Contacts of the helix formed by residues 269 - 288 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ANP 5.5 0.9 - - - +
38B ARG* 4.7 3.4 - - - +
39B VAL 3.3 20.4 - - - -
40B ALA* 4.2 7.6 - - - +
98B GLN* 3.7 13.3 - - - +
106B VAL* 6.3 0.4 - - - +
117B GLY* 4.7 11.4 - - - -
118B ASP* 6.5 0.2 - - + -
265B LYS* 3.6 28.9 - - + -
266B ASP* 3.0 52.6 + - - +
267B PRO 2.7 1.7 - - - +
268B SER* 1.3 84.3 + - - +
270B VAL* 1.3 60.7 + - - +
271B ASP* 2.9 13.0 + - + +
272B ARG* 2.9 12.9 + - + +
273B SER* 3.0 11.4 + - - -
385B MET* 3.0 35.8 + - + -
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 4.1 14.6 - - + -
117B GLY 4.2 0.7 - - - +
118B ASP* 3.7 37.2 - - + +
119B GLN 5.4 2.7 - - - +
122B MET* 2.7 23.5 - - + +
268B SER 3.4 3.5 + - - +
269B LYS* 1.3 70.2 - - - +
271B ASP* 1.3 62.1 - - - +
272B ARG 3.1 0.4 - - - -
273B SER* 3.4 10.8 - - - +
274B ALA* 3.0 20.7 + - + +
300B TYR* 3.7 48.7 - - + -
337B PRO* 5.2 4.9 - - + -
340B LEU* 5.1 6.7 - - + -
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ANP 3.1 33.4 + - - -
118B ASP* 5.1 6.8 - - - +
119B GLN 4.8 9.2 - - - +
120B GLY* 5.4 2.8 - - - -
121B LEU 5.4 0.9 - - - +
122B MET* 3.3 16.7 - - - +
260B GLY* 3.8 22.9 - - - +
261B ALA 3.6 15.3 - - - +
262B PHE* 3.1 11.1 - - - -
265B LYS* 3.2 15.1 + - + +
269B LYS* 2.9 3.6 + - + +
270B VAL* 1.3 81.9 - - - +
272B ARG* 1.3 57.0 + - - +
275B ALA* 3.0 21.3 - - - +
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASP* 2.4 41.4 + - - -
27B LEU* 4.2 0.6 - - - +
261B ALA 4.8 0.9 - - - +
262B PHE* 2.7 46.0 + - + +
263B SER* 3.7 0.2 - - - +
264B GLY 3.9 0.2 - - - +
265B LYS* 3.2 26.3 + - + +
266B ASP 5.1 5.2 - - - +
267B PRO* 5.4 2.0 - - + -
269B LYS* 2.9 10.7 + - + +
271B ASP* 1.3 81.5 - - - +
273B SER* 1.3 59.4 + - - +
274B ALA 3.6 0.4 - - - -
275B ALA* 3.4 0.7 - - - +
276B TYR* 2.7 67.4 + - + -
346B LEU* 6.4 0.2 - - + -
351B TYR* 3.4 25.4 - - - +
354B THR* 3.1 24.9 - - - +
359B HIS* 3.8 5.3 - - - -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PRO* 2.6 32.3 + - - +
269B LYS 3.0 7.7 + - - -
270B VAL* 3.4 8.0 - - - +
272B ARG* 1.3 75.2 - - - +
274B ALA* 1.3 60.8 + - - +
275B ALA 3.1 1.1 - - - -
276B TYR* 3.5 3.6 + - - +
277B ALA* 2.9 29.7 + - - +
340B LEU* 4.0 19.2 - - - +
341B ILE* 5.0 0.9 - - - -
344B LEU* 4.4 3.6 - - - +
346B LEU* 3.7 25.8 - - - -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET* 3.4 11.9 - - + +
270B VAL* 3.0 21.8 + - + +
273B SER* 1.3 75.8 + - - +
275B ALA* 1.3 64.8 + - - +
277B ALA* 3.8 1.4 - - - +
278B ALA* 3.0 25.1 + - - +
298B VAL* 4.2 4.1 - - + +
300B TYR* 3.2 40.6 - - + +
335B LEU* 6.2 0.4 - - - +
340B LEU* 4.2 11.6 - - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 4.1 15.0 - - + +
123B PHE 4.8 6.0 - - - +
124B GLY* 4.8 1.7 - - - -
262B PHE* 3.3 26.0 - - + -
270B VAL 3.6 3.0 + - - -
271B ASP 3.0 24.7 - - - +
272B ARG 3.4 2.5 - - - +
273B SER 3.1 0.2 - - - -
274B ALA* 1.3 79.4 - - - +
276B TYR* 1.3 63.7 + - - +
278B ALA* 3.0 15.3 + - - +
279B ARG* 3.1 12.5 + - - +
360B PHE* 4.5 5.0 - - + -
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B PHE* 4.1 13.4 - + - +
272B ARG* 2.7 61.3 + - + +
273B SER* 3.8 6.3 - - - +
275B ALA* 1.3 79.5 - - + +
277B ALA* 1.3 63.3 + - - +
279B ARG* 3.0 5.2 + - - +
280B TYR* 2.9 21.3 + - - +
344B LEU* 4.3 5.8 - - + -
346B LEU* 4.4 10.3 - - + -
351B TYR* 3.8 9.0 - + - -
354B THR* 3.8 4.0 - - - +
359B HIS* 3.0 28.5 + - + -
360B PHE* 3.8 20.0 - + - -
367B TRP* 3.5 62.2 - + + +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B SER 2.9 19.3 + - - +
274B ALA 3.8 3.6 - - - +
276B TYR* 1.3 75.2 - - - +
278B ALA* 1.3 57.3 + - - +
280B TYR* 3.2 4.4 - - - +
281B VAL* 2.9 33.1 + - - +
335B LEU* 4.2 9.4 - - + -
340B LEU* 3.8 20.2 - - + -
343B MET* 3.2 30.8 - - + +
344B LEU* 3.9 4.6 - - + +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET 4.9 1.3 - - - +
123B PHE 4.2 2.0 - - - -
124B GLY* 3.4 27.1 - - - +
274B ALA 3.0 15.3 + - - +
275B ALA* 3.0 11.6 + - - +
277B ALA* 1.3 75.4 - - - +
279B ARG* 1.3 63.8 + - - +
280B TYR 3.1 1.3 - - - -
281B VAL* 3.6 2.1 + - - +
282B ALA* 3.2 24.8 + - - +
296B ILE* 4.1 21.8 - - + +
298B VAL* 4.9 8.5 - - + -
335B LEU* 6.6 0.2 - - - -
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY* 3.9 0.4 - - - -
125B TYR 3.1 28.2 + - - +
126B ALA* 3.6 4.0 - - - +
132B VAL 3.5 11.9 + - - -
133B LEU 2.9 25.7 + - - -
134B MET* 3.9 16.0 - - - +
251B TYR* 3.3 21.5 + - - +
275B ALA 3.1 4.4 + - - -
276B TYR 3.0 6.7 + - - +
278B ALA* 1.3 75.9 - - - +
280B TYR* 1.3 60.5 + - - +
282B ALA* 4.4 0.2 - - - -
283B LYS* 2.8 52.5 + - + +
360B PHE* 3.3 32.5 - - + -
367B TRP* 3.9 15.9 - - + +
368B GLU* 2.6 48.7 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TYR 2.9 11.6 + - - +
277B ALA* 3.2 13.0 - - - +
279B ARG* 1.3 78.6 - - - +
281B VAL* 1.3 57.8 + - - +
283B LYS* 4.0 0.5 - - - +
284B ASN* 3.0 51.8 + - - -
333B PHE* 3.7 30.7 - + - -
343B MET* 3.5 36.2 + - + +
344B LEU* 4.0 8.3 - - + -
366B PRO 4.1 9.9 - - - -
367B TRP* 3.6 31.0 - - + +
369B LYS* 3.5 10.3 - - + -
371B ASP* 3.0 23.3 + - - -
372B LYS* 3.0 22.6 + - + +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA 2.9 20.6 + - - +
278B ALA* 4.2 4.0 - - - +
280B TYR* 1.3 72.3 - - + +
282B ALA* 1.3 60.2 + - - +
284B ASN* 3.6 0.3 - - - +
285B ILE* 2.7 50.7 + - + +
296B ILE* 3.5 34.3 - - + -
329B VAL* 4.7 7.6 - - + -
333B PHE* 3.6 50.9 - - + -
335B LEU* 5.0 9.0 - - + -
343B MET* 5.6 0.2 - - + -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLY 4.2 2.0 - - - -
125B TYR 3.7 21.1 - - - +
126B ALA* 3.1 10.8 - - - +
278B ALA 3.2 17.9 + - - +
279B ARG 3.9 0.9 - - - +
281B VAL* 1.3 84.4 - - - +
283B LYS* 1.3 64.6 + - - +
285B ILE* 3.2 3.5 + - - +
286B VAL* 3.2 16.5 + - - +
294B CYS* 3.7 34.7 - - - +
296B ILE* 4.4 4.3 - - + -
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA* 3.3 9.1 - - - +
132B VAL 3.2 18.6 + - - -
133B LEU* 3.5 25.4 - - + +
279B ARG* 2.8 40.0 + - + +
280B TYR* 4.0 3.6 - - - +
282B ALA* 1.3 75.3 - - - +
284B ASN* 1.3 59.1 + - - +
286B VAL* 3.1 5.8 + - - +
287B ALA* 2.9 27.5 + - - +
363B GLU* 2.8 23.2 + - - -
367B TRP 4.8 0.7 - - - +
368B GLU* 2.5 60.7 + - - +
369B LYS* 5.6 0.4 - - - +
370B THR* 3.9 14.7 + - + +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B TYR* 3.0 42.8 + - - +
281B VAL* 3.7 5.6 - - - +
283B LYS* 1.3 77.0 - - - +
285B ILE* 1.3 56.0 + - - +
287B ALA* 4.2 0.2 - - - -
288B ALA* 2.9 30.0 + - - +
333B PHE* 4.5 1.8 - - + -
369B LYS 3.1 24.9 + - - -
370B THR* 3.4 17.8 - - - +
371B ASP 4.3 0.4 - - - +
372B LYS* 3.1 15.7 + - - -
373B ALA* 2.8 32.8 + - - +
376B LEU* 4.0 13.6 - - + +
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B VAL* 2.7 46.1 + - + +
282B ALA 3.5 4.5 - - - +
283B LYS 3.2 0.4 - - - -
284B ASN* 1.3 72.4 - - - +
286B VAL* 1.3 65.1 + - - +
288B ALA* 3.1 15.2 + - - +
289B GLY 3.1 7.8 + - - -
290B LEU* 3.1 33.3 + - + +
291B ALA* 4.2 14.1 - - + -
294B CYS* 3.7 27.6 - - - -
296B ILE* 4.5 3.4 - - + -
312B VAL* 5.4 1.3 - - + -
325B LEU* 4.4 16.2 - - + -
328B LEU* 6.4 0.4 - - + -
329B VAL* 4.4 17.3 - - + -
333B PHE* 5.5 0.7 - - + -
376B LEU* 4.3 13.5 - - + -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 4.0 13.9 - - + +
127B THR 4.6 0.2 - - - -
128B ASN* 4.2 12.3 - - + +
133B LEU* 4.0 25.4 - - + -
282B ALA 3.2 9.6 + - - +
283B LYS 3.1 7.6 + - - +
285B ILE* 1.3 79.6 - - + +
287B ALA* 1.3 58.0 + - - +
289B GLY* 2.7 23.7 + - - -
291B ALA* 3.1 26.4 - - + +
292B ASP* 3.7 23.3 - - - +
293B ARG* 3.9 10.5 - - - +
294B CYS 4.3 3.8 - - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 5.2 11.0 - - + +
283B LYS 2.9 15.7 + - - +
284B ASN 3.8 0.4 - - - +
286B VAL* 1.3 73.3 - - - +
288B ALA* 1.3 59.1 + - - +
289B GLY* 2.8 10.9 + - - -
370B THR* 3.7 26.5 - - + +
373B ALA* 3.8 15.6 - - + +
374B GLN* 5.3 2.9 - - - +
377B ARG* 5.7 0.3 - - - -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ASN 2.9 20.2 + - - +
285B ILE 3.1 7.4 + - - +
287B ALA* 1.3 75.3 - - - +
289B GLY* 1.3 59.4 + - - +
290B LEU* 3.4 21.7 + - + +
373B ALA* 3.3 31.4 - - - +
374B GLN* 5.8 0.2 - - - -
376B LEU* 3.9 4.5 - - + -
377B 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
------------------------------------------------------------
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