Contacts of the strand formed by residues 40 - 43 (chain O) in PDB entry 2I2X
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 ILE 40 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32O LEU* 3.8 17.3 - - + -
33O GLU 3.3 26.2 - - - +
34O ILE* 3.9 25.1 - - + -
38O TYR* 3.6 21.5 - - + +
39O THR* 1.3 78.3 - - - +
41O PRO* 1.4 82.6 - - + +
80O ALA* 4.3 5.4 - - + -
81O ILE 4.1 9.6 - - - +
82O ILE* 3.7 27.6 - - + +
308O ASP 3.1 7.4 + - - +
309O CYS* 3.1 7.9 - - - +
310O TRP 3.1 21.7 + - - -
337O CYS* 3.6 3.9 - - - -
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Residues in contact with PRO 41 (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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39O THR 4.4 0.9 - - - +
40O ILE* 1.4 86.3 - - + +
42O GLU* 1.3 58.3 + - - +
43O ILE* 4.0 0.9 - - + -
73O MET* 3.9 5.4 - - + -
80O ALA* 3.5 26.9 - - + +
81O ILE* 3.7 6.0 - - + +
82O ILE* 2.8 26.9 + - - +
310O TRP 3.6 6.1 - - - +
330O SER* 4.7 3.1 - - - +
333O LEU* 3.8 25.6 - - + -
334O ALA* 3.8 25.6 - - + +
337O CYS* 3.6 15.7 - - + -
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Residues in contact with GLU 42 (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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40O ILE 3.7 0.8 + - - -
41O PRO* 1.3 71.9 - - - +
43O ILE* 1.3 61.0 + - - +
44O ASN* 4.3 1.8 - - - +
82O ILE* 3.3 32.7 - - + +
84O GLU* 3.4 25.4 - - + +
123O ARG* 2.7 42.0 + - - -
268O ASP* 5.1 0.5 + - - +
285O THR* 2.9 34.1 + - + +
309O CYS* 4.3 6.7 - - + +
310O TRP 2.9 13.7 + - - +
311O SER* 3.2 30.3 + - - -
312O ASN 3.6 2.8 + - - -
333O LEU* 3.8 3.0 - - - +
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Residues in contact with ILE 43 (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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41O PRO* 4.0 1.4 - - + -
42O GLU* 1.3 71.4 - - - +
44O ASN* 1.3 69.5 + - - +
45O TYR* 3.4 12.8 - - + -
69O VAL* 3.9 11.4 - - + -
81O ILE* 3.3 28.9 - - + -
82O ILE 2.9 9.6 + - - +
83O LEU* 3.9 13.9 - - + -
84O GLU 2.9 27.7 + - - -
312O ASN* 3.4 24.5 - - - +
326O VAL* 3.6 34.5 - - + +
329O TRP* 4.1 5.2 - - + -
330O SER* 3.8 23.6 - - - +
333O LEU* 4.2 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