Contacts of the helix formed by residues 280 - 296 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ARG* 2.9 36.8 + - - -
190C ASN* 2.9 24.0 + - - +
278C GLY 4.8 2.6 - - - +
279C LEU* 1.3 75.8 - - - +
281C HIS* 1.3 67.9 + - - +
282C ALA 4.2 1.1 - - - +
283C GLN* 3.0 48.2 + - + +
284C THR* 3.2 10.0 + - - +
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Residues in contact with HIS 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ASP* 3.0 42.1 + - + -
198C HIS* 4.5 1.0 + - - -
267C HIS* 3.2 34.2 + + + -
271C HIS* 5.8 5.4 + - + -
274C THR* 3.9 15.2 + - + +
279C LEU 3.6 1.6 + - - -
280C ASP* 1.3 71.0 - - - +
282C ALA* 1.3 61.4 + - - +
284C THR* 2.7 25.5 + - - -
285C LEU* 3.3 20.6 + - + +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ASN* 3.3 51.4 - - + +
193C VAL* 3.6 17.8 - - + +
194C ASP* 4.4 4.7 - - + +
280C ASP* 3.2 2.2 - - - +
281C HIS* 1.3 76.4 - - + +
283C GLN* 1.3 65.9 + - - +
285C LEU* 3.2 13.5 + - - +
286C ALA* 3.0 21.1 + - - +
339C VAL* 4.5 2.0 - - + -
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Residues in contact with GLN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ARG* 4.9 7.3 - - - +
190C ASN* 4.4 6.3 + - - +
279C LEU* 3.7 11.8 - - + +
280C ASP* 3.0 52.0 + - + +
282C ALA* 1.3 78.3 - - - +
284C THR* 1.3 61.6 + - - +
286C ALA* 3.4 2.9 + - - +
287C ILE* 3.3 29.2 + - - +
339C VAL* 4.0 17.2 - - + +
340C PRO* 5.6 2.8 - - - +
346C TYR* 3.6 38.5 + - + +
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Residues in contact with THR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLY* 3.2 34.4 + - - +
273C LEU* 3.6 24.2 - - + -
274C THR* 3.2 26.3 + - - +
279C LEU* 3.8 12.8 - - + -
280C ASP 3.2 8.3 + - - +
281C HIS* 2.7 19.9 + - - -
283C GLN* 1.3 77.0 - - - +
285C LEU* 1.3 59.7 + - - +
287C ILE* 3.4 4.4 + - - +
288C VAL* 3.0 34.5 + - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 4.6 0.7 - - + -
194C ASP* 3.2 33.7 - - - +
197C VAL* 3.9 26.9 - - + -
266C THR* 3.8 26.9 - - + +
267C HIS* 3.6 35.0 - - + +
281C HIS* 3.4 29.6 - - + +
282C ALA* 3.2 8.2 + - - +
284C THR* 1.3 79.9 + - - +
286C ALA* 1.3 59.2 + - - +
289C LEU* 3.0 36.1 + - - +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 4.4 3.1 - - + +
282C ALA 3.0 9.1 + - - +
283C GLN 3.8 3.4 - - - +
284C THR 3.4 0.2 - - - -
285C LEU* 1.3 75.6 - - - +
287C ILE* 1.3 57.2 + - - +
290C PRO* 3.2 25.1 - - - +
334C PHE* 3.7 31.3 - - + -
339C VAL* 3.5 32.1 - - + -
340C PRO 3.8 7.9 - - - +
341C THR* 3.4 12.6 - - + +
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 4.4 8.1 - - + -
279C LEU* 3.8 21.1 - - + -
283C GLN 3.3 18.0 + - - +
284C THR* 3.6 8.5 - - - +
286C ALA* 1.3 80.5 - - - +
288C VAL* 1.3 66.0 + - + +
290C PRO* 3.6 9.0 - - - +
291C ALA* 4.0 3.3 + - - +
331C ARG* 4.8 0.7 + - - -
340C PRO 4.0 5.8 - - - +
341C THR 3.5 27.4 - - - +
342C HIS 4.1 3.8 - - - +
343C LEU* 4.2 19.7 - - + -
346C TYR* 3.5 25.6 - - + -
383C TYR* 6.3 0.2 - - + -
386C ALA* 3.6 35.5 - - + +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C THR* 3.8 32.1 - - + +
269C LEU* 3.9 19.1 - - + -
270C GLY 4.1 13.9 - - - +
273C LEU* 3.9 21.8 - - + -
284C THR 3.0 17.8 + - - +
287C ILE* 1.3 78.3 - - + +
289C LEU* 1.3 61.9 + - - +
291C ALA* 3.1 8.0 + - - +
292C LEU* 2.8 30.2 + - + +
382C ILE* 4.1 14.8 - - + -
383C TYR* 4.5 8.1 - - + -
386C ALA* 5.1 1.8 - - + -
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C PHE* 4.8 1.3 - - + -
197C VAL* 4.3 8.5 - - + -
200C VAL* 3.8 23.1 - - + -
201C GLU* 5.7 2.2 - - - +
266C THR* 3.6 28.2 - - + +
285C LEU 3.0 16.9 + - - +
288C VAL* 1.3 76.2 - - - +
290C PRO* 1.3 67.9 - - + +
292C LEU* 3.2 1.5 + - + +
293C TRP* 2.9 75.1 + - + +
330C THR* 4.2 4.0 - - + -
334C PHE* 4.0 26.9 - - + -
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Residues in contact with PRO 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ALA 3.2 25.6 - - - +
287C ILE 3.6 4.0 - - - +
289C LEU* 1.3 98.8 - - + +
291C ALA* 1.3 60.4 + - - +
293C TRP* 3.5 8.4 + - + +
294C ASN* 3.1 23.4 + - - +
327C ILE* 4.0 20.0 - - + +
330C THR* 6.0 2.9 - - + -
331C ARG* 3.5 52.6 + - + +
334C PHE* 4.8 4.7 - - + -
341C THR* 4.6 1.1 - - + -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ILE 4.1 2.2 - - - +
288C VAL 3.1 8.3 + - - +
290C PRO* 1.3 81.0 - - - +
292C LEU* 1.3 62.0 + - - +
294C ASN* 3.4 5.6 + - - +
295C GLU* 3.1 22.9 + - - +
331C ARG* 4.1 6.0 - - - +
382C ILE* 3.4 30.6 - - + +
385C ALA* 4.1 12.9 - - + +
386C ALA* 4.0 24.5 - - + +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ASP* 3.8 8.1 - - - +
265C ALA* 3.6 31.9 - - + +
266C THR* 3.7 24.7 - - - +
269C LEU* 4.6 1.8 - - + -
288C VAL* 2.8 22.8 + - + +
289C LEU* 3.7 3.1 - - + +
291C ALA* 1.3 71.1 - - - +
293C TRP* 1.3 68.1 + - + +
295C GLU* 3.1 2.9 + - - +
296C LYS* 2.9 32.4 + - + +
300C LYS* 3.7 28.0 - - - -
374C ILE* 4.1 7.6 - - + -
382C ILE* 3.9 33.8 - - + +
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Residues in contact with TRP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C PHE* 4.9 0.2 - + - -
200C VAL* 3.7 34.9 + - + +
204C VAL* 3.7 25.4 + - + +
263C ASP* 5.6 0.4 + - - -
289C LEU* 2.9 43.8 + - + +
290C PRO* 3.8 7.6 - - + +
292C LEU* 1.3 86.7 - - + +
294C ASN* 1.3 61.2 + - - +
296C LYS 3.6 0.9 - - - +
297C ARG* 3.0 26.3 + - - +
300C LYS* 3.8 24.7 - - + +
304C LEU* 3.7 18.9 - - + +
307C TYR* 3.6 40.8 - + - -
326C ALA 4.9 0.4 - - - -
327C ILE* 4.1 23.5 - - + +
330C THR* 3.6 20.0 - - + -
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Residues in contact with ASN 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C PRO 3.1 17.3 + - - +
291C ALA* 3.8 6.2 + - - +
293C TRP* 1.3 77.0 - - - +
295C GLU* 1.3 67.2 + - - +
297C ARG* 2.8 55.0 + - - +
324C ASP* 4.7 0.7 - - - +
327C ILE* 3.8 14.6 - - + +
385C ALA* 5.4 8.9 - - - +
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Residues in contact with GLU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ALA 3.1 17.5 + - - +
292C LEU 3.1 4.0 + - - +
294C ASN* 1.3 82.7 + - - +
296C LYS* 1.3 62.6 + - + +
297C ARG* 3.4 1.8 + - - +
298C ASP* 5.0 6.2 - - - +
378C VAL* 3.9 28.6 - - + +
381C ARG* 2.9 55.6 + - - +
382C ILE* 3.8 17.0 - - + -
385C ALA* 6.3 1.1 - - + -
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Residues in contact with LYS 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU* 2.9 18.4 + - + +
293C TRP 3.6 3.6 - - - -
295C GLU* 1.3 83.8 + - + +
297C ARG* 1.3 63.5 + - - +
298C ASP* 3.1 4.8 + - - +
299C THR* 3.3 24.6 + - + +
300C LYS* 3.0 39.8 + - + +
371C ASN* 5.8 0.4 - - - +
373C ASP* 3.1 34.9 + - - +
374C ILE* 3.5 40.4 - - + -
378C VAL* 4.0 17.8 - - + +
382C ILE* 5.4 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
------------------------------------------------------------
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