Contacts of the helix formed by residues 377 - 400 (chain A) in PDB entry 1PV7
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 GLY 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A TYR* 2.6 26.8 + - - -
374A GLU 4.5 0.8 + - - -
376A ILE* 1.3 78.6 - - - +
378A PHE* 1.3 72.2 + - - +
379A GLN 3.6 0.9 - - - -
380A GLY 3.4 1.3 + - - -
381A ALA* 3.2 15.1 + - - +
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Residues in contact with PHE 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 3.2 34.8 - - - -
242A GLN* 3.6 19.3 - - + -
245A ASN* 4.2 12.8 - - + -
246A PHE* 3.2 57.2 - + + -
249A SER* 5.8 3.6 - - - -
373A TYR* 3.8 17.2 + + - -
377A GLY* 1.3 75.7 - - - +
379A GLN* 1.3 65.1 + - + +
381A ALA* 3.3 1.9 + - - +
382A TYR* 2.8 40.8 + - - -
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Residues in contact with GLN 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PHE* 3.9 12.3 - - + -
250A PHE* 4.0 15.1 - - - -
306A SER 2.9 23.4 + - - +
307A SER* 3.0 35.1 + - - +
309A ALA 3.1 21.9 + - - +
377A GLY 3.6 0.2 - - - -
378A PHE* 1.3 81.3 - - + +
380A GLY* 1.3 65.6 + - - +
382A TYR* 3.1 25.2 - - - +
383A LEU* 3.5 4.2 + - - +
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Residues in contact with GLY 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ILE* 3.8 20.1 + - - -
377A GLY 3.4 5.8 + - - -
378A PHE 3.1 1.4 + - - -
379A GLN* 1.3 81.3 - - - +
381A ALA* 1.3 64.3 + - - +
383A LEU* 3.1 26.7 + - - +
384A VAL* 4.0 2.6 + - - +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ALA* 6.0 0.7 - - + -
372A MET* 3.6 45.5 - - + -
373A TYR* 4.4 8.7 - - + +
376A ILE* 3.6 7.4 - - - +
377A GLY 3.2 11.6 + - - +
378A PHE 3.7 7.9 - - - +
380A GLY* 1.3 72.2 - - - +
382A TYR* 1.3 57.0 + - + +
384A VAL* 2.4 39.5 + - - +
385A LEU* 3.3 7.6 + - + +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 4.3 21.0 + + - -
243A PHE* 4.1 16.9 - + - +
246A PHE* 3.6 24.3 - + - +
303A ILE* 4.0 11.6 - - + +
304A ILE* 6.1 1.6 - - - -
306A SER* 3.4 34.1 - - - -
307A SER* 4.5 8.1 - - - +
373A TYR* 3.2 37.5 + + - -
378A PHE* 2.8 37.9 - + - -
379A GLN* 3.1 18.2 - - - +
380A GLY 3.1 0.2 + - - -
381A ALA* 1.3 76.1 - - + +
383A LEU* 1.3 63.2 + - - +
384A VAL 2.8 1.4 + - - -
385A LEU* 3.0 13.3 + - + +
386A GLY* 2.8 25.1 + - - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE* 6.0 7.2 - - + +
307A SER* 3.6 25.7 - - - +
308A PHE* 5.5 9.2 - - + -
379A GLN 3.5 4.7 + - - +
380A GLY* 3.1 20.4 + - - +
381A ALA 2.9 0.4 + - - -
382A TYR* 1.3 77.3 - - - +
384A VAL* 1.3 59.2 + - + +
387A LEU* 2.8 36.2 + - + +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 5.6 4.0 - - + -
372A MET* 3.2 37.5 - - + -
376A ILE* 5.8 2.9 - - + -
380A GLY 4.7 2.2 - - - +
381A ALA* 2.4 32.3 + - - +
383A LEU* 1.3 70.3 - - + +
385A LEU* 1.3 60.7 + - + +
387A LEU* 3.6 3.1 - - - +
388A VAL* 3.0 42.6 + - + +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A THR* 3.8 15.9 - - + +
238A VAL* 4.4 22.0 - - + -
239A PHE* 4.7 13.2 - - + -
303A ILE* 4.6 5.6 - - + -
365A MET* 4.3 24.5 - - + -
368A LEU* 5.7 3.6 - - + -
369A ALA* 4.9 9.0 - - + -
372A MET* 4.8 11.0 - - - -
373A TYR* 4.6 11.4 - - + +
381A ALA* 3.3 9.2 + - + +
382A TYR* 3.0 18.2 + - + +
384A VAL* 1.3 81.8 - - + +
386A GLY* 1.3 55.2 + - - +
388A VAL* 2.9 7.5 + - + +
389A ALA* 2.4 40.2 + - - +
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Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A SER* 4.4 1.8 + - - -
303A ILE* 3.0 39.2 - - - +
304A ILE* 4.0 14.0 - - - +
382A TYR 2.8 10.1 + - - -
385A LEU* 1.3 76.4 - - - +
387A LEU* 1.3 55.5 + - - +
389A ALA* 3.1 1.6 - - - +
390A LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE* 4.4 14.5 - - + +
383A LEU* 2.8 26.6 + - + +
384A VAL* 3.6 3.1 - - - +
385A LEU 3.0 0.8 - - - -
386A GLY* 1.3 70.7 - - - +
388A VAL* 1.3 72.8 + - + +
390A LEU* 2.9 10.2 + - + +
391A GLY* 2.7 24.1 + - - +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A THR* 4.5 14.4 - - + +
365A MET* 5.1 9.2 - - + -
384A VAL* 3.0 25.6 + - + +
385A LEU* 2.9 5.3 + - + +
387A LEU* 1.3 80.7 - - + +
389A ALA* 1.3 70.8 + - - +
391A GLY* 3.1 2.4 + - - +
392A PHE* 2.9 42.0 + - + +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A VAL* 4.3 9.3 - - + +
235A THR* 3.6 23.6 - - + -
236A TYR* 6.6 0.2 - - + -
299A MET* 6.3 0.9 - - + -
300A SER* 3.7 9.9 - - - +
303A ILE* 3.8 10.5 - - + -
385A LEU 2.4 27.2 + - - +
386A GLY* 3.1 15.3 - - - +
387A LEU 2.9 0.4 + - - -
388A VAL* 1.3 74.5 - - - +
390A LEU* 1.3 62.3 + - - +
392A PHE* 2.9 12.5 + - - +
393A THR* 2.9 14.1 + - - -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A THR* 6.4 1.3 - - + -
300A SER* 2.9 29.3 + - - +
301A VAL* 6.1 3.6 - - + -
304A ILE* 4.6 15.7 - - + -
386A GLY 2.8 14.4 + - - +
387A LEU* 3.7 10.8 - - + +
389A ALA* 1.3 72.2 - - - +
391A GLY* 1.3 59.0 + - - +
393A THR* 3.6 4.6 - - + -
394A LEU* 2.7 48.0 + - + +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A LEU* 2.7 19.1 + - - -
388A VAL* 3.6 5.4 - - - -
390A LEU* 1.3 81.6 - - - +
392A PHE* 1.3 61.6 - - - +
394A LEU* 3.7 6.3 + - - +
395A ILE* 3.2 30.7 + - - +
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Residues in contact with PHE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 4.6 26.2 - - + +
228A TYR* 5.5 1.0 - - - -
231A GLY* 3.6 29.2 - - - -
232A VAL* 4.3 13.6 - - + +
388A VAL* 2.9 29.2 + - + +
389A ALA* 2.9 5.6 + - - +
391A GLY* 1.3 79.5 - - - +
393A THR* 1.3 65.0 + - - +
394A LEU 3.3 0.2 - - - -
395A ILE* 3.9 20.0 - - + +
396A SER* 3.2 24.3 + - - -
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Residues in contact with THR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A TYR* 5.0 2.9 - - + -
232A VAL* 3.5 20.0 - - - +
293A LEU* 4.1 12.3 - - + +
296A GLY* 3.6 18.8 + - - -
297A THR* 3.6 34.3 - - - +
300A SER* 4.0 2.6 + - - -
389A ALA 2.9 10.8 + - - -
390A LEU* 3.7 12.6 - - + +
392A PHE* 1.3 74.0 - - - +
394A LEU* 1.3 69.7 + - - +
396A SER* 3.2 8.7 + - - -
397A VAL* 3.2 25.1 + - + +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 2.7 30.6 + - + +
391A GLY* 3.7 7.6 - - - +
393A THR* 1.3 76.9 - - - +
395A ILE* 1.3 59.6 + - + +
397A VAL* 2.8 41.2 + - + +
398A PHE* 3.3 15.9 + - + +
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 5.1 14.6 - - + -
391A GLY 3.2 18.1 + - - +
392A PHE* 3.9 24.0 - - + +
393A THR 3.4 0.2 - - - -
394A LEU* 1.3 84.2 - - + +
396A SER* 1.3 57.3 + - - +
398A PHE* 3.3 7.1 + - - +
399A THR* 2.8 49.8 + - + +
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE 4.6 4.7 + - - -
227A LEU* 5.3 2.3 - - - +
228A TYR* 3.4 45.6 + - - +
293A LEU* 3.8 6.7 - - - -
392A PHE 3.2 12.0 + - - -
393A THR 3.2 10.9 + - - -
394A LEU 3.1 0.6 + - - -
395A ILE* 1.3 78.9 - - - +
397A VAL* 1.3 60.0 + - - +
399A THR* 4.6 2.2 - - - -
400A LEU* 2.5 44.5 + - - +
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS* 3.1 25.7 + - - -
293A LEU* 3.1 36.8 - - + +
297A THR* 5.9 1.1 - - - +
393A THR* 3.2 19.3 - - + +
394A LEU* 2.8 20.8 + - + +
396A SER* 1.3 78.9 - - - +
398A PHE* 1.3 64.1 + - + +
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Residues in contact with PHE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS* 4.9 2.2 - - - -
394A LEU* 3.3 17.8 + - + +
395A ILE* 3.8 9.6 - - - +
396A SER 3.3 0.4 - - - -
397A VAL* 1.3 85.8 - - + +
399A THR* 1.3 61.9 + - - +
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Residues in contact with THR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.1 51.9 - - + +
227A LEU* 5.9 3.4 - - + -
395A ILE* 2.8 32.6 + - + +
396A SER* 2.9 3.9 + - - -
397A VAL 3.1 0.2 - - - -
398A PHE* 1.3 84.8 + - - +
400A LEU* 1.3 64.4 + - - +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LYS 5.7 0.2 - - - +
224A PHE* 4.0 19.7 - - + +
225A LEU* 3.7 14.8 - - + -
228A TYR* 5.2 6.1 - - + -
289A LYS* 2.8 61.3 + - + +
292A LEU* 3.9 18.8 - - + -
293A LEU* 4.7 8.1 - - + -
336A TYR* 3.0 35.9 - - + +
396A SER* 2.5 36.8 + - - +
399A THR* 1.3 74.5 - - - +
401A SER* 1.3 66.1 + - - +
402A GLY 3.7 0.7 + - - -
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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