Contacts of the helix formed by residues 1878 - 1890 (chain A) in PDB entry 3RYT
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 ARG1878 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1874A ALA 4.2 0.2 - - - -
1875A ARG* 3.1 12.4 + - - +
1876A ARG 3.0 20.1 + - - -
1877A GLN* 1.3 82.1 - - - +
1879A LEU* 1.3 62.4 + - - +
1880A ARG* 3.4 3.1 - - - +
1881A SER* 3.7 23.6 + - - +
1882A LYS* 3.8 6.4 + - - +
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Residues in contact with LEU1879 (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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1359A LEU* 3.7 11.9 - - + -
1362A LYS* 4.1 14.4 - - + -
1364A HIS* 4.8 1.1 - - + -
1365A PHE* 3.4 57.7 - - + +
1868A LEU* 3.7 23.3 - - + -
1874A ALA* 2.9 30.6 + - + +
1877A GLN* 2.8 20.5 + - + +
1878A ARG* 1.3 69.2 - - - +
1880A ARG* 1.3 65.3 + - - +
1881A SER 3.1 2.6 + - - -
1882A LYS* 3.1 8.0 + - - +
1883A LEU* 3.0 19.1 + - + -
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Residues in contact with ARG1880 (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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1865A LEU* 4.9 6.4 - - + +
1868A LEU* 3.7 30.5 + - + +
1869A GLU* 4.9 8.3 - - + -
1874A ALA 3.7 3.9 + - - +
1875A ARG* 5.8 1.8 - - - -
1878A ARG* 3.4 1.3 - - - -
1879A LEU* 1.3 80.2 - - - +
1881A SER* 1.3 56.8 + - - +
1883A LEU* 3.4 9.5 - - - +
1884A GLU* 3.1 31.2 + - + +
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Residues in contact with SER1881 (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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1878A ARG* 3.7 21.6 + - - +
1879A LEU 3.1 0.6 - - - -
1880A ARG* 1.3 75.8 - - - +
1882A LYS* 1.3 65.1 + - - +
1883A LEU 3.0 1.6 - - - -
1884A GLU* 3.1 10.3 + - - +
1885A GLN* 3.0 22.7 + - - +
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Residues in contact with LYS1882 (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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1355A LEU* 4.9 8.8 - - + +
1359A LEU* 3.9 21.9 - - + +
1878A ARG 3.8 5.7 + - - +
1879A LEU* 3.1 11.6 + - - +
1881A SER* 1.3 79.2 - - - +
1883A LEU* 1.3 60.5 + - - +
1885A GLN* 3.6 7.9 + - - +
1886A VAL* 3.2 22.5 + - - +
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Residues in contact with LEU1883 (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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1359A LEU* 3.7 17.9 - - + +
1365A PHE* 4.8 1.8 - - + -
1865A LEU* 4.3 10.3 - - + -
1868A LEU* 4.2 20.0 - - + -
1879A LEU* 3.0 12.9 + - + +
1880A ARG* 3.4 14.6 - - - +
1881A SER 3.0 0.2 - - - -
1882A LYS* 1.3 75.6 - - - +
1884A GLU* 1.3 65.6 + - - +
1886A VAL* 3.1 12.0 + - - +
1887A VAL* 3.1 21.5 + - + +
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Residues in contact with GLU1884 (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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1865A LEU* 4.7 22.8 - - + +
1880A ARG 3.1 16.9 + - - +
1881A SER* 3.1 10.3 + - - +
1883A LEU* 1.3 76.2 - - - +
1885A GLN* 1.3 61.6 + - - +
1887A VAL* 4.0 5.6 - - - +
1888A ASP* 3.3 36.3 + - - +
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Residues in contact with GLN1885 (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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1355A LEU* 3.6 12.9 - - + +
1881A SER 3.0 15.3 + - - +
1882A LYS* 3.8 9.0 - - - +
1883A LEU 3.2 0.2 - - - -
1884A GLU* 1.3 77.8 - - - +
1886A VAL* 1.3 61.1 + - - +
1888A ASP* 4.6 2.4 - - - +
1889A THR* 2.7 34.3 + - - +
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Residues in contact with VAL1886 (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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1352A SER* 4.2 5.4 - - - +
1355A LEU* 3.5 28.9 - - + +
1356A PHE* 4.6 15.3 - - + +
1359A LEU* 4.5 9.9 - - + -
1854A TYR* 4.2 3.8 - - - -
1882A LYS 3.2 13.4 + - - +
1883A LEU* 3.1 12.8 + - - +
1885A GLN* 1.3 78.3 - - - +
1887A VAL* 1.3 63.8 + - + +
1889A THR* 4.2 1.0 - - - -
1890A MET* 3.5 22.2 + - - +
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Residues in contact with VAL1887 (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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1854A TYR* 3.3 32.2 + - + +
1857A ILE* 5.6 10.5 - - + +
1858A ALA* 6.3 4.0 - - + -
1861A LYS* 5.9 9.2 - - + -
1865A LEU* 5.7 9.4 - - + -
1883A LEU* 3.1 18.7 + - + +
1884A GLU* 4.0 5.8 - - - +
1886A VAL* 1.3 76.0 - - + +
1888A ASP* 1.3 75.7 + - - +
1890A MET* 3.3 7.6 + - - +
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Residues in contact with ASP1888 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1884A GLU* 3.3 22.9 + - - +
1885A GLN* 4.6 2.4 - - - +
1887A VAL* 1.3 83.4 - - - +
1889A THR* 1.3 66.6 + - - +
1890A MET 3.3 4.2 + - - +
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Residues in contact with THR1889 (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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1348A ASN* 3.9 9.4 - - - +
1351A LYS* 4.5 9.9 - - + +
1352A SER* 3.5 29.8 - - - +
1355A LEU* 3.9 8.7 - - + +
1885A GLN* 2.7 24.6 + - - +
1886A VAL 4.2 0.2 - - - -
1887A VAL 3.3 0.6 - - - -
1888A ASP* 1.3 80.8 - - - +
1890A MET* 1.3 66.0 + - - +
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Residues in contact with MET1890 (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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1348A ASN* 4.1 11.8 - - - +
1349A VAL* 5.5 7.1 - - + +
1352A SER* 3.4 23.3 - - - +
1854A TYR* 3.2 42.6 - - + +
1886A VAL 3.5 12.0 + - - +
1887A VAL 3.3 4.6 + - - -
1888A ASP 3.3 7.4 - - - +
1889A THR* 1.3 85.3 - - - +
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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