Contacts of the helix formed by residues 1584 - 1589 (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 THR1584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1522A ASN 4.8 0.3 + - - -
1523A CYS* 3.2 30.5 - - - +
1524A ASP 3.8 8.1 - - - +
1526A VAL* 5.1 3.6 - - - +
1581A ARG* 4.3 15.6 + - - +
1582A LEU 3.5 10.3 + - - +
1583A ASN* 1.3 77.7 - - - +
1585A LEU* 1.3 65.6 + - - +
1586A ALA* 4.2 3.7 + - - +
1587A HIS* 3.6 21.5 + - - +
1588A TYR* 3.3 27.8 + - - -
1653A HIS* 3.5 20.6 - - + +
1654A LEU* 5.3 1.6 - - + -
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Residues in contact with LEU1585 (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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1501A LEU* 5.6 0.7 - - + -
1521A LEU 4.3 4.7 - - - +
1522A ASN* 3.2 31.6 + - + +
1523A CYS 4.3 0.2 - - - +
1524A ASP 3.9 7.4 + - - +
1584A THR* 1.3 75.0 - - - +
1586A ALA* 1.3 53.1 + - - +
1587A HIS 3.1 1.3 - - - -
1588A TYR* 2.9 7.9 + - - +
1589A GLN 2.6 31.2 + - - -
1590A VAL* 3.2 26.6 + - + -
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Residues in contact with ALA1586 (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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1522A ASN* 3.2 26.3 + - - +
1584A THR* 4.2 2.6 + - - +
1585A LEU* 1.3 77.7 - - - +
1587A HIS* 1.3 59.3 + - - +
1589A GLN* 2.9 35.3 + - - +
1590A VAL 4.7 1.1 - - - +
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Residues in contact with HIS1587 (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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1572A THR 3.3 26.2 - - - -
1573A THR* 3.6 2.1 - - - -
1574A LYS* 2.9 45.3 + - + +
1581A ARG* 5.0 7.6 - - + -
1582A LEU 5.3 0.4 - - - +
1583A ASN* 4.0 12.6 + - - -
1584A THR* 3.6 30.8 + - - +
1585A LEU 3.1 0.4 - - - -
1586A ALA* 1.3 78.8 - - - +
1588A TYR* 1.3 71.8 + + - +
1589A GLN* 3.7 1.6 + - - +
66C ARG* 4.1 32.5 - - + +
67C LEU* 5.3 0.3 - - - +
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Residues in contact with TYR1588 (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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1526A VAL* 4.3 10.1 - - + -
1556A TRP* 4.0 2.5 - - + -
1566A LEU* 3.5 38.8 - - + -
1567A GLN 3.0 12.9 + - - -
1570A ASP* 2.9 18.6 + - - -
1572A THR* 3.1 24.6 + - - -
1583A ASN* 2.8 46.7 + - + -
1584A THR 3.3 18.7 + - - +
1585A LEU* 2.9 8.2 + - - +
1587A HIS* 1.3 86.4 - + - +
1589A GLN* 1.3 73.6 + - - +
1590A VAL* 5.2 1.8 - - + +
66C ARG 4.7 2.5 - - - -
67C LEU* 3.2 41.8 - - + +
70C LEU* 4.1 3.6 - - + -
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Residues in contact with GLN1589 (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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1556A TRP* 3.2 17.7 - - - -
1585A LEU 2.6 10.7 + - - -
1586A ALA* 2.9 23.5 + - - +
1587A HIS 3.3 2.0 - - - +
1588A TYR* 1.3 81.0 - - - +
1590A VAL* 1.3 65.6 + - - +
1591A THR* 5.4 0.2 - - - -
63C ASP* 4.3 18.8 - - - +
64C TYR* 4.8 22.1 + - + -
67C LEU* 4.5 4.0 - - + +
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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