Contacts of the helix formed by residues 1731 - 1743 (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 ASP1731 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1425B LYS* 5.2 1.2 + - - -
1729B ILE 3.5 8.7 - - - +
1730B HIS* 1.3 87.3 - - + +
1732B SER* 1.3 65.2 + - - +
1733B ASP* 3.5 22.6 + - - +
1734B VAL* 3.6 27.4 + - + +
1735B ARG* 3.8 7.8 + - - -
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Residues in contact with SER1732 (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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1730B HIS 3.0 8.0 + - - -
1731B ASP* 1.3 72.1 + - - +
1733B ASP* 1.3 68.0 + - - +
1734B VAL 3.2 1.1 - - - -
1735B ARG* 3.5 14.7 + - - +
1736B HIS* 3.1 28.4 + - - +
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Residues in contact with ASP1733 (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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1425B LYS* 3.4 15.8 + - - +
1731B ASP* 3.2 16.8 - - - +
1732B SER* 1.3 83.2 + - - +
1734B VAL* 1.3 64.3 + - - +
1736B HIS* 3.6 6.7 + - - +
1737B THR* 3.2 25.5 + - - -
1784B THR* 4.4 16.6 - - - +
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Residues in contact with VAL1734 (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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1423B HIS* 5.7 2.2 - - + -
1424B PRO* 3.6 30.5 - - + -
1425B LYS* 3.9 22.0 - - + +
1729B ILE* 5.3 8.5 - - + -
1731B ASP* 3.6 25.1 + - + +
1732B SER 3.2 0.6 - - - -
1733B ASP* 1.3 77.4 - - - +
1735B ARG* 1.3 67.3 + - + +
1736B HIS 3.2 0.2 + - - -
1737B THR* 3.2 4.2 + - - -
1738B TRP* 2.9 58.1 + - + +
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Residues in contact with ARG1735 (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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1720B LEU* 4.6 5.7 - - + +
1721B ASP* 3.7 24.1 + - - +
1724B ALA* 3.2 34.5 - - + +
1725B ASP* 2.8 29.3 + - - -
1729B ILE* 3.2 29.9 + - - -
1730B HIS 4.3 5.7 + - - -
1731B ASP 3.8 7.8 + - - -
1732B SER* 3.5 13.8 + - - +
1733B ASP 3.5 0.2 - - - -
1734B VAL* 1.3 79.8 - - + +
1736B HIS* 1.3 61.4 + - - +
1738B TRP* 3.5 12.6 + - + +
1739B LYS* 3.3 22.5 + - - +
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Residues in contact with HIS1736 (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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1732B SER 3.1 18.4 + - - +
1733B ASP* 3.7 10.3 - - - +
1734B VAL 3.1 0.2 - - - -
1735B ARG* 1.3 75.1 - - - +
1737B THR* 1.3 65.0 + - - +
1738B TRP 3.3 0.2 + - - -
1739B LYS* 3.4 4.9 + - - +
1740B SER* 3.1 32.0 + - - -
1781B SER 5.0 0.7 - - - -
1782B CYS 3.0 30.8 + - - -
1783B SER 4.6 0.9 - - - -
1784B THR* 4.0 21.7 + - - -
1808B LYS 5.1 0.2 + - - -
1811B VAL* 3.6 18.5 - - + +
1812B GLU* 4.7 13.1 - - + +
1815B TYR* 3.4 35.3 + + - -
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Residues in contact with THR1737 (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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1425B LYS* 3.2 47.2 - - + +
1426B LEU* 5.4 0.7 - - - -
1733B ASP 3.2 11.5 + - - -
1734B VAL 3.2 8.2 + - - -
1736B HIS* 1.3 77.9 + - - +
1738B TRP* 1.3 60.0 + - - +
1740B SER* 3.5 5.2 + - - -
1741B ASN* 2.9 43.1 + - - +
1782B CYS 5.5 0.9 - - - -
1783B SER* 6.5 1.1 - - - -
1784B THR* 3.9 17.3 + - - +
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Residues in contact with TRP1738 (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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1414B ILE* 4.0 33.2 - - + -
1418B LEU* 4.5 9.9 - - + -
1424B PRO* 2.9 31.6 + - + -
1425B LYS 4.5 5.2 - - - -
1427B LEU* 4.3 22.6 - - + +
1428B LEU* 4.5 14.5 - - + +
1720B LEU* 4.2 41.5 - - + -
1723B GLN* 4.7 2.9 - - + -
1724B ALA* 4.4 22.7 - - + -
1727B HIS* 5.5 0.9 - + - -
1729B ILE* 5.7 3.4 - - + -
1734B VAL* 2.9 46.9 + - + +
1735B ARG* 3.5 12.3 - - + +
1736B HIS 3.2 0.4 - - - -
1737B THR* 1.3 77.2 - - - +
1739B LYS* 1.3 64.7 + - - +
1741B ASN* 3.1 8.4 + - - +
1742B CYS* 3.1 29.0 + - - -
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Residues in contact with LYS1739 (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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1717B PHE* 3.2 36.2 - - + -
1720B LEU* 4.1 14.3 - - + +
1735B ARG 3.3 13.3 + - - +
1736B HIS* 3.4 2.9 + - - +
1738B TRP* 1.3 77.6 - - - +
1740B SER* 1.3 63.1 + - - +
1742B CYS* 3.0 12.7 + - - +
1743B LEU* 3.1 14.0 + - - +
1744B PRO* 3.2 4.2 - - - +
1815B TYR* 3.7 15.0 - - + -
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Residues in contact with SER1740 (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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1736B HIS* 3.1 17.4 + - - -
1737B THR* 3.7 7.2 - - - -
1738B TRP 3.2 0.2 - - - -
1739B LYS* 1.3 77.8 - - - +
1741B ASN* 1.3 59.1 + - - +
1742B CYS 3.1 0.2 - - - -
1744B PRO* 3.0 8.5 - - - +
1745B LEU* 3.0 38.2 + - - +
1782B CYS* 3.2 38.6 + - - +
1815B TYR* 2.8 22.6 + - - -
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Residues in contact with ASN1741 (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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1425B LYS 3.7 8.1 + - - -
1428B LEU* 3.0 27.2 - - + +
1429B ARG* 3.2 30.6 - - - +
1430B ARG* 3.9 7.6 + - - +
1737B THR* 2.9 41.5 + - - +
1738B TRP* 3.1 5.7 + - - +
1740B SER* 1.3 75.0 - - - +
1742B CYS* 1.3 57.7 + - - +
1745B LEU* 3.1 27.3 - - - +
1746B ARG* 2.8 30.8 + - - +
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Residues in contact with CYS1742 (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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1428B LEU* 3.3 30.3 - - - -
1439B LEU* 4.1 19.1 - - + +
1443B PHE* 3.8 22.7 - - + -
1716B MET* 5.5 2.9 - - + -
1717B PHE* 5.9 2.0 - - + -
1720B LEU* 3.6 24.7 - - + -
1738B TRP 3.1 18.9 + - - -
1739B LYS* 3.0 9.9 + - - +
1741B ASN* 1.3 80.0 - - - +
1743B LEU* 1.3 60.9 + - + +
1746B ARG* 3.2 26.4 - - - +
1747B PHE 4.8 0.5 + - - -
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Residues in contact with LEU1743 (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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1443B PHE* 3.8 25.6 - - + -
1447B LEU* 3.7 24.2 - - + -
1713B ILE* 3.5 35.9 - - + -
1717B PHE* 4.1 24.2 - - + -
1739B LYS 3.1 4.7 + - - +
1742B CYS* 1.3 78.6 - - + +
1744B PRO* 1.3 76.8 - - + +
1745B LEU 3.4 1.6 - - - -
1746B ARG 4.0 0.2 - - - -
1747B PHE* 3.1 32.4 + - + +
1748B TRP* 3.3 23.7 + - + +
1814B TYR* 4.5 7.0 - - + +
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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