Contacts of the helix formed by residues 252 - 266 (chain B) in PDB entry 2R5S
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B LEU 4.8 6.1 - - - -
248B GLY* 3.2 16.6 + - - -
249B ALA 3.9 2.5 - - - -
251B ASP* 1.3 75.0 - - - +
253B GLU* 1.3 56.9 + - - +
254B VAL 3.4 2.5 - - - -
255B LYS* 3.8 5.8 + - - +
256B LYS* 3.1 28.8 + - - +
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Residues in contact with GLU 253 (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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217B GLU* 4.1 23.9 - - - +
220B CYS* 3.9 17.8 - - - +
249B ALA 3.4 0.2 + - - -
250B GLN* 2.9 41.1 + - + +
251B ASP 3.3 2.3 + - - +
252B GLY* 1.3 69.5 - - - +
254B VAL* 1.3 59.3 + - - +
256B LYS* 3.9 13.3 - - + +
257B THR* 2.6 41.3 + - + +
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Residues in contact with VAL 254 (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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216B PHE* 4.1 15.3 - - + +
220B CYS* 3.4 23.6 - - - -
239B LEU* 3.9 27.3 - - + +
242B ILE* 4.0 20.4 - - + -
243B LEU* 3.9 21.3 - - + -
249B ALA* 3.4 19.3 + - + +
250B GLN* 4.0 17.0 - - + -
253B GLU* 1.3 78.7 - - - +
255B LYS* 1.3 63.5 + - - +
257B THR 3.4 0.2 + - - -
258B PHE* 3.2 21.0 + - - +
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Residues in contact with LYS 255 (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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243B LEU* 3.5 27.8 - - + +
247B LEU* 3.9 29.8 + - - +
252B GLY* 3.8 8.4 + - - +
254B VAL* 1.3 79.1 - - - +
256B LYS* 1.3 57.7 + - - +
258B PHE* 3.5 0.5 - - - +
259B MSE 2.8 57.2 + - + +
279B LEU* 4.4 15.5 - - + -
283B LEU* 3.9 29.3 - - - +
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Residues in contact with LYS 256 (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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252B GLY 3.1 19.6 + - - +
253B GLU* 3.9 15.5 - - + +
254B VAL 3.3 0.4 - - - -
255B LYS* 1.3 77.6 - - - +
257B THR* 1.3 64.5 + - + +
259B MSE 3.2 5.5 + - - +
260B ASP* 2.8 51.3 + - - +
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Residues in contact with THR 257 (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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220B CYS* 3.3 39.8 + - + -
223B ALA* 4.4 1.2 - - - +
224B VAL* 4.2 15.4 - - + +
239B LEU* 3.3 14.9 - - + +
253B GLU* 2.6 35.2 + - + +
254B VAL 4.1 2.7 - - - +
256B LYS* 1.3 82.1 - - + +
258B PHE* 1.3 52.9 + - - +
260B ASP* 3.1 8.1 + - - +
261B ILE* 2.7 44.2 + - - +
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Residues in contact with PHE 258 (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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236B LEU* 3.7 36.1 - - + +
239B LEU* 3.3 24.0 - - + +
240B TRP* 4.1 11.0 - + - -
243B LEU* 3.5 25.1 - - + -
254B VAL 3.2 18.1 + - - +
255B LYS 3.5 3.6 - - - +
257B THR* 1.3 74.0 - - - +
259B MSE 1.3 62.3 + - + +
261B ILE* 3.2 3.8 + - - +
262B LEU* 3.1 46.4 + - + +
275B TYR* 3.7 34.5 - + + -
279B LEU* 3.6 39.3 - - + -
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Residues in contact with MSE 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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255B LYS* 2.8 46.1 + - + +
256B LYS* 3.5 7.6 - - - +
257B THR 3.2 0.2 - - - -
258B PHE* 1.3 74.8 - - - +
260B ASP* 1.3 65.9 + - - +
262B LEU* 3.5 11.2 + - - +
263B SER* 3.1 25.5 + - - -
279B LEU* 3.5 28.3 - - + -
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Residues in contact with ASP 260 (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 LYS* 2.8 54.4 + - - +
257B THR* 3.5 8.5 - - - +
259B MSE 1.3 73.0 - - - +
261B ILE* 1.3 70.8 + - + +
263B SER* 3.0 18.9 + - - -
264B ALA* 3.2 11.6 + - - +
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Residues in contact with ILE 261 (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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223B ALA* 4.5 11.4 - - + +
224B VAL* 5.0 9.9 - - + -
227B ASN* 4.0 25.4 - - + +
232B ASP* 3.9 16.8 - - + +
235B ALA* 4.8 6.7 - - + -
236B LEU* 3.7 24.7 - - + -
239B LEU* 5.4 0.9 - - + -
257B THR* 2.7 37.0 + - - +
258B PHE* 3.2 6.0 + - - +
260B ASP* 1.3 79.0 - - + +
262B LEU* 1.3 57.9 + - - +
264B ALA* 3.0 26.9 + - + +
265B LEU* 3.1 27.3 + - + +
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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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236B LEU* 4.1 8.7 - - + -
258B PHE* 3.1 41.7 + - + +
259B MSE 3.8 12.8 - - - +
261B ILE* 1.3 74.0 - - - +
263B SER* 1.3 65.9 + - - +
265B LEU* 3.2 14.5 + - - +
266B GLY 3.3 0.7 + - - -
272B ALA* 3.3 36.1 - - + +
275B TYR* 3.7 18.2 - - + -
276B ARG* 2.9 54.4 + - + +
279B LEU* 4.7 6.5 - - + -
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Residues in contact with SER 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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259B MSE 3.1 12.5 + - - -
260B ASP* 3.0 15.9 + - - -
262B LEU* 1.3 77.9 - - - +
264B ALA* 1.3 67.1 + - - +
265B LEU 3.4 0.5 + - - -
266B GLY* 3.5 10.8 + - - +
276B ARG* 4.7 2.9 - - - +
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Residues in contact with ALA 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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227B ASN* 4.4 16.4 - - - +
260B ASP 3.2 10.0 + - - +
261B ILE* 3.0 17.2 + - + +
263B SER* 1.3 83.0 + - - +
265B LEU* 1.3 60.1 + - + +
266B GLY* 4.8 0.2 - - - -
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Residues in contact with LEU 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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161B THR* 5.2 11.2 + - - +
162B LYS* 5.9 2.7 - - - +
163B GLN* 5.9 0.3 + - - -
227B ASN* 4.6 4.0 - - - +
232B ASP* 3.4 37.5 - - + +
236B LEU* 4.1 13.5 - - + -
261B ILE* 3.1 41.3 + - + +
262B LEU* 3.7 1.8 - - - +
263B SER 3.2 0.6 - - - -
264B ALA* 1.3 80.8 - - + +
266B GLY* 1.3 61.3 + - - +
268B GLY 5.0 0.2 + - - -
269B ASN* 3.3 37.2 + - - +
271B ILE* 5.2 0.9 - - + -
272B ALA* 3.7 23.6 - - + +
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Residues in contact with GLY 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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262B LEU 3.3 8.3 + - - -
263B SER* 3.5 10.7 + - - -
264B ALA 4.8 0.4 - - - -
265B LEU* 1.3 81.0 - - - +
267B GLN* 1.3 62.6 + - - -
268B GLY 3.3 3.4 + - - -
269B ASN* 3.7 8.3 + - - +
272B ALA* 4.0 0.2 - - - +
276B ARG* 2.8 26.5 + - - -
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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