Contacts of the helix formed by residues 282 - 293 (chain A) in PDB entry 2BXO
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 PRO 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A GLU 4.5 0.4 - - - +
281A LYS* 1.3 92.2 - - + +
283A LEU* 1.3 54.7 + - - +
284A LEU* 3.1 5.6 - - + +
285A GLU* 2.6 57.0 + - + +
286A LYS 3.2 7.2 + - - -
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Residues in contact with LEU 283 (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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13A ASP* 3.2 44.6 - - + +
14A LEU* 3.6 17.7 - - + -
258A ALA* 4.5 22.7 - - + -
281A LYS 3.9 0.8 + - - -
282A PRO* 1.3 70.9 - - - +
284A LEU* 1.3 58.3 + - - +
285A GLU 3.1 5.2 + - - -
286A LYS* 3.7 34.4 + - - +
1002A MYR 3.7 27.2 - - + +
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Residues in contact with LEU 284 (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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14A LEU* 4.4 11.2 - - + -
18A ASN* 3.6 30.7 - - + +
22A LEU* 4.4 6.7 - - + -
152A PRO* 4.1 26.5 - - + +
155A LEU* 3.4 33.0 - - + -
159A LYS* 4.7 5.8 - - - +
282A PRO* 2.8 6.8 + - + +
283A LEU* 1.3 76.1 - - - +
285A GLU* 1.3 67.4 - - + +
287A SER* 6.0 0.2 - - - -
288A HIS* 5.0 4.7 + - - +
1002A MYR 3.9 38.0 - - + +
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Residues in contact with GLU 285 (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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156A PHE* 5.2 11.3 - - + -
159A LYS* 5.5 9.7 + - - +
281A LYS* 4.4 23.6 + - + +
282A PRO* 2.6 40.8 + - + +
284A LEU* 1.3 84.8 - - + +
286A LYS* 1.3 67.0 + - - +
287A SER 3.2 2.9 - - - -
288A HIS* 3.0 13.1 + - + +
289A CYS* 2.9 25.5 + - + +
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Residues in contact with LYS 286 (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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258A ALA 5.8 0.4 + - - -
261A ALA* 4.4 14.6 - - + +
262A LYS* 5.0 16.0 - - - +
265A CYS* 4.0 24.0 - - + +
278A CYS 3.4 25.1 - - - +
279A CYS* 4.2 9.9 - - - +
281A LYS* 3.5 18.9 - - - +
282A PRO 3.2 5.1 + - - -
283A LEU* 3.7 34.2 + - - +
285A GLU* 1.3 77.5 - - - +
287A SER* 1.3 63.7 + - - +
289A CYS* 3.3 2.1 + - - +
290A ILE* 3.0 30.1 + - + +
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Residues in contact with SER 287 (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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257A ARG* 3.0 25.8 - - - -
261A ALA* 4.3 7.2 - - - +
284A LEU 6.0 0.2 - - - -
285A GLU 3.2 0.8 - - - -
286A LYS* 1.3 80.4 - - - +
288A HIS* 1.3 61.9 + - - +
290A ILE* 3.3 1.0 + - - -
291A ALA* 3.1 21.0 + - - +
1002A MYR 3.0 28.4 + - - -
2001A OPB 3.4 32.7 - - - -
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Residues in contact with HIS 288 (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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153A GLU* 3.0 41.1 + - - +
156A PHE* 3.3 50.0 - + + -
257A ARG* 3.8 7.4 - - - +
284A LEU 5.0 3.3 + - - +
285A GLU* 3.0 19.4 + - + +
287A SER* 1.3 79.4 - - - +
289A CYS* 1.3 67.8 + - - +
291A ALA* 3.4 6.0 + - - +
292A GLU* 3.3 42.8 + - + +
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Residues in contact with CYS 289 (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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277A GLU* 4.6 10.8 - - - -
278A CYS* 2.0 62.1 - - + +
281A LYS* 4.5 19.5 - - + -
285A GLU* 2.9 11.9 + - + +
286A LYS* 3.4 8.5 - - - +
288A HIS* 1.3 81.6 - - - +
290A ILE* 1.3 55.9 + - - +
292A GLU* 2.9 10.8 + - - +
293A VAL* 2.9 24.4 + - - -
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Residues in contact with ILE 290 (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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223A PHE* 5.2 0.4 - - + -
261A ALA* 4.1 33.4 - - + +
264A ILE* 4.2 26.7 - - + -
265A CYS* 4.2 15.9 - - - -
275A LEU* 4.6 13.5 - - + -
278A CYS* 3.4 20.2 - - + -
279A CYS* 4.6 1.1 - - - -
286A LYS* 3.0 18.5 + - + +
287A SER 3.6 4.5 - - - +
289A CYS* 1.3 70.8 - - - +
291A ALA* 1.3 61.9 + - - +
292A GLU 2.9 6.1 + - - -
293A VAL* 3.0 26.3 - - + +
2001A OPB 3.8 28.6 - - + -
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Residues in contact with ALA 291 (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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222A ARG* 2.7 29.3 + - - -
257A ARG* 5.3 3.1 - - - +
287A SER 3.1 11.4 + - - +
288A HIS* 3.8 6.5 - - - +
289A CYS 3.3 0.2 - - - -
290A ILE* 1.3 76.1 - - - +
292A GLU* 1.3 54.3 + - - +
2001A OPB 3.5 52.9 - - + +
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Residues in contact with GLU 292 (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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222A ARG* 3.9 6.3 + - - +
288A HIS* 3.3 39.5 + - + +
289A CYS* 2.9 12.7 + - - +
291A ALA* 1.3 82.6 - - - +
293A VAL* 1.3 66.9 + - - +
294A GLU* 3.6 1.0 + - - -
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Residues in contact with VAL 293 (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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222A ARG* 3.4 24.8 + - - -
223A PHE* 4.3 16.4 - - + -
272A SER* 5.5 0.2 - - - +
274A LYS* 3.4 33.0 - - + +
275A LEU* 3.9 21.5 - - + -
278A CYS* 4.5 7.0 - - - -
289A CYS 2.9 10.3 + - - +
290A ILE* 3.0 24.5 + - - +
292A GLU* 1.3 80.6 - - - +
294A GLU* 1.3 74.7 + - + +
295A ASN* 4.8 0.2 - - - +
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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