Contacts of the strand formed by residues 81 - 84 (chain O) in PDB entry 1JY3
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 VAL 81 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52N CYS* 4.4 0.4 - - - -
71O GLY* 4.4 1.3 - - - -
72O CYS 3.5 9.9 - - - +
73O LEU* 3.5 22.7 - - + -
79O LEU 3.7 0.9 + - - +
80O GLY* 1.3 71.6 - - - -
82O LEU* 1.3 72.9 + - - +
83O CYS* 4.1 16.8 + - - -
36Q TRP* 3.7 31.2 - - + +
48Q CYS 4.1 0.3 - - - +
49Q PRO* 4.1 1.9 - - - +
50Q SER* 4.0 20.8 + - - -
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Residues in contact with LEU 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O ASP 4.2 0.9 - - - +
71O GLY* 3.2 8.5 - - - -
72O CYS* 2.8 34.8 + - - +
74O HIS* 3.7 34.1 - - + -
79O LEU* 4.2 3.4 - - + +
80O GLY 4.0 2.5 - - - +
81O VAL* 1.3 77.1 - - - +
83O CYS* 1.3 60.4 + - - +
39Q CYS* 3.5 26.7 - - + -
43Q ASP* 5.3 3.8 - - + -
44Q TRP* 4.1 10.5 - - + +
47Q LYS* 3.6 33.2 - - + +
48Q CYS 3.3 2.7 - - - -
49Q PRO* 3.5 35.0 - - + -
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Residues in contact with CYS 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N SER* 3.6 9.4 - - - -
51N GLY* 3.9 8.5 - - - +
52N CYS* 2.1 57.9 - - - +
81O VAL* 4.2 12.6 - - - -
82O LEU* 1.3 76.3 - - - +
84O PRO* 1.3 72.7 - - - +
85O THR* 3.3 0.7 + - - -
47Q LYS* 3.2 4.9 - - - -
48Q CYS* 2.9 30.2 + - - +
50Q SER* 6.6 0.2 - - - -
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Residues in contact with PRO 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N GLY* 3.6 30.1 - - - +
52N CYS 4.1 1.1 - - - +
55N LYS* 4.4 8.3 - - + -
69O ALA 4.1 5.6 - - - +
70O ASP* 3.7 34.8 - - + +
83O CYS* 1.3 90.0 - - + +
85O THR* 1.3 64.0 + - - +
88O LYS* 4.3 11.4 - - + -
89O LEU* 3.9 21.3 - - + +
22P THR* 5.2 0.9 - - - +
46Q THR 3.5 10.1 - - - +
47Q LYS* 4.1 9.8 - - + +
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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