Contacts of the helix formed by residues 255 - 274 (chain B) in PDB entry 4I5L
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 SER 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 4.9 4.5 + - - +
253B GLU* 3.5 6.5 + - - -
254B ALA* 1.3 77.0 - - - +
256B GLU* 1.3 64.2 + - - +
257B PHE* 3.7 7.2 + - - +
258B HIS* 3.3 22.9 + - - +
259B SER* 3.2 25.9 + - - -
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Residues in contact with GLU 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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255B SER* 1.3 73.1 - - - +
257B PHE* 1.3 69.6 + - - +
259B SER* 3.4 7.2 + - - -
260B ARG* 3.0 46.5 + - + +
320B TYR* 2.3 43.5 + - + +
324B TRP* 4.2 11.1 + - - -
330B HIS* 5.8 0.7 - - - -
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.7 17.5 - - + -
255B SER* 3.3 5.8 + - - +
256B GLU* 1.3 91.0 - - - +
258B HIS* 1.3 60.5 + - - +
260B ARG* 4.5 1.1 - - - +
261B TYR* 2.9 33.6 + - - +
313B TYR* 3.5 17.7 - - - -
316B PHE* 3.8 17.8 - + - -
317B TYR* 3.5 37.0 - + - -
320B TYR* 3.6 33.4 - + - -
321B CYS* 5.7 1.8 - - - -
324B TRP* 6.3 0.2 - + - -
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Residues in contact with HIS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLN* 2.8 29.8 + - - -
242B VAL* 3.5 19.7 - - + +
243B ASN* 4.0 6.1 - - - -
251B LEU* 2.7 32.6 + - - +
252B LYS 3.3 17.9 - - - -
253B GLU 2.8 14.7 + - - +
254B ALA* 4.5 4.0 - - - -
255B SER* 3.3 25.8 + - - +
257B PHE* 1.3 79.6 - - - +
259B SER* 1.3 65.2 + - - +
261B TYR* 3.8 2.8 - - - +
262B ILE* 3.3 35.7 + - + +
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Residues in contact with SER 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 SER 3.2 11.6 + - - -
256B GLU* 3.8 4.0 - - - -
258B HIS* 1.3 80.7 - - - +
260B ARG* 1.3 87.2 + - - +
262B ILE* 3.4 8.0 + - - +
263B THR* 3.1 26.3 + - - -
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Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLU* 3.0 31.5 + - - +
257B PHE 4.5 0.4 - - - -
259B SER* 1.3 104.6 + - - +
261B TYR* 1.3 58.5 + - - +
263B THR* 3.3 6.9 + - - -
264B THR* 2.5 39.1 + - - -
316B PHE* 3.5 21.5 - - + -
320B TYR* 3.5 33.7 + - + +
332B LEU* 3.3 43.8 - - - +
374B TYR* 4.0 21.9 - - + -
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 4.1 8.1 - - + -
241B VAL* 4.9 0.8 - - + +
242B VAL* 3.6 31.2 - - + -
248B LEU* 3.6 24.8 - - + +
251B LEU* 4.0 13.2 - - + -
257B PHE 2.9 19.0 + - - +
258B HIS 3.8 2.9 - - - +
260B ARG* 1.3 77.3 - - - +
262B ILE* 1.3 60.3 + - - +
264B THR* 3.2 1.2 + - - -
265B VAL* 2.9 49.4 + - + +
304B ILE* 4.3 0.2 - - - +
311B PHE* 2.6 42.6 + - - +
312B SER 4.3 2.7 - - - -
313B TYR* 4.0 20.4 - + - -
316B PHE* 3.4 34.9 - + + -
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Residues in contact with ILE 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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235B VAL* 4.5 15.0 - - + -
238B LEU* 4.0 24.4 - - + +
239B GLN* 3.6 46.2 - - + +
242B VAL* 4.1 14.1 - - + -
258B HIS* 3.3 26.7 + - + +
259B SER* 3.7 9.2 - - - +
260B ARG 3.3 0.2 - - - -
261B TYR* 1.3 79.3 - - - +
263B THR* 1.3 64.1 + - - +
265B VAL* 3.3 1.6 + - - +
266B ILE* 3.0 45.7 + - + +
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Residues in contact with THR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER* 3.1 15.7 + - - -
260B ARG* 3.6 14.3 + - - -
262B ILE* 1.3 76.5 - - - +
264B THR* 1.3 57.8 + - - +
266B ILE* 3.3 7.4 + - - +
267B GLN* 2.9 48.3 + - + +
374B TYR* 3.8 24.2 - - + -
375B ALA* 4.4 11.7 - - + +
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Residues in contact with THR 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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260B ARG 2.5 21.9 + - - -
261B TYR 3.6 3.4 - - - -
263B THR* 1.3 78.4 - - - +
265B VAL* 1.3 62.7 + - + +
267B GLN* 3.2 9.4 + - - +
268B ARG* 3.1 26.5 + - - +
316B PHE* 3.3 26.6 - - + -
319B ILE* 3.9 30.5 - - + -
374B TYR* 2.7 26.5 + - - +
378B VAL* 4.4 8.4 - - + +
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Residues in contact with VAL 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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238B LEU* 3.6 29.4 - - + -
261B TYR* 2.9 56.3 + - + +
264B THR* 1.3 76.1 - - + +
266B ILE* 1.3 57.7 + - - +
268B ARG* 3.1 6.1 + - - +
269B ILE* 2.9 32.8 + - + +
310B PHE 3.5 27.3 - - - +
311B PHE* 3.9 18.6 - - + +
312B SER 5.5 0.7 - - - +
316B PHE* 5.7 1.3 - - + -
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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
----------------------------------------------------------
231B GLN* 3.7 53.6 - - + +
234B PHE* 3.8 17.0 - - + -
235B VAL* 4.0 13.9 - - + +
238B LEU* 3.6 16.4 - - + -
262B ILE* 3.0 38.5 + - + +
263B THR* 3.7 6.7 - - - +
265B VAL* 1.3 73.2 - - - +
267B GLN* 1.3 66.9 + - - +
269B ILE* 3.1 8.1 + - + +
270B PHE* 3.0 31.6 + - + -
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Residues in contact with GLN 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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231B GLN* 2.7 45.7 + - - +
263B THR* 2.9 32.5 + - - +
264B THR 3.5 7.0 - - - +
266B ILE* 1.3 78.2 - - - +
268B ARG* 1.3 57.8 + - - +
270B PHE* 3.3 2.3 + - - +
271B TYR* 2.8 30.4 + - - +
375B ALA* 3.7 42.6 - - - +
378B VAL* 3.7 21.5 - - + -
379B TRP* 2.9 28.4 + - - +
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Residues in contact with ARG 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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264B THR* 3.1 15.3 + - - +
265B VAL* 3.1 10.5 + - - +
267B GLN* 1.3 75.2 - - - +
269B ILE* 1.3 65.5 + - - +
271B TYR* 3.5 8.7 - - + +
272B ALA* 3.2 18.4 + - - +
308B THR 2.6 29.5 + - - -
309B GLU* 3.1 28.8 + - - +
310B PHE* 3.5 32.6 + - - +
312B SER* 3.7 17.8 + - - +
315B HIS* 3.5 29.8 + - - +
316B PHE* 5.7 1.0 - - - +
319B ILE* 4.5 11.6 - - - +
382B ILE* 3.6 29.5 - - + +
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Residues in contact with ILE 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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234B PHE* 3.9 29.4 - - + -
238B LEU* 4.1 8.1 - - + -
265B VAL* 2.9 33.0 + - + +
266B ILE* 3.1 15.2 + - - +
268B ARG* 1.3 78.4 - - - +
270B PHE* 1.3 60.0 + - + +
272B ALA* 4.2 0.2 - - - +
273B VAL* 2.9 42.8 + - + +
281B ILE* 3.8 20.6 - - + -
291B PHE* 3.5 39.0 - - + -
310B PHE* 3.7 12.8 - - + -
311B PHE* 5.3 0.4 - - + -
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Residues in contact with PHE 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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229B LEU 3.6 8.3 - - - -
230B VAL 3.6 7.0 - - - -
231B GLN* 3.5 51.4 - - + +
234B PHE* 3.8 17.0 - + - -
266B ILE* 3.0 24.5 + - + +
267B GLN 3.9 2.7 - - - +
269B ILE* 1.3 77.2 - - + +
271B TYR* 1.3 61.0 + - - +
274B ASN* 2.9 55.1 + - + +
279B GLY* 3.5 28.5 - - - -
281B ILE* 3.6 26.5 - - + -
362B ARG* 5.7 1.8 - - - -
379B TRP* 3.9 18.0 - - + -
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Residues in contact with TYR 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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267B GLN 2.8 20.8 + - - +
268B ARG* 3.5 14.4 - - + +
270B PHE* 1.3 74.9 - - - +
272B ALA* 1.3 62.6 + - + +
274B ASN 5.4 0.9 - - - +
275B ARG* 4.5 2.8 + - - -
379B TRP* 3.6 46.7 - + - -
382B ILE* 3.7 31.7 - - + +
383B SER* 2.8 38.3 + - - -
386B ASP 4.8 0.2 + - - -
389B THR* 3.8 12.9 - - + +
391B THR* 3.0 51.7 + - + +
392B SER* 3.5 15.1 + - - -
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Residues in contact with ALA 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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268B ARG 3.2 5.4 + - - +
271B TYR* 1.3 81.5 - - + +
273B VAL* 1.3 61.1 + - + +
275B ARG* 3.4 22.4 - - - +
289B SER* 5.0 5.8 - - - -
309B GLU 5.7 1.1 - - - +
310B PHE* 3.7 31.4 - - + -
391B THR* 5.0 0.4 - - - -
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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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269B ILE* 2.9 27.0 + - + +
272B ALA* 1.3 77.7 - - - +
274B ASN* 1.3 57.0 + - - +
275B ARG* 2.9 16.9 + - - +
281B ILE* 3.7 35.4 - - + -
285B GLU* 3.4 35.5 - - + +
286B LEU* 4.0 7.4 - - + +
289B SER* 3.7 24.7 - - - +
291B PHE* 4.1 16.4 - - + -
310B PHE* 4.5 7.2 - - + -
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Residues in contact with ASN 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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270B PHE* 2.9 48.2 + - + +
271B TYR 5.4 0.6 - - - +
273B VAL* 1.3 68.7 - - - +
275B ARG* 1.3 57.3 + - - +
276B SER* 3.1 9.9 + - - -
277B TRP* 3.0 23.7 + - - -
278B SER* 3.4 16.6 + - - -
279B GLY* 2.8 27.5 + - - -
280B ARG 3.3 16.1 + - - -
281B ILE* 3.8 5.6 - - + -
285B GLU* 2.9 26.7 + - - -
362B ARG* 4.3 2.3 + - - -
379B TRP* 5.2 5.0 - - - -
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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
------------------------------------------------------------
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