Contacts of the helix formed by residues 258 - 273 (chain B) in PDB entry 2BT4
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 HIS 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A HIS* 5.1 0.7 - + + +
2401A PO4 3.0 41.9 + - - +
256B SER* 2.9 15.5 + - - +
257B ASN* 1.3 84.5 - - + +
259B GLU* 1.3 65.5 + - - +
261B GLU* 3.5 18.5 - - + +
262B LEU* 3.1 24.0 + - - +
283B TYR* 4.0 2.7 - - - -
460C GLY* 3.3 3.3 - - - -
461C GLU* 3.3 31.6 - - + -
464C ASP* 3.5 19.8 + - - -
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Residues in contact with GLU 259 (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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59A GLU* 4.0 2.6 - - - +
83A TYR* 3.6 27.9 + - - +
2401A PO4 4.6 3.7 + - - +
2405A TRS 2.7 48.4 + - - -
258B HIS* 1.3 70.5 - - - +
260B GLY* 1.4 64.1 + - - +
262B LEU* 3.2 6.9 + - - +
263B VAL* 3.0 24.8 + - - +
283B TYR* 3.5 31.0 + - + +
287B SER* 2.5 31.7 + - - +
289B ALA* 3.9 9.1 - - + +
290B ILE* 4.3 7.1 - - + +
459C GLU* 4.0 2.5 - - - +
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASN* 3.3 25.8 + - - +
58A HIS* 3.4 20.8 - - - +
59A GLU 5.5 0.2 - - - +
83A TYR* 4.4 0.6 + - - -
2401A PO4 3.7 7.5 + - - -
258B HIS 3.2 0.6 - - - -
259B GLU* 1.4 80.2 - - - +
261B GLU* 1.3 56.8 + - - +
263B VAL* 3.2 4.4 + - - +
264B ASP* 2.9 32.7 + - - +
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 3.3 14.6 - - + -
256B SER* 2.5 27.1 + - - +
258B HIS* 3.1 26.1 + - + +
260B GLY* 1.3 73.4 - - - +
262B LEU* 1.3 60.5 + - - +
264B ASP* 3.2 9.5 + - + +
265B TRP* 2.9 71.3 + - + +
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Residues in contact with LEU 262 (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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212B LEU* 4.5 16.6 - - + +
213B ASN 3.8 22.7 - - - +
214B GLY* 4.0 14.8 - - - -
256B SER* 4.0 11.4 - - - +
258B HIS 3.1 15.5 + - - +
259B GLU 3.4 7.0 - - - +
260B GLY 3.2 0.2 - - - -
261B GLU* 1.3 77.8 - - - +
263B VAL* 1.3 62.7 + - - +
265B TRP* 3.3 24.2 + - + +
266B ILE* 3.0 30.5 + - + +
278B ILE* 5.6 4.7 - - + -
280B PRO* 5.3 2.7 - - + +
283B TYR* 3.7 30.7 - - + -
290B ILE* 4.0 16.8 - - + -
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Residues in contact with VAL 263 (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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15A PRO* 4.8 1.1 - - + -
16A ASN* 3.6 23.6 - - - +
57A ASN* 3.5 32.1 - - + +
259B GLU* 3.0 21.1 + - + +
260B GLY* 3.2 9.4 + - - +
262B LEU* 1.3 78.8 - - - +
264B ASP* 1.3 62.1 + - - +
266B ILE* 3.2 9.6 + - - +
267B HIS* 3.0 27.7 + - - +
289B ALA* 3.9 36.1 - - + +
290B ILE* 4.0 8.7 - - + -
293B ALA* 4.1 1.8 - - + -
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Residues in contact with ASP 264 (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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57A ASN* 2.7 36.9 + - - +
58A HIS* 2.9 25.7 + - - -
260B GLY 2.9 14.4 + - - +
261B GLU* 3.3 11.7 - - + +
263B VAL* 1.3 75.4 - - - +
265B TRP* 1.3 69.7 + - + +
267B HIS* 3.2 9.1 + - - +
268B GLU* 3.1 19.8 + - - +
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Residues in contact with TRP 265 (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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210B MET* 3.5 9.6 - - + +
212B LEU* 4.0 20.6 - - + -
254B ARG* 3.4 60.5 - - + +
255B GLN 3.5 22.4 - - - -
256B SER* 3.6 24.0 - - - -
261B GLU* 2.9 44.9 + - + +
262B LEU* 3.7 16.6 - - + +
263B VAL 3.2 0.2 - - - -
264B ASP* 1.3 79.9 - - + +
266B ILE* 1.3 61.4 + - - +
268B GLU* 3.3 12.0 + - - +
269B ALA* 3.0 23.4 + - - +
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Residues in contact with ILE 266 (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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212B LEU* 3.7 20.6 - - + -
262B LEU* 3.0 23.5 + - + +
263B VAL* 3.5 7.0 - - - +
265B TRP* 1.3 75.9 - - - +
267B HIS* 1.4 59.0 + - + +
269B ALA* 3.3 7.3 + - - +
270B ARG* 2.9 27.0 + - - +
276B ILE* 4.3 2.7 - - + -
278B ILE* 4.6 3.1 - - + -
290B ILE* 3.7 30.5 - - + -
293B ALA* 3.6 40.4 - - + +
294B LEU* 3.9 20.4 - - + +
297B CYS* 3.8 14.1 - - - -
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Residues in contact with HIS 267 (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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16A ASN* 2.9 29.8 + - - -
18A ASN* 3.1 41.1 + - - +
19A LEU* 3.8 25.3 - - + +
57A ASN* 3.8 11.1 + - - -
263B VAL* 3.0 27.3 + - + +
264B ASP* 3.4 9.2 - - - +
266B ILE* 1.4 77.6 - - - +
268B GLU* 1.3 61.8 + - - +
270B ARG* 3.3 20.6 + - - +
271B LEU* 3.7 14.0 + - - +
293B ALA* 4.5 4.9 - - + -
296B THR* 4.3 6.5 - - - -
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Residues in contact with GLU 268 (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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210B MET* 4.4 0.4 - - + -
254B ARG* 2.9 43.4 + - - -
264B ASP 3.1 11.0 + - - +
265B TRP* 3.5 14.6 - - - +
266B ILE 3.2 0.2 - - - -
267B HIS* 1.3 78.2 - - - +
269B ALA* 1.3 57.9 + - - +
271B LEU* 3.2 2.2 + - - -
272B ASN* 2.8 48.8 + - - +
273B HIS* 4.1 10.9 - - + -
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Residues in contact with ALA 269 (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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210B MET* 3.8 18.8 - - + +
265B TRP 3.0 14.2 + - - +
266B ILE* 3.3 8.5 + - - +
268B GLU* 1.3 71.6 - - - +
270B ARG* 1.3 66.7 + - - +
271B LEU 3.0 3.7 + - - -
273B HIS* 3.1 40.5 + - + +
276B ILE* 4.0 28.0 - - + -
300B LEU* 4.0 5.3 - - + +
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Residues in contact with ARG 270 (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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19A LEU* 3.8 25.1 - - - +
22A GLN* 2.8 45.0 + - - +
23A ARG* 5.4 3.4 - - - +
266B ILE 2.9 13.4 + - - +
267B HIS* 3.3 14.5 + - - +
268B GLU 3.3 0.2 - - - -
269B ALA* 1.3 77.0 - - - +
271B LEU* 1.3 83.9 + - + +
273B HIS 5.1 0.7 - - - +
296B THR* 2.7 50.8 + - - +
297B CYS* 3.8 17.9 - - - -
298B ASP* 5.4 0.6 + - - -
300B LEU* 4.2 12.6 - - - +
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Residues in contact with LEU 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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22A GLN* 5.4 0.2 - - - +
202B ARG* 2.9 27.2 + - - -
267B HIS 3.9 12.3 - - - +
268B GLU* 3.2 2.5 + - - +
269B ALA 3.0 0.6 - - - -
270B ARG* 1.3 111.1 - - + +
272B ASN* 1.3 73.8 + - - +
273B HIS 3.9 0.4 - - - -
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Residues in contact with ASN 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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202B ARG* 3.8 18.8 + - - +
207B ALA* 3.6 15.1 - - - +
208B PRO* 4.0 6.6 - - - +
268B GLU* 2.8 37.3 + - + +
271B LEU* 1.3 93.1 - - - +
273B HIS* 1.3 75.7 + - + +
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Residues in contact with HIS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 3.9 13.9 - - - +
207B ALA* 4.1 1.3 - - - -
208B PRO* 3.1 35.8 - - + +
210B MET* 3.4 37.8 - - + +
252B ASP* 3.0 27.4 + - + +
268B GLU* 4.1 11.7 - - + -
269B ALA* 3.1 25.7 + - + +
270B ARG 5.1 1.0 - - - +
271B LEU 5.4 0.2 - - - -
272B ASN* 1.3 100.7 + - + +
274B CYS* 1.3 60.5 + - - +
275B GLY 3.4 13.2 - - - +
300B LEU* 3.4 15.8 - - - +
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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