Contacts of the helix formed by residues 1825 - 1840 (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 SER1825 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1823B ALA 3.7 3.8 + - - -
1824B ILE* 1.3 74.8 - - - +
1826B ASP* 1.3 65.2 + - - +
1827B GLN* 3.0 8.9 + - - +
1828B ASP* 2.7 54.4 + - - -
1829B MET* 3.0 11.8 + - - +
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Residues in contact with ASP1826 (chain B).
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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1715B TYR* 6.3 2.0 - - - -
1824B ILE 3.6 3.0 + - - -
1825B SER* 1.3 71.8 - - - +
1827B GLN* 1.3 59.1 + - - +
1829B MET* 4.0 7.2 - - - +
1830B SER* 3.0 29.5 + - - -
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Residues in contact with GLN1827 (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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1825B SER* 3.0 7.5 - - - +
1826B ASP* 1.3 78.7 - - - +
1828B ASP* 1.3 68.1 + - - +
1830B SER* 3.7 4.7 + - - -
1831B ALA* 3.5 18.4 + - - +
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Residues in contact with ASP1828 (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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1711B LEU* 4.5 4.0 - - + +
1824B ILE* 4.1 14.0 - - + +
1825B SER* 2.7 29.7 + - - +
1827B GLN* 1.3 78.6 - - - +
1829B MET* 1.3 67.1 + - - +
1831B ALA* 3.2 9.0 + - - +
1832B TYR* 3.1 20.8 + - - +
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Residues in contact with MET1829 (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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1442B TRP* 4.5 2.9 - - + -
1711B LEU* 3.7 33.9 - - - +
1712B ALA* 4.3 3.8 - - - +
1715B TYR* 3.5 58.3 - - + -
1824B ILE* 4.2 12.3 - - + +
1825B SER 3.0 14.2 + - - +
1826B ASP* 4.1 8.3 - - - +
1828B ASP* 1.3 78.2 - - - +
1830B SER* 1.3 58.4 + - - +
1832B TYR* 3.2 10.2 + - + +
1833B LEU* 2.9 65.6 + - + +
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Residues in contact with SER1830 (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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1651A LEU* 4.7 20.2 - - - +
1400B GLU* 3.9 15.8 - - - +
1826B ASP 3.0 18.7 + - - -
1827B GLN* 4.0 5.8 - - - -
1828B ASP 3.3 0.2 - - - -
1829B MET* 1.3 77.9 - - - +
1831B ALA* 1.3 57.2 + - - +
1833B LEU* 4.5 10.3 - - - +
1834B ALA* 3.0 30.7 + - - +
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Residues in contact with ALA1831 (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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1477A ALA 5.2 4.7 - - - +
1478A ILE* 3.6 26.8 - - + +
1827B GLN 3.5 11.1 + - - +
1828B ASP* 3.2 12.3 + - - +
1829B MET 3.1 0.4 - - - -
1830B SER* 1.3 76.7 - - - +
1832B TYR* 1.3 60.7 + - - +
1834B ALA* 3.2 5.3 + - - +
1835B GLU* 2.9 31.4 + - - +
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Residues in contact with TYR1832 (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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1446B LEU* 3.4 36.7 + - + +
1710B PRO* 4.8 3.7 - - + +
1711B LEU* 3.3 56.7 + - + -
1712B ALA* 4.0 11.8 + - - +
1828B ASP 3.1 4.0 + - - +
1829B MET* 3.2 14.3 + - + +
1831B ALA* 1.3 79.6 - - - +
1833B LEU* 1.3 77.5 + - + +
1835B GLU* 3.0 43.9 - - - +
1836B GLN* 3.2 30.0 + - + +
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Residues in contact with LEU1833 (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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1399B MET* 3.5 13.0 - - + +
1400B GLU* 4.0 24.2 - - - +
1403B THR* 3.4 36.3 - - + +
1442B TRP* 4.6 0.4 - - + -
1446B LEU* 3.8 25.6 - - + -
1715B TYR* 5.9 0.2 - - + -
1829B MET* 2.9 53.9 + - + +
1830B SER* 4.0 7.6 - - - +
1832B TYR* 1.3 80.8 - - + +
1834B ALA* 1.3 57.7 + - - +
1836B GLN* 3.5 4.8 + - - +
1837B SER* 3.1 30.0 + - - -
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Residues in contact with ALA1834 (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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1478A ILE* 3.4 28.3 - - + +
1651A LEU* 4.2 3.6 - - + +
1400B GLU* 3.1 26.5 - - - +
1830B SER 3.0 16.4 + - - +
1831B ALA 3.2 1.5 + - - +
1833B LEU* 1.3 75.5 - - - +
1835B GLU* 1.3 59.9 + - - +
1837B SER* 2.9 18.3 + - - -
1838B ARG* 2.9 22.3 + - - +
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Residues in contact with GLU1835 (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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1478A ILE 3.8 14.4 + - - +
1479A THR* 4.1 27.2 - - - +
1490A LYS* 5.1 7.1 + - - -
1831B ALA 2.9 11.8 + - - +
1832B TYR* 3.0 41.2 - - - +
1834B ALA* 1.3 78.3 - - - +
1836B GLN* 1.3 74.9 + - + +
1838B ARG* 4.5 0.5 - - - +
1839B LEU* 3.3 27.7 + - - +
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Residues in contact with GLN1836 (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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1322B TYR* 5.6 0.4 + - - -
1396B GLN* 3.9 4.9 + - - +
1399B MET* 5.2 2.2 - - + -
1445B PHE 4.6 12.7 + - - -
1446B LEU* 4.3 21.0 + - + +
1448B TYR* 5.9 1.6 - - - +
1449B LYS* 4.2 21.9 - - - +
1832B TYR* 3.2 44.7 + - + +
1833B LEU 4.0 3.8 - - - +
1835B GLU* 1.3 90.5 - - + +
1837B SER* 1.3 61.1 + - - +
1839B LEU* 4.3 2.6 - - - +
1840B HIS* 3.1 52.8 + - - -
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Residues in contact with SER1837 (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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1396B GLN* 3.0 28.4 - - - +
1397B GLY 3.9 10.9 + - - -
1398B GLU* 5.1 0.2 - - - -
1399B MET* 3.6 20.0 + - - +
1400B GLU* 5.0 2.1 + - - -
1833B LEU 3.1 15.6 + - - -
1834B ALA* 2.9 17.5 + - - -
1836B GLN* 1.3 76.7 - - - +
1838B ARG* 1.3 63.8 + - - +
1839B LEU 3.2 1.6 - - - -
1840B HIS 3.4 0.5 - - - -
1841B LEU* 2.8 39.7 + - - +
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Residues in contact with ARG1838 (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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1478A ILE* 6.1 0.4 - - + -
1479A THR* 4.1 22.2 - - + -
1481A GLU* 6.0 0.2 - - - -
1655A VAL 5.9 2.7 - - - +
1656A LYS* 6.3 0.7 - - - -
1657A ASN* 3.6 33.4 + - - +
1397B GLY 5.8 1.1 - - - -
1834B ALA 2.9 17.1 + - - +
1835B GLU 4.5 0.4 - - - +
1837B SER* 1.3 81.5 + - - +
1839B LEU* 1.3 62.3 + - - +
1841B LEU* 3.7 9.1 - - - +
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Residues in contact with LEU1839 (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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1481A GLU* 4.6 17.9 - - - +
1489A ASP* 5.3 9.2 - - + +
1657A ASN* 5.5 5.1 + - - +
1835B GLU 3.3 18.3 + - - +
1836B GLN* 5.8 2.7 - - - +
1837B SER 3.2 0.6 - - - -
1838B ARG* 1.3 83.3 - - - +
1840B HIS* 1.3 88.2 + - + +
1841B LEU 3.3 2.9 + - - -
1842B SER 4.8 2.4 + - - -
1843B GLN* 4.5 4.8 + - - +
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Residues in contact with HIS1840 (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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1322B TYR* 3.5 35.8 - + + -
1396B GLN* 2.8 29.2 - - - +
1448B TYR* 4.7 15.4 - + - -
1836B GLN* 3.1 41.7 + - - -
1837B SER 3.4 2.6 + - - -
1839B LEU* 1.3 100.1 - - + +
1841B LEU* 1.3 60.4 + - - +
1842B SER 3.4 2.0 - - - -
1843B GLN* 2.9 38.0 + - - +
1844B PHE* 3.8 5.5 - - - -
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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