Contacts of the helix formed by residues 1731 - 1741 (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 ASP1731 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1425A LYS* 5.6 0.5 + - - -
1729A ILE* 3.2 8.8 - - + +
1730A HIS* 1.3 75.7 - - - +
1732A SER* 1.3 64.6 + - - +
1733A ASP* 3.1 30.9 + - - +
1734A VAL* 3.1 38.6 + - + +
1735A ARG* 3.7 5.8 + - - +
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Residues in contact with SER1732 (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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1730A HIS 3.0 7.6 + - - -
1731A ASP* 1.3 72.6 + - - +
1733A ASP* 1.3 75.2 + - - +
1735A ARG* 3.5 14.2 + - - +
1736A HIS* 3.0 27.3 + - - +
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Residues in contact with ASP1733 (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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1425A LYS* 3.7 20.6 + - - +
1731A ASP* 3.1 19.9 + - - +
1732A SER* 1.3 87.8 + - - +
1734A VAL* 1.3 65.2 + - - +
1736A HIS* 3.5 6.7 + - - +
1737A THR* 3.2 24.6 + - - -
1784A THR* 4.2 15.7 - - - +
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Residues in contact with VAL1734 (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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1423A HIS* 6.3 1.8 - - + -
1424A PRO* 3.7 28.9 - - + -
1425A LYS* 4.8 12.5 - - + +
1729A ILE* 3.7 21.3 - - + -
1731A ASP* 3.1 34.3 + - + +
1732A SER 3.1 0.8 - - - -
1733A ASP* 1.3 77.3 - - + +
1735A ARG* 1.3 60.4 + - + +
1736A HIS 3.0 0.2 - - - -
1737A THR* 2.9 20.6 + - - -
1738A TRP* 3.1 44.3 + - + +
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Residues in contact with ARG1735 (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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1720A LEU* 5.3 2.2 - - + +
1721A ASP* 3.5 30.3 + - - +
1724A ALA* 3.6 26.4 - - + +
1725A ASP* 2.7 33.2 + - - +
1729A ILE* 3.0 29.2 + - + +
1730A HIS* 4.7 4.7 + - - +
1731A ASP 3.7 2.8 + - - -
1732A SER* 3.5 16.9 + - - +
1734A VAL* 1.3 79.5 - - + +
1736A HIS* 1.3 60.3 + - - +
1737A THR 3.2 0.2 - - - -
1738A TRP* 3.8 15.9 - - + +
1739A LYS* 3.1 42.6 + - - +
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Residues in contact with HIS1736 (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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1732A SER 3.0 19.9 + - - +
1733A ASP* 3.5 8.1 - - - +
1734A VAL 3.0 0.2 - - - -
1735A ARG* 1.3 79.6 - - - +
1737A THR* 1.3 57.7 + - - +
1739A LYS* 3.7 1.5 + - - +
1740A SER* 3.3 22.4 + - - -
1782A CYS 3.5 23.5 + - - -
1783A SER 5.3 0.4 - - - -
1784A THR* 3.2 24.2 - - + +
1811A VAL* 3.7 22.3 - - + +
1812A GLU* 4.0 19.3 - - + +
1815A TYR* 3.6 38.2 - + + -
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Residues in contact with THR1737 (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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1425A LYS* 3.5 34.0 - - + +
1733A ASP 3.2 11.9 + - - -
1734A VAL 2.9 9.0 + - - -
1736A HIS* 1.3 77.0 - - - +
1738A TRP* 1.3 63.6 + - - +
1739A LYS 3.3 0.2 - - - -
1740A SER* 3.9 7.4 - - - -
1741A ASN* 3.0 44.2 + - - +
1783A SER* 5.9 0.6 - - - -
1784A THR* 3.4 24.6 + - - +
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Residues in contact with TRP1738 (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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1414A ILE* 4.1 28.3 - - + -
1418A LEU* 4.5 8.5 - - + -
1424A PRO* 3.2 27.0 + - + -
1425A LYS* 5.0 2.0 - - - -
1427A LEU* 3.9 25.8 - - + +
1428A LEU* 4.0 16.1 - - + +
1720A LEU* 3.9 40.4 - - + -
1723A GLN 4.5 2.5 - - - -
1724A ALA* 4.2 16.6 - - + -
1729A ILE* 3.5 26.5 - - + -
1734A VAL* 3.1 39.0 + - + +
1735A ARG* 3.9 11.7 - - + +
1736A HIS 3.4 0.2 - - - -
1737A THR* 1.3 82.5 - - - +
1739A LYS* 1.3 60.0 + - - +
1741A ASN* 3.5 2.6 + - - -
1742A CYS* 2.9 30.7 + - - -
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Residues in contact with LYS1739 (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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1717A PHE* 3.5 46.5 - - + -
1720A LEU* 4.1 20.0 - - + -
1721A ASP* 3.5 33.2 + - - -
1735A ARG* 3.1 32.4 + - - +
1736A HIS* 3.9 4.9 - - - +
1737A THR 3.3 0.4 - - - -
1738A TRP* 1.3 72.6 - - - +
1740A SER* 1.3 65.3 + - - +
1742A CYS* 3.0 12.4 + - - +
1743A LEU* 3.1 14.2 + - - +
1744A PRO* 3.2 4.2 - - - +
1815A TYR* 3.8 38.5 + - + +
1819A ALA* 5.3 3.8 - - - +
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Residues in contact with SER1740 (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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1736A HIS* 3.3 15.1 + - - -
1737A THR* 4.1 8.3 - - - -
1738A TRP 3.4 0.2 - - - -
1739A LYS* 1.3 76.4 - - - +
1741A ASN* 1.3 60.0 + - - +
1742A CYS 2.9 5.7 + - - -
1744A PRO* 3.1 8.7 - - - +
1745A LEU* 3.0 43.1 + - - -
1782A CYS* 3.3 29.8 + - - +
1783A SER* 5.8 0.4 - - - -
1815A TYR* 3.0 23.3 + - - -
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Residues in contact with ASN1741 (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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1425A LYS 3.9 7.9 + - - -
1428A LEU* 3.8 24.2 - - + +
1429A ARG* 3.2 33.1 - - + +
1737A THR* 3.0 38.1 + - - +
1738A TRP* 3.8 3.4 - - - +
1739A LYS 3.3 0.2 - - - -
1740A SER* 1.3 74.3 - - - +
1742A CYS* 1.3 57.9 + - - +
1745A LEU* 3.3 27.2 - - - +
1746A ARG* 2.8 32.7 + - - +
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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