Contacts of the helix formed by residues 2032 - 2038 (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 PRO2032 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2014X GLN* 5.7 5.8 - - - +
2031X SER* 1.4 93.2 - - - +
2033X ILE* 1.3 61.1 + - + +
2034X ASN* 3.2 17.0 - - - +
2035X LYS* 2.9 44.1 + - + +
2036X LEU 3.4 4.3 + - - -
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Residues in contact with ILE2033 (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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1734X LEU 3.8 22.2 - - - +
1735X ASN* 4.7 4.7 - - - +
1736X ASP* 2.9 26.2 - - - +
1914X ILE* 3.4 28.3 - - + -
1919X LEU* 5.4 0.4 - - + -
1922X LEU* 4.4 12.3 - - + -
2011X VAL* 4.8 2.9 - - + -
2031X SER 4.0 6.7 - - - +
2032X PRO* 1.3 70.8 - - + +
2034X ASN* 1.3 64.3 + - - +
2035X LYS 3.2 0.2 - - - -
2036X LEU* 3.4 20.8 + - + -
2037X LEU* 3.1 35.0 + - + +
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Residues in contact with ASN2034 (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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2011X VAL* 3.6 39.5 - - + +
2014X GLN* 3.5 24.1 + - + +
2015X THR* 3.4 26.3 + - - +
2018X ASP* 2.9 24.4 + - - +
2032X PRO* 3.2 13.2 + - - +
2033X ILE* 1.3 78.2 - - - +
2035X LYS* 1.3 75.2 + - - +
2037X LEU 3.3 0.3 + - - -
2038X TYR* 2.8 36.7 + - - +
2042X ILE* 4.3 2.6 - - - +
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Residues in contact with LYS2035 (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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2018X ASP* 2.9 40.5 + - - +
2031X SER* 4.7 12.6 - - - +
2032X PRO* 2.9 35.6 + - + +
2034X ASN* 1.3 90.4 + - - +
2036X LEU* 1.3 60.0 + - - +
2039X ALA* 3.3 24.1 + - - +
2042X ILE* 4.2 11.3 - - + +
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Residues in contact with LEU2036 (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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1914X ILE* 4.6 4.3 - - + -
1919X LEU* 4.3 26.2 - - + -
1923X LEU* 4.9 3.1 - - - +
2031X SER* 4.3 23.1 - - - +
2032X PRO 3.4 1.2 + - - -
2033X ILE* 3.4 39.0 + - + +
2034X ASN 3.2 0.2 - - - -
2035X LYS* 1.3 81.2 - - - +
2037X LEU* 1.3 66.6 + - + +
2038X TYR 3.5 0.5 + - - -
2039X ALA* 3.6 12.9 + - - +
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Residues in contact with LEU2037 (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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1734X LEU* 3.4 49.1 - - + +
1919X LEU* 4.7 10.5 - - + +
1922X LEU* 3.8 21.1 - - + +
1923X LEU* 3.4 36.7 - - + +
1926X LYS* 3.1 33.0 + - + +
2011X VAL* 4.6 5.8 - - + -
2033X ILE* 3.1 24.4 + - + +
2036X LEU* 1.3 81.0 - - + +
2038X TYR* 1.3 71.8 + - + +
2039X ALA 3.6 0.6 + - - -
2040X ARG* 5.4 0.3 + - - +
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Residues in contact with TYR2038 (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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1734X LEU* 3.6 21.7 - - + +
1926X LYS* 3.6 32.0 + - + +
1929X LEU* 5.6 1.7 - - - +
1930X GLN* 3.4 23.0 + - - -
1933X VAL* 4.3 16.1 - - + +
2011X VAL* 3.9 20.9 - - + -
2012X ILE* 3.8 13.5 - - + +
2015X THR* 3.1 43.1 - - + +
2034X ASN* 2.8 18.7 + - - +
2035X LYS 4.0 0.2 - - - -
2037X LEU* 1.3 83.7 - - + +
2039X ALA* 1.3 62.3 + - - +
2040X ARG 3.3 2.2 - - - -
2041X ASP* 3.7 16.8 - - + +
2042X ILE* 3.0 32.1 + - + +
2045X TYR* 4.8 0.9 - + - -
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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