Contacts of the helix formed by residues 399 - 422 (chain A) in PDB entry 4PYP
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 PRO 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLU* 4.8 0.2 - - - +
257A VAL* 3.4 25.1 - - + +
262A LEU* 3.8 7.8 - - + +
268A TYR* 3.3 33.4 - - + +
395A PHE* 3.7 23.1 - - + -
396A SER* 3.1 28.0 - - - +
398A GLY* 1.3 82.9 - - - +
400A ARG* 1.3 62.9 + - - +
401A PRO* 3.3 2.8 - - - -
402A ALA* 3.3 4.6 + - - +
403A ALA* 2.9 22.9 + - - +
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Residues in contact with ARG 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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251A MET* 5.3 8.5 - - - -
391A VAL 4.2 1.3 - - - +
392A ALA* 3.4 36.5 + - - +
395A PHE* 2.9 32.0 + - + +
396A SER* 3.0 15.4 + - - +
397A GLN* 3.0 52.4 - - - +
399A PRO* 1.3 77.9 - - - +
401A PRO* 1.4 69.2 - - + +
403A ALA* 3.3 3.5 - - - +
404A ILE* 2.9 34.9 + - + +
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Residues in contact with PRO 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS* 4.7 11.0 - - + -
257A VAL 4.5 4.7 - - - +
397A GLN 3.9 9.6 - - - +
398A GLY 3.3 19.7 - - - +
399A PRO 3.4 0.2 - - - -
400A ARG* 1.4 93.2 - - + +
402A ALA* 1.3 58.7 + - - +
404A ILE* 2.8 29.4 + - + +
405A ALA* 3.2 11.4 + - - +
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Residues in contact with ALA 402 (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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257A VAL 3.1 24.2 + - - +
258A THR* 3.4 24.7 - - - +
259A ILE* 3.4 16.8 - - - +
262A LEU* 4.0 10.5 - - + -
399A PRO 3.3 7.1 + - - +
401A PRO* 1.3 79.5 - - - +
403A ALA* 1.3 59.7 + - - +
404A ILE 3.3 0.7 + - - -
405A ALA* 3.4 2.1 + - - +
406A VAL* 3.0 28.6 + - - +
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Residues in contact with ALA 403 (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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262A LEU* 3.7 11.8 - - - +
272A ILE* 5.7 1.5 - - - +
275A ALA* 5.5 1.7 - - - +
391A VAL* 3.8 10.1 - - + +
395A PHE* 3.4 41.5 - - + -
399A PRO 2.9 13.6 + - - +
400A ARG 3.3 10.8 - - - +
402A ALA* 1.3 76.0 - - - +
404A ILE* 1.3 57.9 + - - +
406A VAL* 3.6 3.3 + - - +
407A ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TRP* 4.2 24.0 - - + +
391A VAL* 4.0 21.8 - - + -
392A ALA* 4.9 8.1 - - + +
400A ARG* 2.9 30.3 - - + +
401A PRO* 2.8 16.8 + - + +
403A ALA* 1.3 71.2 - - - +
405A ALA* 1.3 59.2 + - - +
407A ALA* 3.5 3.5 - - - +
408A GLY* 2.8 29.3 + - - -
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Residues in contact with ALA 405 (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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80A SER 5.6 6.3 - - - +
81A PHE* 4.6 14.4 - - + -
259A ILE* 3.5 29.8 - - + -
401A PRO 3.2 9.2 + - - +
402A ALA* 3.4 3.8 + - - +
404A ILE* 1.3 77.1 - - - +
406A VAL* 1.3 56.7 + - - +
408A GLY* 3.7 1.7 + - - -
409A PHE* 2.9 27.9 + - - +
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Residues in contact with VAL 406 (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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259A ILE* 3.5 25.1 - - + -
262A LEU* 4.1 13.0 - - + -
263A PHE* 3.5 28.7 - - + -
272A ILE* 4.2 4.5 - - + -
276A VAL* 4.1 17.5 - - + -
402A ALA 3.0 21.5 - - - +
403A ALA 3.9 4.0 - - - +
404A ILE 3.2 0.2 - - - -
405A ALA* 1.3 73.8 - - - +
407A ALA* 1.3 65.8 + - - +
409A PHE* 3.0 14.1 + - + +
410A SER* 3.0 26.8 + - - +
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Residues in contact with ALA 407 (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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275A ALA* 5.1 3.4 - - + +
276A VAL* 5.0 6.2 - - - +
279A GLN* 3.2 34.0 - - - +
388A TRP* 3.9 11.9 - - + -
391A VAL* 4.4 14.1 - - + -
403A ALA 3.0 15.4 + - - +
404A ILE* 3.5 9.4 - - - +
406A VAL* 1.3 75.5 - - - +
408A GLY* 1.3 58.3 + - - +
410A SER* 2.9 21.9 + - - -
411A ASN 3.0 9.5 + - - -
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Residues in contact with GLY 408 (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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80A SER* 5.7 5.6 - - - -
388A TRP* 3.7 19.1 - - - -
404A ILE* 2.8 19.4 + - - -
405A ALA* 3.7 2.7 - - - -
407A ALA* 1.3 72.7 - - - +
409A PHE* 1.3 55.8 + - - +
411A ASN* 3.7 4.4 - - - +
412A TRP* 3.1 41.2 + - - -
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Residues in contact with PHE 409 (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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77A MET* 3.5 28.0 - - + -
81A PHE* 3.2 36.3 - + + -
405A ALA 2.9 19.7 + - - +
406A VAL* 3.5 15.3 - - + +
407A ALA 3.0 0.6 - - - -
408A GLY* 1.3 75.2 - - - +
410A SER* 1.3 62.6 + - - +
412A TRP* 3.8 3.2 + - - -
413A THR* 2.3 55.8 + - + -
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Residues in contact with SER 410 (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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276A VAL* 3.4 29.9 - - - +
279A GLN* 3.5 17.9 - - - -
280A LEU* 4.0 12.6 - - - +
406A VAL* 3.0 13.9 + - - +
407A ALA 2.9 8.2 + - - -
409A PHE* 1.3 79.2 - - - +
411A ASN* 1.3 54.7 + - - +
413A THR* 2.9 5.9 + - - -
414A SER* 2.7 40.3 + - - -
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Residues in contact with ASN 411 (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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279A GLN* 3.6 31.2 - - + +
282A GLN* 2.6 29.6 + - - +
283A GLN* 3.3 23.0 + - - +
388A TRP* 3.9 13.5 - - + +
407A ALA 3.0 6.0 + - - +
408A GLY* 3.7 12.3 - - - +
410A SER* 1.3 77.2 - - - +
412A TRP* 1.3 63.5 + - + +
414A SER* 3.9 5.2 - - - -
415A ASN* 3.1 28.1 + - - +
601A BNG 4.4 5.2 + - - -
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Residues in contact with TRP 412 (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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26A PHE* 3.9 30.5 - + - -
72A PHE* 4.2 19.3 - + - -
73A SER* 3.1 44.1 - - - +
76A GLY* 3.0 38.3 + - - -
77A MET* 3.4 29.4 - - + +
80A SER* 2.9 25.9 + - - -
130A GLY 4.6 0.4 - - - -
133A CYS 4.5 0.7 - - - -
134A GLY* 3.6 17.3 - - - -
137A THR* 4.2 5.1 + - + +
408A GLY* 3.1 32.1 + - - +
409A PHE 4.4 2.2 - - - +
411A ASN* 1.3 77.6 - - + +
413A THR* 1.3 61.7 + - - +
415A ASN* 3.7 9.7 - - + +
416A PHE* 3.3 16.8 + - - +
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Residues in contact with THR 413 (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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77A MET* 4.9 5.9 - - + +
280A LEU* 6.0 0.9 - - - -
409A PHE* 2.3 52.1 + - + -
410A SER* 2.9 8.3 + - - -
412A TRP* 1.3 76.4 - - - +
414A SER* 1.3 64.6 + - - +
415A ASN 3.0 4.3 - - - -
416A PHE* 3.1 17.3 + - + +
417A ILE* 3.1 27.9 + - + +
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Residues in contact with SER 414 (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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279A GLN 3.8 3.3 + - - -
280A LEU* 3.6 26.1 - - - +
283A GLN* 3.2 27.8 - - - +
284A LEU* 3.8 17.2 - - - +
410A SER 2.7 23.9 + - - -
413A THR* 1.3 73.8 - - - +
415A ASN* 1.3 59.7 + - - +
417A ILE* 3.6 15.4 + - - +
418A VAL* 3.3 26.9 + - - +
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Residues in contact with ASN 415 (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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30A THR* 6.2 0.8 - - - +
73A SER* 3.4 19.7 + - - +
283A GLN* 2.3 30.9 + - - +
288A ASN* 3.1 14.8 + - - +
292A TYR* 2.7 28.0 + - - -
411A ASN* 3.1 22.7 + - - +
412A TRP* 3.7 8.7 - - - +
413A THR 3.0 0.2 - - - -
414A SER* 1.3 76.2 + - - +
416A PHE* 1.3 65.9 + - - +
417A ILE 3.1 0.5 + - - -
418A VAL* 3.3 4.6 + - - +
419A GLY* 2.9 21.5 + - - -
601A BNG 3.9 6.7 + - - -
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Residues in contact with PHE 416 (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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67A LEU* 5.0 7.0 - - + -
70A ALA* 4.1 28.2 - - + +
71A ILE* 4.7 1.6 - - - -
73A SER* 4.1 8.9 - - - -
74A VAL* 3.5 35.7 - - + +
77A MET* 6.1 2.5 - - + -
412A TRP 3.3 10.8 + - - +
413A THR* 3.1 12.6 + - + +
415A ASN* 1.3 77.5 - - - +
417A ILE* 1.3 61.9 + - + +
419A GLY* 4.7 0.7 - - - +
420A MET* 2.7 68.4 + - + +
421A CYS* 5.7 1.6 - - - -
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Residues in contact with ILE 417 (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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280A LEU* 6.3 0.4 - - + -
284A LEU* 4.6 18.2 - - + -
413A THR* 3.1 28.3 - - + +
414A SER* 3.7 17.9 - - - +
415A ASN 3.1 0.8 - - - -
416A PHE* 1.3 82.6 - - + +
418A VAL* 1.3 60.3 + - - +
421A CYS* 2.9 52.7 + - + +
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Residues in contact with VAL 418 (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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283A GLN 3.2 27.1 - - - +
284A LEU* 4.0 15.0 - - + -
286A GLY* 4.5 8.3 - - - -
288A ASN* 4.3 11.4 - - + +
289A ALA* 3.8 35.2 - - + +
293A TYR* 5.9 0.2 - - + -
414A SER 3.3 12.7 + - - +
415A ASN* 3.9 4.5 - - - +
417A ILE* 1.3 78.3 - - - +
419A GLY* 1.3 59.9 + - - +
422A PHE* 2.8 41.0 + - + +
437A PHE* 4.6 11.0 - - + -
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Residues in contact with GLY 419 (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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66A SER* 4.1 7.8 + - - +
69A VAL* 4.3 0.8 - - - +
70A ALA* 4.2 11.2 - - - -
292A TYR* 3.9 27.6 - - - -
293A TYR* 3.2 23.1 + - - -
415A ASN 2.9 15.4 + - - -
416A PHE 3.9 0.4 - - - -
418A VAL* 1.3 79.1 - - - +
420A MET* 1.3 60.7 + - - +
422A PHE 4.3 1.2 + - - -
423A GLN 5.2 0.2 + - - -
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Residues in contact with MET 420 (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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63A THR* 3.9 26.2 - - - +
66A SER* 3.4 29.0 + - - -
67A LEU* 3.9 23.1 - - + -
70A ALA* 3.8 12.4 - - + +
416A PHE* 2.7 49.3 + - + +
419A GLY* 1.3 74.1 - - - +
421A CYS* 1.3 68.1 + - - +
422A PHE 3.7 0.2 - - - -
423A GLN 4.7 0.5 + - - -
424A TYR* 4.8 5.0 + - - +
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Residues in contact with CYS 421 (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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416A PHE* 5.7 1.8 - - - -
417A ILE* 2.9 36.9 + - + +
420A MET* 1.3 92.9 - - - +
422A PHE* 1.3 63.4 + - - +
423A GLN 3.2 2.7 - - - -
424A TYR* 3.2 20.9 + - + +
425A VAL* 3.2 31.6 + - + +
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Residues in contact with PHE 422 (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 ALA* 3.6 22.9 - - + -
293A TYR* 3.5 34.1 - + + -
297A ILE* 3.5 31.9 - - + -
417A ILE 4.1 0.2 + - - -
418A VAL* 2.8 25.9 + - + +
419A GLY 4.3 0.4 + - - -
420A MET 3.7 0.6 - - - -
421A CYS* 1.3 79.4 - - - +
423A GLN* 1.3 61.0 - - + +
425A VAL* 3.3 6.0 + - + -
426A GLU* 3.0 48.2 + - + +
433A VAL* 4.4 19.1 - - + -
434A PHE* 4.7 6.5 - + - -
437A PHE* 3.6 27.8 - + + -
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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