Contacts of the helix formed by residues 1681 - 1688 (chain B) 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 LEU1681 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485B SER 3.4 18.6 - - - +
1486B LEU* 3.5 22.1 - - - +
1488B GLU* 4.2 28.9 - - + +
1491B LEU* 3.3 31.0 - - + -
1677B TYR 4.6 11.2 + - - +
1678B LEU* 4.4 11.2 - - - +
1679B THR 3.1 0.8 - - - -
1680B ARG* 1.3 78.6 - - - +
1682B LEU* 1.3 62.7 + - - +
1683B ALA 2.9 6.0 + - - -
1684B THR* 3.1 7.7 + - - -
1685B LYS* 3.0 20.0 + - - +
1795B SER* 5.7 2.5 - - - +
1799B LEU* 4.4 21.8 - - + -
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Residues in contact with LEU1682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283B MET* 4.4 22.2 - - + +
1286B LEU* 4.1 11.9 - - + +
1287B GLU* 3.9 37.5 - - + +
1290B VAL* 4.2 12.2 - - + +
1294B CYS* 4.0 4.9 - - - -
1678B LEU 3.3 23.6 - - - +
1679B THR* 3.6 8.9 + - - +
1681B LEU* 1.3 73.3 - - - +
1683B ALA* 1.3 60.7 + - - +
1685B LYS* 3.5 10.5 - - + -
1686B GLY* 2.8 27.2 + - - -
1799B LEU* 3.9 22.7 - - + -
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Residues in contact with ALA1683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290B VAL* 4.8 10.0 - - + +
1293B GLU* 6.2 3.1 - - + -
1294B CYS* 4.0 8.0 - - - -
1484B TYR* 5.6 9.0 - - + -
1679B THR 3.8 7.5 + - - +
1680B ARG* 3.9 23.1 - - - +
1681B LEU 2.9 0.4 - - - -
1682B LEU* 1.3 80.3 - - - +
1684B THR* 1.3 56.6 + - - +
1687B THR* 2.7 33.9 + - - -
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Residues in contact with THR1684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466B ILE* 5.8 4.5 - - + -
1469B GLN* 4.3 18.3 + - + +
1470B MET* 4.6 3.6 - - + -
1484B TYR* 3.2 44.4 + - - +
1485B SER 4.8 1.6 + - - -
1486B LEU* 4.5 25.8 - - + +
1680B ARG 5.1 3.1 + - - -
1681B LEU* 3.1 6.7 + - - -
1683B ALA* 1.3 75.5 - - - +
1685B LYS* 1.3 64.8 + - - +
1686B GLY 3.3 0.7 - - - -
1687B THR* 3.9 6.7 - - + -
1688B LEU* 3.3 31.0 + - + +
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Residues in contact with LYS1685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486B LEU* 4.4 14.3 - - + +
1681B LEU 3.0 17.6 + - - +
1682B LEU* 3.2 15.4 + - + -
1684B THR* 1.3 79.1 - - - +
1686B GLY* 1.3 56.2 + - - +
1688B LEU 4.6 0.2 - - - -
1689B GLN* 2.9 32.7 + - - +
1799B LEU* 4.4 19.5 - - + -
1800B TYR* 4.8 11.2 + - + +
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Residues in contact with GLY1686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294B CYS* 3.7 22.1 - - - +
1298B PHE* 5.5 0.3 - - - +
1682B LEU 2.8 14.7 + - - -
1685B LYS* 1.3 76.2 - - - +
1687B THR* 1.3 66.9 + - - +
1688B LEU 3.5 0.4 - - - -
1689B GLN* 3.1 20.4 - - - +
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Residues in contact with THR1687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294B CYS* 3.9 14.0 - - - -
1297B ALA* 3.5 22.8 - - + +
1298B PHE* 3.5 48.6 - - + +
1301B LEU* 4.4 18.6 - - + -
1469B GLN* 4.5 11.6 - - + +
1683B ALA 2.7 24.0 + - - -
1684B THR* 3.7 7.6 + - + -
1686B GLY* 1.3 80.7 - - - +
1688B LEU* 1.3 60.9 + - + +
1689B GLN 3.2 2.3 + - - -
1690B LYS* 4.1 1.9 + - - +
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Residues in contact with LEU1688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1301B LEU* 6.0 2.7 - - + -
1462B LEU* 5.5 0.2 - - + -
1465B ALA* 5.4 3.4 - - + +
1466B ILE* 4.4 22.0 - - + -
1469B GLN* 6.5 0.9 - - + -
1486B LEU* 6.3 2.7 - - + -
1684B THR* 3.3 19.8 + - + +
1685B LYS 4.6 1.1 - - - -
1687B THR* 1.3 78.4 - - + +
1689B GLN* 1.3 64.0 + - - +
1690B LYS 3.0 5.0 + - - -
1691B PHE* 3.3 26.7 + - + +
1692B VAL* 3.3 20.8 + - + +
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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