Contacts of the strand formed by residues 288 - 291 (chain B) 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 TYR 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B HIS* 5.3 6.9 - + + -
14B SER 3.3 7.1 + - - -
15B VAL* 3.3 15.5 - - + -
16B VAL* 3.0 27.2 + - - +
36B TYR* 5.6 1.3 - + - -
271B VAL* 4.3 5.4 - - - -
286B ALA* 3.7 2.4 - - - +
287B ASP* 1.3 97.9 - - + +
289B ALA* 1.3 59.9 + - - +
453B LYS* 3.5 23.1 - - + +
455B TYR* 4.1 12.8 - + + -
482B ILE* 4.0 26.9 - - + -
485B ARG* 3.7 41.1 + - - +
486B VAL* 3.7 32.9 - - + +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.2 17.3 - - + +
18B LEU* 4.1 11.4 - - + -
264B MET* 5.0 1.8 - - - -
271B VAL* 3.7 29.1 - - + +
273B VAL* 5.0 0.4 - - + -
288B TYR* 1.3 75.8 - - - +
290B ILE* 1.3 63.8 + - - +
291B CYS 4.0 0.4 - - - -
453B LYS 3.1 7.9 + - - +
454B ILE* 4.4 11.2 - - + -
455B TYR* 2.9 30.7 + - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 4.0 6.1 - - + -
16B VAL 2.9 7.9 + - - -
17B VAL* 3.4 11.2 - - + +
18B LEU* 2.8 28.9 + - - +
27B SER* 3.8 33.0 - - - +
31B LEU* 3.9 17.3 - - + -
289B ALA* 1.3 74.3 - - - +
291B CYS* 1.3 60.9 + - - +
292B THR* 3.7 9.7 + - + -
455B TYR* 3.3 5.6 - - + +
457B ALA* 3.9 26.9 - - + -
478B VAL* 3.9 14.8 - - + -
479B VAL* 4.4 4.3 - - + -
482B ILE* 3.7 29.6 - - + -
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Residues in contact with CYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.1 14.1 - - + -
264B MET* 3.9 31.2 - - - -
289B ALA 4.0 1.0 - - - -
290B ILE* 1.3 70.4 - - - +
292B THR* 1.3 61.1 + - - +
293B ILE* 4.0 18.3 - - - +
298B VAL* 4.1 24.2 - - - -
301B LEU* 5.2 0.9 - - - -
454B ILE* 4.6 2.7 - - + -
455B TYR 2.8 10.0 + - - +
456B PHE* 3.5 25.8 - - + +
457B ALA 3.1 19.8 + - - +
460B HIS* 5.7 0.5 - - - -
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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