Contacts of the helix formed by residues 269 - 288 (chain C) in PDB entry 1P7L
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 LYS 269 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 4.5 2.4 - - - +
39C VAL 3.2 25.2 + - - +
40C ALA* 4.1 7.0 - - - -
98C GLN* 3.9 8.5 - - - +
117C GLY* 4.7 9.8 - - - -
118C ASP* 6.5 0.4 - - + -
265C LYS* 3.6 29.6 - - + -
266C ASP* 3.0 51.0 + - - +
267C PRO 2.8 1.9 - - - +
268C SER* 1.3 82.8 + - - +
270C VAL* 1.3 58.7 + - - +
271C ASP* 2.9 12.9 + - + +
272C ARG* 2.9 13.3 + - + +
273C SER* 3.1 9.9 + - - -
885C SAM 3.0 39.2 + - + +
884D PPK 5.8 1.3 - - - +
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 4.0 14.8 - - + -
117C GLY 4.2 0.4 - - - +
118C ASP* 3.6 38.6 - - + +
119C GLN 5.2 2.5 - - - +
122C MET* 2.8 18.5 - - + +
268C SER 3.6 3.3 + - - +
269C LYS* 1.3 69.3 - - - +
271C ASP* 1.3 64.6 + - - +
272C ARG 3.1 0.2 - - - -
273C SER* 3.3 10.5 + - - +
274C ALA* 3.0 25.7 + - + +
275C ALA 3.6 0.2 + - - -
300C TYR* 3.8 44.2 - - + -
337C PRO* 5.2 5.2 - - + -
340C LEU* 5.0 6.7 - - + -
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Residues in contact with ASP 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ASP* 5.1 4.7 - - - +
119C GLN 4.9 3.9 - - - +
120C GLY* 5.4 1.9 - - - -
121C LEU 5.3 1.2 - - - +
122C MET* 3.3 16.9 - - - +
260C GLY* 3.6 21.3 - - - +
261C ALA 3.6 16.6 - - - +
262C PHE* 3.2 8.8 - - - -
265C LYS* 3.1 13.2 + - + +
269C LYS* 2.9 3.6 + - + +
270C VAL* 1.3 80.8 - - - +
272C ARG* 1.3 57.9 + - - +
275C ALA* 3.2 20.6 - - - +
887C MG 3.0 27.6 - - - -
884D PPK 3.0 21.8 + - - -
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 2.6 41.6 + - - -
27C LEU* 4.3 0.4 - - - +
261C ALA 4.8 0.4 - - - +
262C PHE* 2.7 45.7 + - + +
263C SER* 3.5 0.6 - - - +
264C GLY 3.8 0.4 - - - +
265C LYS* 3.3 25.6 + - + +
266C ASP 5.0 5.6 - - - +
267C PRO* 5.3 2.0 - - + -
269C LYS* 2.9 11.4 + - + +
271C ASP* 1.3 79.2 - - + +
273C SER* 1.3 60.4 + - - +
274C ALA 3.6 0.2 - - - -
275C ALA* 3.4 1.6 - - - +
276C TYR* 2.7 64.3 + - + -
346C LEU* 6.4 0.2 - - + -
351C TYR* 3.4 25.9 - - + +
354C THR* 3.1 25.9 - - - +
359C HIS* 3.7 5.3 - - - -
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Residues in contact with SER 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PRO* 2.6 31.0 + - - -
269C LYS 3.1 8.2 + - - -
270C VAL* 3.3 8.1 - - - +
272C ARG* 1.3 77.1 - - - +
274C ALA* 1.3 61.2 + - - +
275C ALA 3.1 1.3 - - - -
276C TYR* 3.4 3.8 + - - +
277C ALA* 2.9 29.6 + - - +
340C LEU* 4.0 18.1 - - - +
341C ILE* 5.1 0.2 - - - -
344C LEU* 4.4 3.8 - - - +
346C LEU* 3.7 26.9 - - - -
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C MET* 3.5 11.2 - - + -
270C VAL* 3.0 22.9 + - + +
273C SER* 1.3 76.7 + - - +
275C ALA* 1.3 64.1 + - - +
277C ALA* 3.6 1.7 + - - +
278C ALA* 3.0 23.9 + - - +
298C VAL* 4.1 6.4 - - + +
300C TYR* 3.3 40.8 - - + +
340C LEU* 4.2 11.6 - - + +
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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
----------------------------------------------------------
122C MET* 4.1 15.6 - - + +
123C PHE 4.8 7.3 - - - +
262C PHE* 3.4 26.5 - - + -
270C VAL 3.6 2.2 + - - -
271C ASP 3.2 22.9 - - - +
272C ARG 3.4 2.0 + - - +
273C SER 3.1 0.4 - - - -
274C ALA* 1.3 77.1 - - - +
276C TYR* 1.3 68.4 + - - +
278C ALA* 2.9 16.4 + - - +
279C ARG* 3.1 11.6 + - - +
360C PHE* 4.5 4.8 - - + -
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Residues in contact with TYR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C PHE* 4.1 15.0 - + - +
272C ARG* 2.7 60.1 + - + +
273C SER* 3.4 6.3 + - - +
275C ALA* 1.3 81.0 - - + +
277C ALA* 1.3 62.8 + - - +
279C ARG* 3.0 5.2 + - - +
280C TYR* 3.0 21.3 + - - +
344C LEU* 4.3 6.3 - - + -
346C LEU* 4.4 10.5 - - + -
351C TYR* 3.8 7.8 - + - -
354C THR* 3.8 4.2 - - - +
359C HIS* 2.9 33.0 + - + -
360C PHE* 3.8 17.5 - + - -
367C TRP* 3.5 60.8 - + + +
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Residues in contact with ALA 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 SER 2.9 17.2 + - - +
274C ALA 3.8 3.8 - - - +
276C TYR* 1.3 76.4 - - - +
278C ALA* 1.3 58.0 + - - +
280C TYR* 3.2 8.8 - - - +
281C VAL* 2.9 26.0 - - - +
335C LEU* 4.4 9.0 - - + -
340C LEU* 3.8 21.8 - - + -
343C MET* 3.3 31.2 - - + +
344C LEU* 3.9 3.7 - - + +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C MET 5.0 0.4 - - - +
123C PHE* 4.1 3.1 - - - +
124C GLY* 3.4 27.7 - - - +
274C ALA 3.0 13.7 + - - +
275C ALA* 2.9 12.9 + - - +
277C ALA* 1.3 75.8 - - - +
279C ARG* 1.3 62.9 + - - +
280C TYR 3.1 1.3 - - - -
281C VAL* 4.4 4.5 - - - -
282C ALA* 3.2 24.8 + - - +
296C ILE* 4.1 20.0 - - + +
298C VAL* 4.9 9.0 - - + -
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Residues in contact with ARG 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLY* 3.9 0.8 - - - -
125C TYR 3.1 28.1 + - - +
126C ALA* 3.7 2.6 - - - +
132C VAL 3.5 11.9 + - - -
133C LEU 2.8 27.7 + - - -
134C MET* 3.7 18.2 - - - +
251C TYR* 3.3 20.8 + - - +
275C ALA 3.1 4.4 + - - -
276C TYR 3.0 6.3 + - - +
278C ALA* 1.3 77.2 - - - +
280C TYR* 1.3 57.2 + - - +
283C LYS* 2.8 53.6 + - - +
360C PHE* 3.3 33.7 - - + -
367C TRP* 3.8 15.9 - - + +
368C GLU* 2.7 52.1 + - - +
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Residues in contact with TYR 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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276C TYR 3.0 11.6 + - - +
277C ALA* 3.2 13.5 - - - +
278C ALA 3.1 0.2 - - - -
279C ARG* 1.3 78.4 - - - +
281C VAL* 1.3 56.9 + - - +
283C LYS* 4.1 0.7 - - - +
284C ASN* 2.8 51.3 + - - -
333C PHE* 3.7 29.4 - + - -
343C MET* 3.3 36.0 + - + +
344C LEU* 4.0 13.9 - - + -
366C PRO 4.1 9.2 - - - -
367C TRP* 3.5 25.6 - - + +
369C LYS* 3.5 11.0 - - + -
371C ASP* 3.0 15.5 + - - -
372C LYS* 3.0 30.7 + - + +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ALA 2.9 19.9 + - - +
278C ALA* 4.4 3.8 - - - +
280C TYR* 1.3 72.5 - - + +
282C ALA* 1.3 60.3 + - - +
284C ASN* 3.1 0.9 + - - +
285C ILE* 2.6 52.0 + - + +
296C ILE* 3.6 31.9 - - + -
329C VAL* 4.7 8.5 - - + -
333C PHE* 3.5 50.3 - - + -
335C LEU* 5.0 8.5 - - + -
343C MET* 5.5 0.2 - - + -
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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
----------------------------------------------------------
124C GLY 4.2 2.0 - - - -
125C TYR 3.7 28.7 - - - +
126C ALA* 3.3 8.3 - - - +
278C ALA 3.2 17.2 + - - +
279C ARG 3.8 1.3 - - - +
281C VAL* 1.3 86.8 - - - +
283C LYS* 1.3 63.5 + - - +
285C ILE* 3.1 9.4 + - - +
286C VAL* 3.2 11.8 + - - +
294C CYS* 3.7 25.3 - - - +
296C ILE* 4.5 4.9 - - + -
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Residues in contact with LYS 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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126C ALA* 3.3 9.1 - - - +
132C VAL 3.2 19.9 + - - -
133C LEU* 3.6 26.1 - - + +
279C ARG* 2.8 40.2 + - - +
280C TYR* 4.1 3.4 - - - +
282C ALA* 1.3 72.3 - - - +
284C ASN* 1.3 60.3 + - - +
286C VAL* 3.1 4.9 + - - +
287C ALA* 2.9 28.4 + - - +
363C GLU* 2.9 23.6 + - - -
367C TRP 4.8 0.7 - - - +
368C GLU* 2.5 60.5 + - - +
369C LYS* 5.6 0.4 - - - +
370C THR* 4.0 12.8 + - + +
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Residues in contact with ASN 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 TYR* 2.8 41.6 + - - +
281C VAL* 3.1 6.3 + - - +
283C LYS* 1.3 81.8 - - - +
285C ILE* 1.3 55.8 + - - +
287C ALA 3.9 0.2 - - - -
288C ALA* 2.9 29.6 + - - +
333C PHE* 4.6 2.2 - - + -
369C LYS 3.1 24.2 + - - -
370C THR* 3.2 19.8 - - - +
371C ASP 4.4 0.2 - - - +
372C LYS* 3.2 14.3 + - - -
373C ALA* 2.9 30.9 + - - +
376C LEU* 4.0 14.0 - - + +
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Residues in contact with ILE 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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281C VAL* 2.6 44.1 + - + +
282C ALA 3.1 4.5 + - - +
284C ASN* 1.3 72.5 - - - +
286C VAL* 1.3 63.8 + - - +
288C ALA* 3.1 8.0 + - - +
289C GLY 3.1 4.3 + - - -
290C LEU* 3.0 43.9 + - + -
291C ALA* 4.2 13.2 - - + -
294C CYS* 3.8 26.5 - - - -
296C ILE* 4.6 4.0 - - + -
312C VAL* 5.4 1.3 - - + -
325C LEU* 4.3 20.2 - - + -
328C LEU* 6.4 0.4 - - + -
329C VAL* 4.4 17.0 - - + -
333C PHE* 5.5 0.4 - - + -
376C LEU* 4.3 13.9 - - + -
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Residues in contact with VAL 286 (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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126C ALA* 3.9 15.0 - - + +
127C THR 4.6 0.2 - - - -
128C ASN* 4.2 11.9 - - + +
133C LEU* 4.0 24.9 - - + -
282C ALA 3.2 9.8 + - - +
283C LYS 3.1 7.4 + - - +
285C ILE* 1.3 76.0 - - + +
287C ALA* 1.3 58.0 + - - +
289C GLY* 2.7 24.4 + - - -
291C ALA* 3.2 26.3 - - + +
292C ASP* 3.7 24.2 - - - +
293C ARG* 3.9 11.0 - - - +
294C CYS* 4.3 3.8 - - - +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 5.1 11.1 - - + +
283C LYS 2.9 15.5 + - - +
284C ASN 3.9 0.2 - - - +
286C VAL* 1.3 78.7 - - - +
288C ALA* 1.3 59.2 + - - +
289C GLY* 3.0 5.4 + - - -
370C THR* 3.7 26.7 - - + +
373C ALA* 3.8 14.5 - - + +
374C GLN* 5.3 3.6 - - - +
377C ARG* 5.7 0.5 - - - -
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ASN 2.9 20.2 + - - +
285C ILE 3.3 7.0 - - - +
286C VAL 3.1 0.4 - - - -
287C ALA* 1.3 75.7 - - - +
289C GLY* 1.3 60.2 + - - +
290C LEU* 3.4 23.0 + - + +
373C ALA* 3.5 30.9 - - - +
374C GLN* 5.8 0.4 - - - -
376C LEU* 3.9 3.1 - - + -
377C ARG* 2.8 35.6 + - - +
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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
------------------------------------------------------------
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