Contacts of the helix formed by residues 269 - 285 (chain C) in PDB entry 2QMR
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 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C PRO* 3.6 25.5 - - + +
232C ARG* 4.8 1.1 - - - +
267C ASP* 3.1 8.1 + - - +
268C GLN* 1.3 79.2 - - + +
270C GLU* 1.3 58.8 + - - +
271C ASN* 3.0 37.7 + - - +
272C VAL* 3.2 30.5 + - + +
273C ALA* 3.1 27.9 + - - +
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Residues in contact with GLU 270 (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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267C ASP 5.7 0.9 - - - +
268C GLN 3.6 7.2 + - - +
269C ASP* 1.3 72.2 + - - +
271C ASN* 1.3 67.2 + - - +
273C ALA* 3.9 4.6 - - - +
274C LEU* 3.3 25.9 + - + +
311C SER* 5.0 12.7 + - - -
313C ILE* 6.6 0.4 - - - -
374C ASN* 6.1 0.3 - - - +
375C LEU* 3.8 34.3 + - + +
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Residues in contact with ASN 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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230C GLU* 5.8 1.4 + - - -
233C LYS* 4.4 23.8 - - + +
269C ASP* 3.0 15.1 + - - +
270C GLU* 1.3 77.6 - - - +
272C VAL* 1.3 64.4 + - + +
274C LEU* 4.2 6.4 - - - +
275C GLU* 3.3 27.7 + - - +
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Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO 3.5 24.0 - - - +
232C ARG* 3.6 30.1 - - + +
233C LYS* 4.0 15.0 - - + +
236C CYS* 4.5 3.6 - - - -
264C ARG* 4.2 10.3 - - - +
267C ASP* 3.7 24.0 - - + +
269C ASP* 3.2 32.2 + - + +
271C ASN* 1.3 73.0 - - - +
273C ALA* 1.3 66.6 + - - +
275C GLU* 3.3 3.5 + - - +
276C ALA* 2.9 22.0 + - - +
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Residues in contact with ALA 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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264C ARG 3.4 15.0 + - - +
265C THR* 3.5 22.3 - - - +
267C ASP 4.3 9.6 - - - +
269C ASP 3.1 16.8 + - - +
270C GLU* 4.0 9.0 - - - +
271C ASN 3.3 0.2 - - - -
272C VAL* 1.3 76.5 - - - +
274C LEU* 1.3 52.9 + - - +
276C ALA* 3.0 4.9 + - - +
277C CYS* 2.8 34.8 + - - +
375C LEU* 4.2 17.3 - - + -
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Residues in contact with LEU 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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270C GLU* 3.3 17.0 + - + +
271C ASN* 4.2 5.6 - - - +
273C ALA* 1.3 78.5 - - - +
275C GLU* 1.3 66.7 + - - +
277C CYS* 3.5 0.9 + - - +
278C GLU* 3.3 24.1 + - - +
373C TRP* 3.8 30.5 - - + +
374C ASN* 3.7 39.9 - - - +
375C LEU* 4.0 17.8 - - + +
378C CYS* 3.8 9.9 - - + -
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Residues in contact with GLU 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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233C LYS* 3.8 39.0 - - + +
236C CYS* 4.3 5.6 - - + +
237C ARG* 3.6 37.0 + - - +
240C VAL* 3.6 15.2 - - - +
261C MET* 4.2 0.2 - - - +
271C ASN 3.3 17.6 + - - +
272C VAL 3.6 4.3 - - - +
273C ALA 3.2 0.6 - - - -
274C LEU* 1.3 80.7 - - + +
276C ALA* 1.3 65.5 + - - +
278C GLU* 3.5 26.3 - - - +
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Residues in contact with ALA 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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236C CYS* 3.9 5.6 - - - +
261C MET* 3.5 14.6 - - + +
264C ARG* 3.4 33.4 - - + -
265C THR* 3.5 17.9 + - - +
272C VAL 2.9 11.9 + - - +
273C ALA 3.0 7.6 + - - +
275C GLU* 1.3 74.9 - - - +
277C CYS* 1.3 57.5 + - - +
279C PHE* 2.8 35.5 + - - +
280C TRP* 4.0 0.7 + - - -
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Residues in contact with CYS 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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265C THR* 4.0 7.2 - - + -
273C ALA 2.8 15.3 + - - +
274C LEU* 3.6 7.2 - - - +
276C ALA* 1.3 77.7 - - - +
278C GLU* 1.3 54.9 + - - +
280C TRP* 3.0 37.2 + - - +
281C LEU 3.7 3.1 + - - -
304C LEU* 4.2 11.9 - - - -
375C LEU* 3.7 14.8 - - + -
378C CYS* 3.5 22.1 - - - -
379C SER* 3.5 35.7 - - - -
382C ALA* 5.0 0.6 - - - +
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Residues in contact with GLU 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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240C VAL* 4.2 15.0 - - + -
274C LEU* 3.3 18.1 + - - +
275C GLU* 3.5 25.9 - - - +
277C CYS* 1.3 74.0 - - - +
279C PHE* 1.3 62.5 + - - +
280C TRP 3.2 0.2 - - - -
281C LEU* 3.5 12.3 + - + +
282C THR* 3.0 33.1 + - - +
373C TRP* 3.3 38.9 + - - -
378C CYS* 3.7 8.9 - - - -
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Residues in contact with PHE 279 (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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239C LEU 4.0 12.8 - - - -
240C VAL* 3.7 14.3 - - + +
243C LEU* 3.3 34.2 - - + +
250C LEU* 5.7 0.9 - - + -
254C MET* 4.3 9.2 - - - -
257C ILE* 3.5 31.0 - - + -
258C VAL* 4.4 8.3 - - + -
261C MET* 3.5 35.2 - - + -
276C ALA 2.8 20.3 + - - +
278C GLU* 1.3 78.6 - - - +
280C TRP* 1.3 75.5 + + + +
282C THR* 3.3 4.2 + - - -
283C LEU* 2.7 56.4 + - + +
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Residues in contact with TRP 280 (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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258C VAL* 3.6 26.2 - - + -
261C MET* 3.6 11.9 - - + -
262C LEU* 3.4 36.3 - - + -
265C THR* 2.6 24.7 + - + +
276C ALA 4.0 3.5 + - - -
277C CYS* 3.0 27.9 + - - +
279C PHE* 1.3 93.6 - + - +
281C LEU* 1.3 56.3 + - - +
283C LEU* 3.9 6.3 - - + +
284C ALA* 2.8 37.4 + - - +
293C LEU* 4.0 25.0 - - + +
300C LEU* 3.5 33.8 - - + +
304C LEU* 4.0 19.1 - - + -
382C ALA* 4.0 17.3 - - + -
386C LEU* 5.1 4.4 - - + +
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Residues in contact with LEU 281 (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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277C CYS 3.7 2.9 + - - +
278C GLU* 3.7 21.3 - - + +
280C TRP* 1.3 79.9 - - - +
282C THR* 1.3 62.4 + - - +
284C ALA* 3.7 5.0 + - - +
285C GLU* 3.5 44.6 + - - +
373C TRP* 3.7 30.5 - - + -
378C CYS* 4.0 11.0 - - - +
381C ALA* 4.1 12.8 - - + -
382C ALA* 4.1 21.8 - - + +
385C VAL* 4.3 16.2 - - + -
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Residues in contact with THR 282 (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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240C VAL* 3.6 18.5 - - - +
243C LEU* 4.0 22.9 - - + -
244C GLU* 3.7 33.6 - - + +
278C GLU* 3.0 20.3 + - - +
279C PHE 3.7 2.9 - - - -
281C LEU* 1.3 77.0 - - - +
283C LEU* 1.3 67.2 + - - +
285C GLU* 3.1 16.5 + - - +
286C GLN* 3.3 22.2 + - - +
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Residues in contact with LEU 283 (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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243C LEU* 3.9 24.4 - - + +
254C MET* 5.3 2.9 - - - -
258C VAL* 4.8 1.1 - - + -
279C PHE* 2.7 39.8 + - + +
280C TRP* 3.9 7.0 - - + +
282C THR* 1.3 73.4 - - - +
284C ALA* 1.3 55.2 + - - +
286C GLN* 2.8 39.3 + - + +
288C ILE* 4.9 5.4 - - + -
289C CYS* 3.4 26.5 - - - +
292C VAL* 4.3 22.4 - - + -
293C LEU* 3.8 40.6 - - + -
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Residues in contact with ALA 284 (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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280C TRP 2.8 18.9 + - - +
281C LEU* 3.7 8.1 - - - +
282C THR 3.2 0.2 - - - -
283C LEU* 1.3 76.7 - - - +
285C GLU* 1.3 59.3 + - - +
286C GLN 3.3 1.7 + - - +
289C CYS* 3.7 17.5 - - - +
293C LEU* 5.7 0.2 - - - +
382C ALA 5.0 0.7 - - - +
385C VAL* 3.8 25.7 - - + +
386C LEU* 3.9 21.3 - - + -
389C VAL* 3.5 21.6 - - + +
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Residues in contact with GLU 285 (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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244C GLU* 5.3 4.9 - - - +
281C LEU* 3.5 34.4 + - - +
282C THR* 3.1 12.3 + - - +
283C LEU 2.9 1.6 + - - -
284C ALA* 1.3 79.1 - - - +
286C GLN* 1.3 69.2 + - - +
287C PRO* 3.8 6.1 - - - +
385C VAL* 4.4 16.6 - - + +
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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