Contacts of the strand formed by residues 232 - 235 (chain A) in PDB entry 2JB2
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 MET 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.9 20.0 - - + -
85A ILE 3.5 14.6 - - - +
86A PRO* 3.5 31.6 - - + -
104A GLY* 3.6 3.6 - - - -
105A PHE* 2.9 40.1 + - + +
107A ASN* 3.7 14.8 - - + +
227A ASP 3.2 26.5 - - - +
228A GLN* 3.4 26.0 - - - +
229A ALA 3.5 18.6 - - - +
230A MET* 3.7 5.8 - - - +
231A MET* 1.3 72.8 - - - +
233A PHE* 1.3 70.8 + - - +
467A TRP* 4.6 0.7 - - + -
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Residues in contact with PHE 233 (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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84A ARG* 3.5 2.6 - - - -
85A ILE* 2.8 46.9 + - - +
87A GLN* 3.8 9.9 - - + -
92A LEU* 4.3 15.5 - - + -
102A ILE* 4.1 27.4 - - + -
103A GLN 3.4 18.8 - - - +
104A GLY* 4.1 5.8 - - - -
105A PHE* 3.9 4.2 - - - +
231A MET* 3.6 35.9 - - + -
232A MET* 1.3 80.3 - - - +
234A THR* 1.3 64.2 + - - +
340B TYR* 3.3 42.6 - + + -
360B TYR* 3.6 28.9 - + - -
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Residues in contact with THR 234 (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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79A ASN* 4.0 2.8 + - - -
83A THR 2.6 27.2 + - - -
85A ILE* 4.5 1.1 - - - -
102A ILE* 4.3 4.3 - - - -
103A GLN* 2.8 40.2 + - + +
104A GLY 4.5 0.2 - - - +
105A PHE* 4.2 11.2 - - + -
233A PHE* 1.3 76.5 - - - +
235A PRO* 1.3 77.1 + - - +
239A MET* 3.6 3.7 + - - +
357A TYR* 3.5 45.2 + - + -
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Residues in contact with PRO 235 (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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85A ILE* 4.2 3.1 - - + -
95A CYS* 4.4 6.7 - - - -
100A VAL* 3.8 21.1 - - + -
101A GLU 3.4 6.7 - - - +
102A ILE* 4.1 2.0 - - + -
103A GLN* 4.2 2.2 + - - -
234A THR* 1.3 99.3 + - - +
236A VAL* 1.3 66.4 + - - +
237A GLY 3.3 2.8 + - - -
238A GLY* 3.3 24.5 + - - +
239A MET* 3.3 35.9 - - + -
241A ARG* 4.6 0.4 - - + -
242A ILE* 3.9 20.9 - - + -
357A TYR* 4.8 2.8 + - - -
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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