Contacts of the helix formed by residues 280 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PRO* 5.8 3.5 - - - +
68A ASN* 5.2 6.7 + - - +
186A ARG* 2.8 46.2 + - - +
187A GLN* 4.0 6.1 - - - +
190A ASN* 3.0 26.7 - - - +
278A GLY 3.6 3.2 + - - +
279A LEU* 1.3 75.4 - - - +
281A HIS* 1.3 67.7 + - - +
283A GLN* 2.9 31.1 + - + +
284A THR* 3.2 10.2 + - - +
1389A BO3 3.4 3.6 + - - -
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 4.6 8.0 + - - +
160A LYS* 4.7 1.2 - - - -
194A ASP* 3.2 32.7 + - - -
267A HIS* 3.3 21.9 + + + -
271A HIS* 4.0 17.3 - + - -
274A THR* 3.8 10.6 + - - +
279A LEU 3.6 1.8 + - - -
280A ASP* 1.3 72.3 - - - +
282A ALA* 1.3 62.2 + - - +
284A THR* 2.7 25.7 + - - -
285A LEU* 3.4 20.3 + - + +
1388A NZQ 3.0 70.7 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASN* 3.2 51.3 - - + +
193A VAL* 3.7 16.4 - - + +
194A ASP* 4.4 5.8 - - + +
280A ASP* 3.3 2.0 - - - +
281A HIS* 1.3 77.2 - - - +
283A GLN* 1.3 65.9 + - - +
285A LEU* 3.2 13.3 + - - +
286A ALA* 3.0 20.4 + - - +
339A VAL* 4.5 1.8 - - - -
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 4.0 17.3 + - - +
190A ASN* 4.2 0.4 - - - +
279A LEU* 3.8 9.7 - - + +
280A ASP* 2.9 40.1 + - + +
282A ALA* 1.3 77.5 - - - +
284A THR* 1.3 61.8 + - - +
286A ALA* 3.4 3.1 + - - +
287A ILE* 3.2 29.5 + - - +
339A VAL* 3.9 8.7 - - + -
346A TYR* 3.4 40.0 + - + +
1389A BO3 2.4 44.3 + - - +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY* 3.2 34.1 + - - +
273A LEU* 3.7 18.8 - - + -
274A THR* 3.3 24.4 + - - +
279A LEU* 3.8 12.6 - - + -
280A ASP 3.2 8.9 + - - +
281A HIS* 2.7 18.9 + - - -
283A GLN* 1.3 75.7 - - - +
285A LEU* 1.3 61.1 + - - +
287A ILE* 3.5 8.7 + - - +
288A VAL* 3.0 33.4 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL* 4.5 1.1 - - + +
194A ASP* 3.3 30.1 - - - +
197A VAL* 3.9 26.2 - - + -
266A THR* 4.0 14.4 - - + +
267A HIS* 3.6 45.1 - - + +
281A HIS* 3.4 29.8 - - + +
282A ALA* 3.2 13.2 + - - +
284A THR* 1.3 77.4 - - - +
286A ALA* 1.3 59.7 + - - +
288A VAL* 4.8 0.2 - - - -
289A LEU* 2.9 36.3 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL* 4.5 2.8 - - + +
282A ALA 3.0 8.5 + - - +
283A GLN 3.7 3.6 - - - +
285A LEU* 1.3 76.7 - - - +
287A ILE* 1.3 57.5 + - - +
290A PRO* 3.1 26.2 - - - +
334A PHE* 3.7 27.7 - - + -
339A VAL* 3.6 35.4 - - + +
340A PRO 3.8 7.9 - - - +
341A THR* 3.4 12.1 - - + +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU* 4.7 3.1 - - + -
279A LEU* 3.6 22.0 - - + -
283A GLN 3.2 17.1 + - - +
284A THR* 3.7 7.4 - - - +
286A ALA* 1.3 79.9 - - - +
288A VAL* 1.3 70.6 + - + +
290A PRO* 3.6 6.8 - - - +
291A ALA* 4.2 2.9 + - - +
331A ARG* 5.2 0.3 + - - -
340A PRO 4.1 1.3 - - - +
341A THR 3.5 21.8 - - - +
342A HIS 4.0 2.5 - - - +
343A LEU* 4.0 24.5 - - + +
346A TYR* 3.5 32.8 - - + -
383A TYR* 6.3 0.4 - - + -
386A ALA* 3.6 38.2 - - + +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A THR* 3.9 26.5 - - + +
269A LEU* 3.8 38.6 - - + -
270A GLY 4.4 4.3 - - - +
273A LEU* 3.9 22.2 - - + -
284A THR 3.0 18.7 + - - +
287A ILE* 1.3 79.3 - - + +
289A LEU* 1.3 61.4 + - - +
291A ALA* 3.2 7.1 + - - +
292A LEU* 2.8 28.3 + - + -
382A ILE* 4.2 8.1 - - + -
383A TYR* 4.4 9.2 - - + -
386A ALA* 5.0 2.5 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 5.1 1.1 - - + -
197A VAL* 4.2 9.0 - - + -
200A VAL* 4.0 25.1 - - + -
201A GLU* 5.6 2.2 - - - +
266A THR* 3.5 29.5 - - + +
285A LEU 2.9 19.3 + - - +
288A VAL* 1.3 76.7 - - - +
290A PRO* 1.3 61.6 - - + +
292A LEU* 3.2 2.2 + - + +
293A TRP* 2.8 73.6 + - + +
330A THR* 4.3 5.8 - - + -
334A PHE* 4.0 27.6 - - + -
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Residues in contact with PRO 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ALA 3.1 24.0 - - - +
287A ILE 3.6 2.9 - - - +
288A VAL 3.5 2.7 - - - -
289A LEU* 1.3 96.3 - - + +
291A ALA* 1.3 60.7 + - - +
293A TRP* 3.6 4.9 + - + -
294A ASN* 3.2 23.0 + - - +
327A ILE* 3.9 24.6 - - + +
330A THR* 6.0 3.1 - - + -
331A ARG* 3.3 54.2 + - + +
334A PHE* 5.1 4.7 - - + -
341A THR* 4.6 0.4 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ILE 4.2 1.7 + - - +
288A VAL 3.2 8.1 + - - +
290A PRO* 1.3 79.0 - - - +
292A LEU* 1.3 66.0 + - - +
294A ASN* 3.4 7.6 + - - +
295A GLU* 3.1 22.3 + - - +
331A ARG* 4.4 5.0 - - - +
382A ILE* 3.5 30.5 - - + +
385A ALA* 4.1 17.5 - - + +
386A ALA* 4.0 17.7 - - + +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP* 3.8 20.4 - - - +
265A ALA* 3.7 27.1 - - + -
266A THR* 3.6 25.4 - - - +
269A LEU* 4.0 18.2 - - + -
288A VAL* 2.8 20.5 + - + +
289A LEU* 3.6 2.9 - - + +
291A ALA* 1.3 73.5 - - - +
293A TRP* 1.3 64.1 + - + +
295A GLU* 3.2 2.1 + - - +
296A LYS* 2.8 43.9 + - + +
300A LYS* 3.8 16.6 - - - -
374A ILE* 4.1 3.8 - - + -
382A ILE* 3.9 20.8 - - + +
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Residues in contact with TRP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.6 36.6 + - + +
204A VAL* 3.8 23.8 + - + +
263A ASP* 5.5 0.2 + - - -
289A LEU* 2.8 44.1 + - + +
290A PRO* 3.9 5.6 - - + +
292A LEU* 1.3 81.1 - - + +
294A ASN* 1.3 56.7 + - - +
296A LYS* 3.4 2.1 - - - +
297A ARG* 3.0 31.9 + - - +
300A LYS* 3.8 26.4 - - + +
304A LEU* 3.8 17.3 - - + +
307A TYR* 3.6 32.8 - + - -
326A ALA 4.9 0.7 - - - -
327A ILE* 3.9 26.6 - - + +
330A THR* 3.5 30.5 - - + -
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Residues in contact with ASN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PRO 3.2 14.8 + - - +
291A ALA* 3.7 7.1 + - - +
292A LEU 3.3 0.2 - - - -
293A TRP* 1.3 79.6 - - - +
295A GLU* 1.3 65.1 + - - +
297A ARG* 3.0 51.9 + - - +
327A ILE* 3.7 12.9 - - + +
385A ALA* 5.8 6.3 - - - +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA 3.1 12.0 + - - +
292A LEU 3.5 7.4 - - - +
294A ASN* 1.3 83.7 + - - +
296A LYS* 1.3 67.0 + - + +
297A ARG* 3.4 3.2 + - - +
298A ASP 5.2 0.5 + - - -
378A VAL* 3.9 15.0 - - + +
381A ARG* 3.0 53.5 + - - +
382A ILE* 3.9 22.9 - - + -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 2.8 36.4 + - + +
293A TRP 3.4 2.7 - - - -
295A GLU* 1.3 93.2 + - + +
297A ARG* 1.3 61.2 + - - +
298A ASP 3.1 3.9 + - - -
299A THR* 3.2 23.1 + - - +
300A LYS* 3.1 43.5 + - + +
369A GLY* 6.2 0.2 - - - -
370A GLU* 6.2 1.3 - - - -
371A ASN* 5.3 2.0 - - - +
373A ASP* 2.7 44.3 + - - -
374A ILE* 3.8 22.9 - - + +
378A VAL* 4.8 3.9 - - + +
382A ILE* 5.2 0.4 - - + -
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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