - - - -
1943X THR* 4.1 8.5 + - - -
1947X VAL* 5.5 4.9 - - + +
1948X PRO* 5.4 4.7 - - - +
1951X VAL* 4.0 7.1 - - - +
1955X PHE* 4.8 0.2 - + - -
1981X LEU* 3.9 23.3 - - + +
1982X PRO* 5.6 3.1 - - + -
1986X TRP* 4.8 7.4 + + - -
2048X MET 3.0 15.1 + - - +
2049X VAL* 3.2 10.5 + - - +
2051X ARG* 1.3 76.0 - - - +
2053X TYR* 1.3 84.3 + + - +
2055X ASP* 3.3 3.3 + - + +
2056X ILE* 3.1 55.2 + - + +
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Residues in contact with TYR2053 (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* 3.5 31.4 - + - -
1974X HIS* 3.4 55.0 - + + -
1977X LYS* 3.9 27.4 + - + +
1978X THR* 2.8 32.1 + - - -
1982X PRO* 3.5 14.2 - - + +
2020X CYS* 4.4 0.3 - - - +
2049X VAL* 3.1 23.9 + - + +
2050X GLU* 4.2 4.5 - - - +
2052X TYR* 1.3 93.2 - + - +
2054X ALA* 1.3 57.4 + - - +
2056X ILE* 3.5 6.5 + - - +
2057X ARG* 3.1 28.5 + - - +
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Residues in contact with ALA2054 (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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2050X GLU 3.2 12.9 + - - +
2051X ARG* 3.2 12.4 + - - +
2053X TYR* 1.3 76.5 - - - +
2055X ASP* 1.3 64.3 + - - +
2057X ARG* 3.4 7.4 + - - +
2058X GLN* 3.1 26.6 + - - +
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Residues in contact with ASP2055 (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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11X UNX 2.6 27.3 - - - -
1942X SER 4.7 1.0 - - - +
1943X THR* 3.2 50.4 - - + +
1945X ARG 4.9 0.7 - - - +
1947X VAL* 3.6 17.5 - - - +
2051X ARG* 2.7 14.9 + - - +
2052X TYR* 3.3 5.2 + - + +
2054X ALA* 1.3 70.2 - - - +
2056X ILE* 1.3 60.9 + - - +
2058X GLN* 3.3 6.4 + - - +
2059X THR* 2.6 35.5 + - - +
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Residues in contact with ILE2056 (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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1947X VAL* 4.0 18.4 - - + -
1951X VAL* 3.4 26.2 - - + +
1952X LYS* 2.6 52.4 + - + +
1955X PHE* 3.7 40.2 - - + -
1956X ASP* 5.3 0.2 - - - +
1977X LYS* 5.9 0.4 - - - +
2052X TYR* 3.1 43.2 + - + +
2053X TYR 3.7 4.5 - - - +
2054X ALA 3.3 0.2 - - - -
2055X ASP* 1.3 76.3 - - + +
2057X ARG* 1.3 52.1 + - - +
2059X THR* 3.1 17.3 + - - -
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Residues in contact with ARG2057 (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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1952X LYS* 2.8 18.4 + - - +
1955X PHE* 6.4 0.2 - - - -
1956X ASP* 4.7 2.0 - - - +
1959X ASP* 3.0 43.9 + - - +
1970X GLN* 3.2 34.5 + - - +
1973X ILE* 3.8 16.2 - - - +
1977X LYS* 3.9 8.0 - - - +
2053X TYR 3.1 17.2 + - - +
2054X ALA* 3.7 8.3 - - - +
2056X ILE* 1.3 77.3 - - - +
2058X GLN* 1.3 60.1 + - + +
2059X THR 4.0 0.5 - - - +
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Residues in contact with GLN2058 (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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2054X ALA 3.1 18.2 + - - +
2055X ASP* 3.8 6.5 - - - +
2057X ARG* 1.3 75.5 - - + +
2059X THR* 1.3 65.5 + - + +
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Residues in contact with THR2059 (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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11X UNX 3.4 24.9 - - - -
1947X VAL* 3.9 21.7 - - + +
1952X LYS* 3.3 26.3 + - - +
2055X ASP* 2.6 34.2 + - - +
2056X ILE* 3.1 13.2 + - - -
2057X ARG 4.0 0.7 - - - +
2058X GLN* 1.3 81.6 - - - +
2060X VAL* 1.3 70.4 + - - +
2061X PRO* 3.4 2.6 - - - +
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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