Contacts of the helix formed by residues 280 - 296 (chain B) in PDB entry 1OJ7
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 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B PRO* 5.9 2.9 - - - +
68B ASN* 5.5 5.4 + - - +
186B ARG* 5.9 1.2 - - - +
187B GLN* 3.8 14.4 + - - -
190B ASN* 3.0 31.0 + - - +
278B GLY 3.6 3.7 + - - +
279B LEU* 1.3 74.5 - - - +
281B HIS* 1.3 66.8 + - - +
282B ALA 4.4 0.4 - - - +
283B GLN* 3.0 44.7 + - + +
284B THR* 3.2 9.9 + - - +
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Residues in contact with HIS 281 (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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68B ASN* 4.9 7.1 + - - +
160B LYS* 4.6 1.4 - - - +
194B ASP* 3.3 20.4 + - + -
267B HIS* 3.2 15.9 + + - -
271B HIS* 3.6 19.1 - + - -
274B THR* 3.9 11.5 + - - +
279B LEU 3.5 1.8 + - - -
280B ASP* 1.3 70.4 - - - +
282B ALA* 1.3 62.0 + - - +
284B THR* 2.6 26.1 + - - -
285B LEU* 3.2 21.9 + - + +
1388B NZQ 2.9 52.8 + - - +
1389B ZN 2.1 36.2 - - - -
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Residues in contact with ALA 282 (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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190B ASN* 3.1 52.5 - - + +
193B VAL* 3.6 18.5 - - + +
194B ASP* 4.4 4.9 - - + +
280B ASP* 3.3 1.4 - - - +
281B HIS* 1.3 80.5 - - + +
283B GLN* 1.3 62.1 + - - +
285B LEU* 3.3 11.8 + - - -
286B ALA* 3.0 20.6 + - - +
339B VAL* 4.4 2.2 - - + -
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Residues in contact with GLN 283 (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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186B ARG* 5.6 12.3 - - - +
190B ASN* 4.3 6.7 + - - +
279B LEU* 3.9 12.9 - - + +
280B ASP* 3.0 46.8 + - + +
282B ALA* 1.3 77.1 - - - +
284B THR* 1.3 61.7 + - - +
286B ALA* 3.3 2.6 + - - +
287B ILE* 3.2 30.2 + - - +
339B VAL* 3.9 17.5 - - + +
340B PRO* 5.6 2.6 - - - +
346B TYR* 3.5 39.2 + - + +
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Residues in contact with THR 284 (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 GLY* 3.2 35.5 + - - +
273B LEU* 3.7 17.9 - - + -
274B THR* 3.2 25.1 + - - +
279B LEU* 3.8 13.9 - - + -
280B ASP 3.4 8.5 - - - +
281B HIS* 2.6 20.1 + - - -
283B GLN* 1.3 76.3 - - - +
285B LEU* 1.3 59.9 + - - +
287B ILE* 3.5 10.2 + - - +
288B VAL* 3.1 33.7 + - - +
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Residues in contact with LEU 285 (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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193B VAL* 4.5 0.9 - - + -
194B ASP* 3.3 30.5 - - - +
197B VAL* 3.9 24.5 - - + -
266B THR* 4.0 15.3 - - + +
267B HIS* 3.6 46.9 - - + +
281B HIS* 3.4 30.5 - - + +
282B ALA* 3.6 11.2 - - - +
283B GLN 3.2 0.4 - - - -
284B THR* 1.3 78.8 - - - +
286B ALA* 1.3 59.8 + - - +
289B LEU* 3.0 35.2 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.5 2.4 - - + +
282B ALA 3.0 8.4 + - - +
283B GLN 3.7 2.9 - - - +
285B LEU* 1.3 76.2 - - - +
287B ILE* 1.3 57.2 + - - +
290B PRO* 3.2 20.8 - - - +
334B PHE* 3.7 27.8 - - + -
339B VAL* 3.5 33.2 - - + +
340B PRO 3.8 8.3 - - - +
341B THR* 3.3 21.1 - - + +
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Residues in contact with ILE 287 (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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273B LEU* 4.6 3.1 - - + -
279B LEU* 4.0 19.1 - - + -
283B GLN 3.2 17.6 + - - +
284B THR* 3.7 8.7 - - - +
285B LEU 3.2 0.2 - - - -
286B ALA* 1.3 77.8 - - - +
288B VAL* 1.3 68.4 + - + +
290B PRO* 3.5 9.0 - - - +
291B ALA* 4.2 3.6 + - - +
331B ARG* 5.2 0.9 + - - -
340B PRO 4.0 1.1 - - - +
341B THR 3.4 23.3 - - - +
342B HIS 4.0 1.6 - - - +
343B LEU* 4.0 22.2 - - + +
346B TYR* 3.4 35.4 - - + -
383B TYR* 6.3 0.4 - - + -
386B ALA* 3.6 39.2 - - + +
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Residues in contact with VAL 288 (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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266B THR* 3.9 32.1 - - + +
269B LEU* 4.0 34.8 - - + -
270B GLY 4.4 4.3 - - - +
273B LEU* 4.0 22.2 - - + -
284B THR 3.1 17.6 + - - +
287B ILE* 1.3 78.1 - - + +
289B LEU* 1.3 61.9 + - - +
291B ALA* 3.1 7.4 + - - +
292B LEU* 2.8 29.5 + - + +
382B ILE* 4.2 7.2 - - + -
383B TYR* 4.4 8.7 - - + -
386B ALA* 4.9 2.2 - - + -
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Residues in contact with LEU 289 (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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196B PHE* 5.0 0.9 - - + -
197B VAL* 4.1 9.4 - - + -
200B VAL* 4.0 19.7 - - + -
201B GLU* 5.7 2.0 - - - +
266B THR* 3.5 28.4 - - + +
285B LEU 3.0 19.3 + - - +
288B VAL* 1.3 76.3 - - - +
290B PRO* 1.3 60.5 - - + +
292B LEU* 3.2 1.7 + - + +
293B TRP* 2.9 78.0 + - + +
330B THR* 4.2 6.7 - - + -
334B PHE* 4.0 26.7 - - + -
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Residues in contact with PRO 290 (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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286B ALA* 3.2 25.1 - - - +
287B ILE 3.5 7.2 - - - +
289B LEU* 1.3 96.7 - - + +
291B ALA* 1.3 59.2 + - - +
293B TRP* 3.6 7.1 + - + +
294B ASN* 3.1 23.0 + - - +
327B ILE* 3.9 23.4 - - + +
330B THR* 5.9 3.6 - - + -
331B ARG* 3.3 50.0 + - + +
334B PHE* 5.0 4.5 - - + -
341B THR* 4.6 0.7 - - + -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE 4.2 2.0 + - - +
288B VAL 3.1 7.5 + - - +
290B PRO* 1.3 76.7 - - - +
292B LEU* 1.3 65.8 + - - +
294B ASN* 3.4 6.9 + - - +
295B GLU* 3.1 22.3 + - - +
331B ARG* 4.3 6.3 - - - +
382B ILE* 3.5 29.5 - - + +
385B ALA* 4.2 12.0 - - + +
386B ALA* 3.9 23.6 - - + +
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Residues in contact with LEU 292 (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 ASP* 3.9 8.5 - - - +
265B ALA* 3.7 29.2 - - + +
266B THR* 3.6 26.5 - - - +
269B LEU* 4.6 2.5 - - + -
288B VAL* 2.8 24.4 + - + +
289B LEU* 3.7 3.1 - - + +
291B ALA* 1.3 73.1 - - - +
293B TRP* 1.3 64.2 + - + +
295B GLU* 3.2 2.8 + - - +
296B LYS* 2.9 41.0 + - + +
300B LYS* 3.8 27.1 - - - -
374B ILE* 4.1 4.3 - - + -
382B ILE* 3.9 32.6 - - + +
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Residues in contact with TRP 293 (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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200B VAL* 3.7 34.1 + - + +
204B VAL* 3.8 23.9 + - + +
263B ASP* 5.5 0.6 + - - -
289B LEU* 2.9 43.9 + - + +
290B PRO* 3.8 7.9 - - + +
292B LEU* 1.3 83.9 - - + +
294B ASN* 1.3 61.6 + - - +
296B LYS* 3.3 2.7 + - - -
297B ARG* 3.0 26.0 + - - +
300B LYS* 3.8 23.5 - - + +
304B LEU* 3.8 19.0 - - + +
307B TYR* 3.6 32.8 - + - -
326B ALA 4.9 0.9 - - - -
327B ILE* 4.0 24.5 - - + -
330B THR* 3.6 30.3 - - + -
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Residues in contact with ASN 294 (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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290B PRO 3.1 17.1 + - - +
291B ALA* 3.8 6.6 + - - +
292B LEU 3.3 0.2 - - - -
293B TRP* 1.3 74.8 - - - +
295B GLU* 1.3 66.6 + - - +
297B ARG* 3.0 48.7 + - - +
327B ILE* 3.8 14.5 - - + +
385B ALA* 5.6 7.3 - - - +
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Residues in contact with GLU 295 (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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291B ALA 3.1 14.1 + - - +
292B LEU 3.2 8.3 + - - +
294B ASN* 1.3 80.5 + - - +
296B LYS* 1.3 64.0 + - + +
297B ARG* 3.4 2.9 + - - +
298B ASP* 4.0 7.8 - - - +
378B VAL* 3.8 15.9 - - + +
381B ARG* 2.7 53.8 + - - +
382B ILE* 3.8 24.9 - - + -
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Residues in contact with LYS 296 (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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292B LEU* 2.9 35.5 + - + +
293B TRP 3.4 2.9 - - - -
295B GLU* 1.3 91.4 + - + +
297B ARG* 1.3 58.1 + - - +
298B ASP* 3.1 11.6 + - - -
299B THR* 3.4 20.4 + - - +
300B LYS* 3.0 48.0 + - + +
370B GLU* 6.1 1.6 - - - -
371B ASN* 5.4 1.3 - - - +
373B ASP* 2.8 43.6 + - - -
374B ILE* 3.9 22.2 - - + +
378B VAL* 4.6 5.3 - - + +
382B ILE* 5.1 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