Contacts of the helix formed by residues 1835 - 1840 (chain X) in PDB entry 3SU8
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 THR1835 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1773X ASP 3.6 8.4 + - - -
1774X CYS* 3.4 23.1 - - - +
1775X ASP 3.4 11.7 - - - +
1776X THR 4.4 0.4 - - - +
1777X ILE* 4.2 4.5 - - - -
1832X ARG* 5.7 4.5 - - - +
1833X LEU 3.3 9.3 + - - +
1834X ASN* 1.3 73.0 - - - +
1836X LEU* 1.3 62.9 + - - +
1837X GLN* 3.6 6.9 + - - +
1838X HIS* 3.2 28.0 + - - +
1839X TYR* 3.3 21.5 - - - -
1885X HIS* 3.5 24.0 - - + +
1886X LEU* 5.9 1.1 - - + -
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Residues in contact with LEU1836 (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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1749X LEU* 4.5 8.3 - - + -
1751X LEU* 4.5 10.1 - - + -
1771X VAL* 3.8 24.5 - - + -
1772X LEU 3.5 21.8 - - - +
1773X ASP* 3.2 11.4 + - - +
1775X ASP* 3.2 11.5 + - + +
1777X ILE* 4.1 16.6 - - + -
1780X ALA* 4.1 22.0 - - + -
1805X VAL* 5.9 2.5 - - + -
1817X LEU* 4.7 4.9 - - + -
1835X THR* 1.3 73.6 - - - +
1837X GLN* 1.4 58.0 + - - +
1839X TYR 3.5 1.9 + - - -
1840X LYS 3.1 7.3 + - - -
1841X VAL* 3.0 59.1 + - + +
1847X VAL* 5.7 2.5 - - + -
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Residues in contact with GLN1837 (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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66A ARG* 4.3 8.8 + - - +
1745X GLU* 4.1 15.3 - - - +
1747X ARG* 5.4 1.5 - - - -
1773X ASP* 2.9 50.1 + - + +
1774X CYS* 5.1 2.7 + - - -
1835X THR* 3.3 5.6 - - - +
1836X LEU* 1.4 74.5 - - - +
1838X HIS* 1.4 63.0 + - - +
1840X LYS* 3.3 22.6 + - + +
1841X VAL 5.7 0.7 - - - -
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Residues in contact with HIS1838 (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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66A ARG* 3.3 47.7 - - + +
1823X THR* 3.0 43.0 + - - -
1825X GLU* 2.8 39.7 + - + +
1832X ARG* 6.2 0.4 - - - -
1833X LEU 5.8 0.2 + - - -
1834X ASN* 3.0 31.3 + - + -
1835X THR* 3.2 29.5 + - - +
1836X LEU 3.3 0.2 - - - -
1837X GLN* 1.4 78.3 - - - +
1839X TYR* 1.3 69.8 + + - +
1840X LYS* 3.2 2.6 + - - +
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Residues in contact with TYR1839 (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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66A ARG* 5.2 0.9 - - - -
67A LEU* 3.3 37.3 - - + +
70A LEU* 3.6 25.8 - - + -
1777X ILE* 3.6 26.9 - - + -
1807X TRP* 3.4 10.4 - - + -
1817X LEU* 3.7 25.4 - - + -
1818X SER 2.9 16.0 + - - -
1821X ASP* 2.8 23.4 + - - -
1823X THR* 3.4 20.6 - - - -
1834X ASN* 3.4 21.7 + - + -
1835X THR 3.3 17.5 - - - -
1836X LEU* 3.5 2.7 + - - +
1837X GLN 3.4 0.2 - - - -
1838X HIS* 1.3 79.2 - + - +
1840X LYS* 1.4 67.0 + - - +
1841X VAL* 3.9 16.2 - - + -
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Residues in contact with LYS1840 (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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63A ASP* 3.0 53.6 + - + +
64A TYR* 4.8 20.2 - - + -
66A ARG* 4.8 18.4 - - + +
67A LEU* 5.2 0.4 - - + -
1807X TRP* 3.7 6.3 - - - -
1836X LEU 3.1 3.8 + - - -
1837X GLN* 3.3 19.2 + - + +
1838X HIS 3.2 4.8 - - - +
1839X TYR* 1.4 80.9 - - - +
1841X VAL* 1.3 62.2 + - - +
1842X PRO* 3.5 9.7 - - - +
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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
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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