Contacts of the strand formed by residues 270 - 277 (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 GLY 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ASN* 3.7 0.3 - - - -
267B VAL* 2.9 20.8 + - - +
268B SER 3.4 2.0 + - - -
269B GLU* 1.3 80.5 - - - +
271B VAL* 1.3 66.7 + - - +
285B THR* 4.6 0.2 - - - -
286B ALA 3.4 8.5 - - - -
287B ASP* 4.0 5.8 - - - -
453B LYS* 2.9 34.6 + - - +
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Residues in contact with VAL 271 (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* 4.8 3.8 - - + +
264B MET* 4.3 6.1 - - + -
265B LYS 3.3 17.9 - - - +
266B ASN* 3.9 8.3 - - - +
270B GLY* 1.3 79.5 - - - +
272B THR* 1.3 69.1 + - - +
273B VAL* 4.1 4.7 + - + -
284B ILE 3.8 0.9 - - - +
285B THR* 3.3 4.1 - - - +
286B ALA* 2.8 33.1 + - - +
288B TYR* 4.3 2.7 - - - -
289B ALA* 3.7 29.8 - - + +
453B LYS* 3.6 37.0 - - + +
454B ILE* 4.0 12.6 - - + -
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Residues in contact with THR 272 (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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263B SER* 4.0 2.1 + - - +
264B MET* 3.5 2.3 + - - -
265B LYS* 2.9 34.9 + - - +
267B VAL* 3.5 29.0 - - - +
269B GLU* 4.2 5.2 + - - -
271B VAL* 1.3 71.9 - - - +
273B VAL* 1.3 65.6 + - - +
274B GLU* 4.4 9.5 + - + +
283B SER* 3.5 23.1 - - - +
284B ILE 3.4 5.8 - - - +
285B THR* 2.8 18.5 + - - +
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Residues in contact with VAL 273 (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* 4.0 25.1 - - + -
18B LEU* 4.3 10.1 - - + -
41B LEU* 3.8 22.2 - - + -
261B VAL* 3.5 22.2 - - + -
263B SER 3.2 11.2 - - - +
264B MET* 4.3 19.1 - - + -
271B VAL* 4.3 5.4 - - + -
272B THR* 1.3 78.6 - - - +
274B GLU* 1.3 66.6 + - - +
275B TYR* 4.2 1.4 - - - -
283B SER* 3.4 1.4 - - - -
284B ILE* 2.8 47.0 + - + +
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Residues in contact with GLU 274 (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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261B VAL* 3.5 4.7 - - - +
262B THR* 2.9 33.2 + - - +
263B SER* 3.0 31.6 + - - +
272B THR* 4.7 8.5 - - + +
273B VAL* 1.3 74.8 - - - +
275B TYR* 1.3 62.1 + - - +
282B LYS 3.4 10.5 - - - +
283B SER* 4.2 16.3 + - - +
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Residues in contact with TYR 275 (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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41B LEU* 3.8 31.1 - - + +
256B VAL* 4.0 18.2 - - + +
259B ALA* 3.6 24.5 - - + -
260B GLU 3.2 16.6 - - - +
261B VAL* 3.7 14.6 - - + +
262B THR* 4.0 4.0 + - - -
273B VAL 4.2 4.7 - - - -
274B GLU* 1.3 77.6 - - - +
276B THR* 1.3 62.3 + - - +
277B ALA* 3.9 16.8 - - + -
281B LYS* 3.8 2.6 - - - -
282B LYS* 2.9 70.0 + - + +
283B SER 4.3 3.6 + - - -
284B ILE* 4.2 14.1 - - + +
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Residues in contact with THR 276 (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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258B GLY 3.2 4.2 - - - +
259B ALA* 3.4 0.5 - - - -
260B GLU* 2.9 38.8 + - - +
262B THR* 4.2 13.8 + - - +
275B TYR* 1.3 71.4 - - - +
277B ALA* 1.3 63.4 + - - +
278B GLY 4.4 0.2 - - - -
279B GLY* 3.8 27.6 - - - +
280B SER 3.4 12.3 - - - +
281B LYS* 3.4 27.0 - - - +
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Residues in contact with ALA 277 (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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256B VAL* 4.3 11.4 - - + -
257B PHE 4.6 2.5 - - - +
258B GLY 3.4 13.5 - - - +
259B ALA* 4.2 3.1 - - - -
275B TYR* 3.9 24.7 + - + -
276B THR* 1.3 74.8 - - - +
278B GLY* 1.3 66.0 + - - +
279B GLY 3.2 0.9 - - - -
280B SER* 3.0 25.7 + - - +
282B LYS* 4.8 8.7 - - + -
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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