Contacts of the helix formed by residues 264 - 278 (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 TRP 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C HIS* 3.6 37.0 - + - -
201C GLU* 2.8 42.8 + - + -
202C GLN* 4.0 18.2 - - + -
262C GLN* 2.9 41.7 + - + +
263C ASP* 1.3 75.1 - - - +
265C ALA* 1.3 62.1 + - - -
266C THR 3.2 2.2 - - - -
267C HIS* 3.2 37.8 + + + +
268C MET* 3.0 37.1 + - + +
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Residues in contact with ALA 265 (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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263C ASP* 3.0 20.8 + - - +
264C TRP* 1.3 75.0 - - - +
266C THR* 1.3 61.2 + - - +
268C MET* 3.8 3.3 - - - +
269C LEU* 2.9 35.3 + - + +
292C LEU* 3.6 19.5 - - + -
368C LEU* 3.9 16.6 - - + -
369C GLY 3.9 9.2 - - - +
374C ILE* 3.7 18.2 - - + -
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C VAL* 4.2 5.6 - - + -
201C GLU* 3.4 17.6 + - - -
263C ASP* 4.7 0.7 + - - -
264C TRP 3.2 0.2 - - - -
265C ALA* 1.3 79.7 - - - +
267C HIS* 1.3 56.8 + - - +
270C GLY* 2.9 27.0 + - - -
285C LEU* 3.8 19.8 - - + +
288C VAL* 3.8 15.4 - - + +
289C LEU* 3.6 51.2 - - + +
292C LEU* 3.7 16.9 - - - +
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Residues in contact with HIS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C VAL* 3.9 8.1 - - + -
198C HIS* 3.1 40.1 + + - -
201C GLU* 2.8 27.7 + - + +
264C TRP* 3.2 29.2 + + + +
266C THR* 1.3 77.1 - - - +
268C MET* 1.3 70.8 + - + +
270C GLY* 3.3 0.7 + - - -
271C HIS* 2.9 30.3 + - - +
281C HIS* 3.2 31.2 + + - -
285C LEU* 3.6 25.7 - - + +
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Residues in contact with MET 268 (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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264C TRP* 3.0 29.9 + - + +
265C ALA 3.2 4.4 + - - +
267C HIS* 1.3 89.9 - - + +
269C LEU* 1.3 64.8 + - - +
271C HIS* 3.4 18.0 + - + +
272C GLU* 3.6 13.2 + - - +
360C LEU* 4.1 2.1 - - - +
365C MET* 3.7 34.0 - - + +
368C LEU* 3.9 33.4 - - + -
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Residues in contact with LEU 269 (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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265C ALA* 2.9 19.5 + - + +
268C MET* 1.3 76.4 - - - +
270C GLY* 1.3 61.9 + - - +
272C GLU 3.4 6.6 + - - -
273C LEU* 3.7 4.5 + - - +
288C VAL* 3.9 15.0 - - + -
292C LEU* 4.6 2.9 - - + -
360C LEU* 3.5 35.4 - - + -
368C LEU* 3.9 11.4 - - + -
374C ILE* 5.1 1.3 - - + -
379C SER* 3.5 18.6 - - - +
382C ILE* 3.7 45.5 - - + -
383C TYR* 2.6 39.1 + - + +
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C THR 2.9 19.0 + - - -
267C HIS 3.7 1.1 - - - -
269C LEU* 1.3 75.4 - - - +
271C HIS* 1.3 64.3 + - - +
273C LEU* 3.1 11.8 + - - -
274C THR* 3.2 5.0 + - - -
281C HIS* 5.9 0.7 - - - -
284C THR* 3.2 41.5 + - - +
285C LEU* 4.9 1.6 - - - -
288C VAL* 4.1 9.1 - - - +
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Residues in contact with HIS 271 (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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160C LYS* 3.4 31.9 + - + -
267C HIS 2.9 18.1 + - - +
268C MET* 3.6 11.2 - - + +
269C LEU 3.3 0.4 - - - -
270C GLY* 1.3 77.3 - - - +
272C GLU* 1.3 74.2 + - - +
274C THR* 3.2 13.0 + - + +
275C ALA* 3.0 34.4 + - + +
281C HIS* 5.8 4.6 + - + +
363C HIS* 4.9 8.9 + - - -
365C MET* 6.3 2.7 - - + -
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Residues in contact with GLU 272 (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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268C MET 3.9 5.0 - - - +
269C LEU 3.4 1.0 + - - -
270C GLY 3.2 0.8 - - - -
271C HIS* 1.3 87.4 - - - +
273C LEU* 1.3 57.9 + - - +
275C ALA* 3.8 7.7 - - - +
276C MET* 3.0 32.1 + - - +
356C LEU* 3.5 16.4 - - + +
359C LYS* 3.5 21.7 - - + +
360C LEU* 3.5 35.7 - - + +
363C HIS* 2.7 42.7 + - - +
365C MET* 4.6 3.3 - - - +
383C TYR* 3.7 13.7 - - - +
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Residues in contact with LEU 273 (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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269C LEU 3.7 7.8 + - - +
270C GLY 3.1 7.0 + - - +
272C GLU* 1.3 75.1 - - - +
274C THR* 1.3 59.2 + - - +
277C HIS* 2.9 42.9 + - + +
278C GLY 3.5 0.7 + - - -
279C LEU* 4.1 8.2 + - + +
284C THR* 3.6 24.0 - - + +
287C ILE* 4.4 9.0 - - + -
288C VAL* 3.9 28.0 - - + -
343C LEU* 4.0 30.7 - - + -
356C LEU* 3.6 33.0 - - + -
383C TYR* 4.1 9.0 - - + -
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Residues in contact with THR 274 (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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160C LYS* 6.1 1.8 - - - +
270C GLY 3.2 7.0 + - - -
271C HIS* 3.2 17.3 + - + +
273C LEU* 1.3 74.8 - - - +
275C ALA* 1.3 61.1 - - - +
278C GLY* 2.9 27.5 + - - -
279C LEU 2.9 27.6 + - - +
281C HIS* 3.9 16.3 + - + +
284C THR* 3.2 14.6 + - - +
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Residues in contact with ALA 275 (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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271C HIS* 3.0 28.0 + - + +
272C GLU* 3.8 16.4 - - - +
273C LEU 3.3 0.2 - - - -
274C THR* 1.3 79.7 - - - +
276C MET* 1.3 60.2 + - + +
278C GLY 4.9 0.2 + - - -
359C LYS* 6.2 2.5 - - + -
363C HIS* 5.7 3.1 - - + -
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Residues in contact with MET 276 (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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272C GLU 3.0 17.2 + - - +
275C ALA* 1.3 78.6 - - + +
277C HIS* 1.3 86.1 + - + +
278C GLY 3.8 0.4 - - - -
352C SER* 4.1 7.4 - - - -
355C ALA* 3.6 41.7 - - + +
356C LEU* 3.6 21.8 - - + +
359C LYS* 4.1 19.5 - - + -
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Residues in contact with HIS 277 (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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273C LEU* 2.9 32.5 + - + +
276C MET* 1.3 100.9 + - + +
278C GLY* 1.3 62.8 + - - +
279C LEU* 3.2 14.1 + - + +
348C LEU* 3.5 46.6 - - + +
352C SER* 2.8 40.4 + - - -
356C LEU* 4.5 1.2 - - + +
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Residues in contact with GLY 278 (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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274C THR* 2.9 18.5 + - - -
275C ALA 4.9 0.2 + - - -
276C MET 3.8 0.8 - - - -
277C HIS* 1.3 76.5 - - - +
279C LEU* 1.3 66.3 + - - +
280C ASP* 3.7 3.5 + - - +
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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