Contacts of the helix formed by residues 259 - 278 (chain B) in PDB entry 6XWQ
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 ASP 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B LYS* 5.9 0.4 - - - -
257B GLY 3.5 9.0 - - - +
258B ILE* 1.3 85.9 - - - +
260B PRO* 1.3 70.9 - - + +
261B ILE* 4.6 6.1 - - + +
262B LYS* 3.3 34.8 + - + +
263B PHE 3.2 14.9 + - - -
428B TRP* 4.8 4.2 - - - -
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Residues in contact with PRO 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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250B PHE* 3.4 62.8 - - + +
253B LEU* 4.2 8.3 - - + -
254B LYS* 4.0 22.4 - - + +
258B ILE 3.7 4.2 - - - +
259B ASP* 1.3 82.8 - - + +
261B ILE* 1.3 73.7 + - + +
263B PHE* 3.0 10.8 + - + +
264B ILE* 2.9 26.2 + - - +
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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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250B PHE* 4.4 20.4 - - + -
259B ASP* 3.3 5.3 - - + -
260B PRO* 1.3 82.5 - - + +
262B LYS* 1.3 60.2 + - + +
264B ILE* 3.3 6.1 + - + +
265B ARG* 2.9 41.1 + - - +
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Residues in contact with LYS 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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259B ASP* 3.3 31.7 + - + +
260B PRO 3.3 0.4 - - - -
261B ILE* 1.3 78.3 - - + +
263B PHE* 1.3 56.1 + - - +
265B ARG* 4.2 10.3 - - - +
266B LYS* 2.9 44.2 + - - +
427B LYS 5.4 1.6 - - - +
428B TRP* 3.6 50.7 - - + +
429B ILE* 6.0 0.2 - - - +
430B SER* 5.7 3.8 + - - -
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Residues in contact with PHE 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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249B TYR* 5.1 4.9 - - + -
250B PHE* 5.3 2.5 - + - -
253B LEU* 3.4 30.7 - - + -
258B ILE* 4.2 11.7 - - + -
259B ASP 3.2 9.9 + - - +
260B PRO 3.0 8.6 + - - +
262B LYS* 1.3 77.8 - - - +
264B ILE* 1.3 74.4 + - + +
267B ALA* 2.9 37.9 + - + +
295B MET* 3.4 28.8 - - + +
407B THR* 3.3 45.3 - - + -
410B LEU* 3.7 16.4 - - + -
411B ALA* 3.4 27.4 - - + -
414B VAL* 4.7 5.4 - - + -
428B TRP* 4.8 1.0 - - - +
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Residues in contact with ILE 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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245B ILE* 4.5 9.6 - - + -
250B PHE* 3.6 35.2 - - + -
260B PRO 2.9 9.1 + - - +
261B ILE* 3.8 8.3 - - + +
263B PHE* 1.3 96.4 - - + +
265B ARG* 1.3 58.8 + - - +
267B ALA* 4.6 1.8 - - - -
268B LYS* 2.9 32.6 + - + +
271B MET* 3.9 30.2 - - + +
407B THR* 4.3 5.4 - - + -
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Residues in contact with ARG 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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261B ILE* 2.9 29.4 + - + +
262B LYS* 3.7 10.7 - - - +
264B ILE* 1.3 79.6 - - - +
266B LYS* 1.3 67.5 + - + +
268B LYS* 3.4 36.7 - - + +
269B ASP* 5.1 1.7 - - - +
294B GLU* 4.4 2.8 - - - +
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Residues in contact with LYS 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 LYS* 2.9 28.6 + - - +
265B ARG* 1.3 82.9 - - + +
267B ALA* 1.3 59.0 + - - +
268B LYS 3.5 0.2 - - - -
269B ASP* 4.6 3.1 + - - +
290B VAL* 3.1 24.8 - - - +
294B GLU* 3.2 50.7 + - + +
295B MET* 3.9 14.3 - - + +
427B LYS* 4.0 34.8 + - + +
428B TRP* 4.8 20.6 - - + +
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Residues in contact with ALA 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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263B PHE* 2.9 28.3 + - + +
264B ILE 3.3 1.1 + - - +
266B LYS* 1.3 76.6 - - - +
268B LYS* 1.3 65.2 + - - +
269B ASP 3.1 2.9 - - - -
270B ALA* 2.9 8.4 + - - +
271B MET* 2.9 33.5 + - + +
290B VAL* 4.6 2.7 - - - -
295B MET* 3.7 8.7 - - + -
407B THR* 5.9 0.2 - - - -
410B LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 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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15B LEU* 5.7 1.6 - - - +
264B ILE* 2.9 16.9 + - + +
265B ARG* 3.4 31.0 - - + +
267B ALA* 1.3 77.2 - - - +
269B ASP* 1.3 84.6 + - - +
271B MET* 3.9 16.4 - - + -
272B ILE* 2.9 50.6 + - + +
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Residues in contact with ASP 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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15B LEU* 4.1 28.4 - - + +
265B ARG 5.1 1.3 - - - +
266B LYS 5.0 1.8 - - - -
267B ALA 3.1 1.2 + - - -
268B LYS* 1.3 107.4 + - - +
270B ALA* 1.3 56.8 + - - +
272B ILE* 4.6 1.3 - - - +
273B THR* 3.8 11.5 + - - -
286B VAL* 3.8 13.0 - - - +
290B VAL* 4.8 12.1 - - + -
294B GLU* 3.8 18.5 - - - +
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Residues in contact with ALA 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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267B ALA 2.9 7.5 + - - +
269B ASP* 1.3 78.6 - - - +
271B MET* 1.3 65.2 + - - +
272B ILE 3.2 1.6 - - - -
273B THR* 3.3 2.9 + - - +
274B ALA* 2.9 25.5 + - - +
283B THR* 4.7 2.9 + - - +
286B VAL* 3.7 22.0 - - + -
287B THR* 4.2 11.4 - - - -
290B VAL* 3.8 23.0 - - + +
406B VAL* 4.6 6.2 - - + +
410B LEU* 4.5 7.6 - - + -
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Residues in contact with MET 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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245B ILE* 5.4 4.3 - - + -
264B ILE* 3.9 32.3 - - + -
267B ALA* 2.9 31.9 + - + +
268B LYS* 3.8 12.1 - - + +
270B ALA* 1.3 78.3 - - - +
272B ILE* 1.3 58.7 + - + +
274B ALA* 3.8 3.4 - - - +
275B PHE* 2.9 25.0 + - - +
403B MET* 3.2 34.8 - - + +
406B VAL* 5.2 3.1 - - + +
407B THR* 2.6 44.4 - - - +
410B LEU* 5.5 1.8 - - + -
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Residues in contact with ILE 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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15B LEU* 3.7 27.8 - - + -
18B ILE* 5.5 0.2 - - + -
19B LEU* 3.8 39.3 - - + -
268B LYS* 2.9 40.4 + - + +
271B MET* 1.3 78.1 - - + +
273B THR* 1.3 59.5 + - - +
275B PHE* 3.2 8.2 + - + +
276B VAL* 2.9 30.4 + - + +
403B MET* 5.8 0.4 - - - -
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Residues in contact with THR 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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14B VAL* 6.0 3.1 - - + +
15B LEU* 3.4 24.6 - - - +
18B ILE* 4.2 16.5 - - + +
204B MET* 4.7 14.1 - - + -
269B ASP 3.8 9.3 + - - -
270B ALA* 3.3 10.2 + - - +
272B ILE* 1.3 78.6 - - - +
274B ALA* 1.3 56.7 + - - +
276B VAL* 3.8 0.9 - - - +
277B THR* 2.9 40.2 + - + +
283B THR* 3.7 22.0 - - - +
286B VAL* 4.5 16.5 - - + +
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Residues in contact with ALA 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 ALA 2.9 18.2 + - - +
271B MET 3.8 2.9 - - - +
273B THR* 1.3 74.7 - - - +
275B PHE* 1.3 67.0 + - - +
277B THR* 4.1 7.9 - - - -
278B ARG* 3.0 19.4 + - - -
283B THR* 4.3 8.5 + - + -
402B THR* 3.2 20.8 - - + +
403B MET* 4.0 5.8 - - - -
406B VAL* 3.5 34.8 - - + -
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Residues in contact with PHE 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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19B LEU* 5.8 2.0 - - + -
22B LEU* 4.4 12.3 - - + -
238B TYR* 4.2 20.9 - + - -
271B MET 2.9 20.2 + - - +
272B ILE* 3.4 9.9 - - + +
274B ALA* 1.3 77.3 - - - +
276B VAL* 1.3 69.5 + - + +
399B MET* 2.9 68.7 - - + +
400B GLY* 4.0 10.3 - - - -
403B MET* 3.5 34.5 - - + +
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Residues in contact with VAL 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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18B ILE* 3.1 42.4 - - + +
19B LEU* 3.7 22.7 - - + -
22B LEU* 3.6 29.4 - - + -
211B VAL* 3.2 33.4 - - + +
272B ILE* 2.9 23.0 + - + +
273B THR 3.9 2.5 - - - +
275B PHE* 1.3 79.2 - - + +
277B THR* 1.3 60.0 + - - +
278B ARG* 3.0 15.9 + - - +
399B MET* 4.0 5.2 - - - +
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Residues in contact with THR 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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18B ILE* 5.2 4.3 - - - -
52B PHE* 3.2 28.3 - - - -
56B LEU* 3.5 4.2 - - - +
204B MET* 3.4 29.5 - - + +
211B VAL* 4.4 7.0 - - - -
273B THR* 2.9 31.5 + - + +
274B ALA* 4.1 2.7 - - - -
276B VAL* 1.3 74.8 - - - +
278B ARG* 1.3 73.4 + - - +
279B SER* 2.9 34.1 + - - +
283B THR* 4.8 2.2 - - - -
359B PRO* 4.2 1.9 - - - +
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Residues in contact with ARG 278 (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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52B PHE* 6.0 0.4 - - + -
53B VAL* 5.9 0.6 - - - +
211B VAL* 5.4 2.9 - - + -
214B LEU* 4.5 25.2 - - + +
218B VAL* 5.3 2.6 - - - +
274B ALA 3.0 15.2 + - - -
275B PHE 4.5 0.7 - - - -
276B VAL 3.0 8.1 + - - +
277B THR* 1.3 84.4 - - - +
279B SER* 1.3 58.8 + - - +
359B PRO* 3.3 29.0 - - + +
360B GLY* 3.0 35.2 - - - +
394B ASP* 4.3 6.1 + - - +
395B ALA* 3.3 36.8 - - - +
398B ASP* 3.0 34.4 + - - +
399B MET* 3.6 32.5 - - + +
402B THR* 3.5 12.8 + - - -
501B ASP 4.4 0.3 + - - -
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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