Contacts of the helix formed by residues 390 - 413 (chain A) in PDB entry 3IFS
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 ASN 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A HIS* 6.0 1.2 - - - -
95A MSE 5.6 0.2 - - - +
96A LEU* 3.5 11.5 - - - +
388A GLU* 2.8 38.0 + - + +
389A LEU* 1.3 74.9 - - - +
391A GLU* 1.3 73.2 + - - +
392A TYR* 3.6 9.4 + - - +
393A THR* 2.7 33.5 + - - -
394A PHE* 3.0 22.9 + - - +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.9 14.9 - - + +
224A GLY 4.7 1.0 - - - +
225A LEU* 3.5 28.5 - - + +
226A ASN* 2.8 57.2 + - - +
229A GLU* 4.2 5.8 - - + +
230A MSE 3.4 21.8 - - + +
390A ASN* 1.3 81.3 - - - +
392A TYR* 1.3 64.0 + - - +
394A PHE* 3.2 2.6 + - - +
395A GLY 3.0 19.4 + - - -
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.8 40.9 - + + +
229A GLU* 3.4 38.5 + - + +
232A LYS* 3.9 11.2 - - + -
233A GLY* 3.2 38.5 - - - -
236A ALA* 3.4 20.3 - - + +
390A ASN* 3.4 10.6 + - - +
391A GLU* 1.3 78.2 - - - +
393A THR* 1.3 59.7 + - - +
395A GLY 3.3 1.2 + - - -
396A TYR* 3.0 27.3 + + - +
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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
----------------------------------------------------------
4A HIS* 2.7 38.6 + - + +
5A VAL* 4.4 5.6 - - + -
95A MSE 6.5 0.4 - - - -
386A ILE* 3.5 22.2 - - + -
387A PRO* 4.2 5.4 - - + -
388A GLU* 3.2 26.3 + - - +
389A LEU* 5.5 0.4 - - + -
390A ASN* 2.7 26.4 + - - -
392A TYR* 1.3 72.9 - - - +
394A PHE* 1.3 60.6 + - - +
396A TYR* 3.2 1.3 + - - +
397A LEU* 2.8 31.1 + - + +
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Residues in contact with PHE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY* 4.1 9.2 - - - -
91A ALA* 4.3 3.1 - - + -
92A ALA* 3.4 39.9 - - + -
95A MSE 3.7 27.5 - - + -
96A LEU* 4.1 11.7 - - + -
211A VAL* 4.4 13.2 - - + -
212A LEU* 5.0 2.2 - - + -
230A MSE 3.5 30.7 - - + -
281A PHE* 4.0 23.8 - + - -
284A TRP* 6.2 1.1 - + - -
390A ASN 3.0 13.3 + - - +
391A GLU 3.2 7.4 + - - +
393A THR* 1.3 76.4 - - - +
395A GLY* 1.3 63.1 + - - +
397A LEU* 3.7 4.7 - - + +
398A VAL* 2.9 47.2 + - + +
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Residues in contact with GLY 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 5.1 2.7 - - - -
230A MSE 3.6 30.3 - - - -
234A ALA* 3.4 22.4 - - - +
391A GLU 3.0 11.7 + - - -
392A TYR 3.7 0.9 - - - -
394A PHE* 1.3 80.3 - - - +
396A TYR* 1.3 60.9 + - - +
398A VAL* 3.5 5.1 + - - +
399A TYR 3.3 16.6 + - - -
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.1 17.7 - - - -
4A HIS* 3.3 25.5 + + + -
5A VAL* 3.4 34.1 - - + -
233A GLY* 3.3 25.9 - - - +
234A ALA* 4.3 1.1 - - - +
236A ALA* 3.7 10.5 - - + -
237A GLY* 3.5 14.4 - - - -
240A ASP* 2.2 38.2 + - - +
241A PHE* 3.5 26.9 - + - -
392A TYR* 3.0 19.3 + + + +
393A THR* 3.6 8.3 - - - +
395A GLY* 1.3 75.7 - - - +
397A LEU* 1.3 58.3 + - - +
399A TYR* 3.3 5.3 + - - +
400A PHE* 2.9 24.3 + - + +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.1 17.0 - - + -
95A MSE 4.8 12.6 - - + -
278A LEU* 5.8 0.2 - - + -
281A PHE* 3.5 35.7 - - + -
330A LEU* 5.2 0.2 - - + -
384A VAL* 3.9 21.3 - - + -
386A ILE* 3.7 31.4 - - + -
393A THR* 2.8 22.5 + - + +
394A PHE* 3.7 5.2 - - - +
396A TYR* 1.3 71.9 - - - +
398A VAL* 1.3 65.4 + - - +
400A PHE* 3.3 8.1 + - + +
401A PHE* 3.1 44.2 + - + -
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A VAL* 3.7 17.0 - - + -
212A LEU* 4.2 11.2 - - + -
281A PHE* 4.2 7.2 - - + -
284A TRP* 3.8 25.0 - - + -
394A PHE* 2.9 54.4 + - + +
395A GLY* 3.8 5.4 - - - +
397A LEU* 1.3 75.3 - - - +
399A TYR* 1.3 59.2 + - - +
401A PHE 3.3 1.7 + - - -
402A GLU* 2.9 54.4 + - - +
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 5.2 0.5 - - - -
48A TRP* 3.6 22.0 - + - -
49A VAL* 2.7 45.5 + - - +
52A PRO* 3.8 22.0 - - + -
212A LEU* 5.4 2.0 - - + -
234A ALA* 3.9 14.1 - - + +
237A GLY* 3.6 8.7 - - - -
238A ARG* 3.3 35.8 + - - +
241A PHE* 4.2 5.4 - + + -
395A GLY 3.3 11.3 + - - +
396A TYR 3.7 7.0 - - - +
397A LEU 3.2 0.6 - - - -
398A VAL* 1.3 76.8 - - + +
400A PHE* 1.3 67.7 + - - +
402A GLU* 4.1 14.4 - - - -
403A LYS* 2.9 46.9 + - + +
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Residues in contact with PHE 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.7 11.2 - - + -
6A THR 5.6 0.2 - - - -
7A PHE* 4.3 12.8 - - + -
241A PHE* 3.7 36.0 - + + -
250A PRO* 3.8 11.7 - - + -
251A ALA* 3.6 30.6 - - - +
254A TYR* 4.1 24.9 - + + -
384A VAL* 4.0 18.2 - - + -
396A TYR* 2.9 16.1 + - + +
397A LEU* 3.4 15.9 - - + +
399A TYR* 1.3 76.3 - - - +
401A PHE* 1.3 97.7 + + - +
404A ALA* 3.0 28.8 + - - +
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.5 34.5 - + - -
271A LEU* 4.5 4.0 - - + -
281A PHE* 3.7 29.2 - + - -
284A TRP* 4.0 5.2 - + + -
285A TRP* 3.7 27.4 - + - -
288A LEU* 3.6 16.7 - - + +
289A PHE* 3.8 4.8 - + + -
330A LEU* 3.9 20.0 - - + -
384A VAL* 4.3 6.7 - - + -
397A LEU* 3.1 43.0 + - + +
398A VAL 3.9 2.7 - - - +
400A PHE* 1.3 94.4 - + - +
402A GLU* 1.3 59.5 + - - +
404A ALA* 3.7 2.2 - - - +
405A CYS* 2.8 30.7 + - - +
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.6 38.1 - - + +
209A PHE* 3.6 49.6 - - + +
211A VAL* 4.2 4.3 - - - +
212A LEU* 5.0 5.6 - - - +
284A TRP* 4.1 13.5 - - + -
288A LEU* 4.0 8.1 - - + -
398A VAL* 2.9 42.4 + - + +
399A TYR* 3.3 15.0 + - - +
401A PHE* 1.3 75.7 - - - +
403A LYS* 1.3 62.5 + - - +
405A CYS* 3.3 3.7 + - - +
406A ALA* 3.1 18.4 + - - +
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Residues in contact with LYS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.3 16.2 - - + -
36A HIS* 2.8 35.1 + - - -
48A TRP* 4.0 18.6 - - + -
49A VAL* 4.3 3.1 - - - -
238A ARG 6.0 0.4 - - - -
241A PHE* 3.0 35.9 + - + +
242A GLY* 4.3 0.4 - - - -
251A ALA* 4.4 7.6 - - + -
252A TYR* 2.7 38.3 + - + +
399A TYR* 2.9 39.8 + - + +
400A PHE 4.0 1.8 - - - +
402A GLU* 1.3 74.3 - - - +
404A ALA* 1.3 66.3 + - - +
406A ALA* 3.4 3.6 + - - +
407A MSE 3.2 21.7 + - - +
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Residues in contact with ALA 404 (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 ALA* 3.4 29.8 - - + +
254A TYR* 3.7 27.8 - - + -
255A ALA* 3.5 6.5 - - - +
289A PHE* 4.5 1.3 - - - -
400A PHE* 3.0 20.1 + - + +
401A PHE* 3.7 6.1 - - - +
403A LYS* 1.3 76.3 - - - +
405A CYS* 1.3 57.8 + - - +
407A MSE 3.4 1.3 + - - -
408A SER* 2.9 31.3 + - - -
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Residues in contact with CYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.6 3.8 - - + -
288A LEU* 3.5 25.8 - - + -
289A PHE* 3.6 25.3 - - + -
292A SER* 3.2 37.2 - - - -
293A GLU* 4.4 1.9 - - - +
401A PHE 2.8 19.2 + - - +
402A GLU* 3.5 5.6 - - - +
403A LYS 3.2 0.2 - - - -
404A ALA* 1.3 74.2 - - - +
406A ALA* 1.3 66.0 + - - +
408A SER* 3.3 0.7 + - - -
409A GLY* 3.0 22.3 + - - -
416A PRO* 4.6 2.2 - - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.9 17.7 - - + -
48A TRP* 3.8 19.3 - - + -
209A PHE* 5.2 0.6 - - - -
402A GLU 3.1 12.9 + - - +
403A LYS* 3.7 9.2 - - - +
405A CYS* 1.3 75.1 - - - +
407A MSE 1.3 63.0 + - - +
409A GLY 3.5 0.2 + - - -
410A TYR* 3.1 30.4 + - - -
416A PRO* 3.9 5.2 - - - +
417A PHE* 3.9 24.5 - - + -
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Residues in contact with MSE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.6 32.5 - - + +
31A THR* 3.5 24.7 - - + -
32A HIS* 3.7 13.5 - - - +
35A ILE* 4.2 6.7 - - + +
252A TYR* 3.5 54.3 - - + +
255A ALA* 3.6 16.4 - - + -
403A LYS 3.2 5.4 + - - +
404A ALA 3.7 7.0 - - - +
406A ALA* 1.3 75.8 - - - +
408A SER* 1.3 60.6 + - - +
410A TYR* 3.3 2.9 + - - -
411A LEU* 2.9 52.8 + - + +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 3.6 13.2 - - - +
258A ARG* 2.8 22.1 + - - +
259A ASN* 3.1 26.3 + - - +
289A PHE* 4.4 2.7 - - - -
293A GLU* 2.5 24.6 + - - +
404A ALA 2.9 18.4 + - - -
405A CYS* 3.7 6.3 - - - -
407A MSE 1.3 75.7 - - - +
409A GLY* 1.3 55.7 + - - +
411A LEU* 3.3 0.7 + - - -
412A LEU* 3.0 25.6 + - - +
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Residues in contact with GLY 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 3.1 15.0 + - - -
405A CYS 3.0 16.3 + - - -
406A ALA 4.0 0.9 - - - -
408A SER* 1.3 75.3 - - - +
410A TYR* 1.3 61.8 + - - +
412A LEU* 3.2 2.6 + - - +
413A GLY 3.1 16.8 + - - -
414A VAL* 3.1 27.0 + - - +
416A PRO* 4.0 13.7 - - - -
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Residues in contact with TYR 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 3.5 34.3 - - + +
34A ALA* 5.3 6.0 + - + -
35A ILE* 3.7 27.6 - - + -
40A GLY* 3.7 15.1 + - - -
41A ALA* 2.6 42.8 + - + -
43A ASN 4.7 1.7 + - - -
46A LEU* 4.8 6.8 - - + +
406A ALA 3.1 22.3 + - - +
407A MSE 3.3 0.9 + - - +
409A GLY* 1.3 74.8 - - - +
411A LEU* 1.3 62.9 + - - +
413A GLY* 3.2 12.5 + - - -
414A VAL 4.1 6.1 - - - -
416A PRO* 3.8 13.8 - - + +
417A PHE* 3.5 23.6 - + - -
23D TYR* 5.5 3.2 - - + +
24D LEU* 5.7 0.5 - - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.4 22.2 - - + -
27A ALA* 4.4 13.2 - - + +
28A VAL* 4.5 1.3 - - + -
31A THR* 4.4 11.9 - - - +
255A ALA 4.4 3.6 - - - +
256A VAL* 3.8 35.4 - - + +
259A ASN* 4.0 14.4 - - + +
407A MSE 2.9 51.7 + - + +
408A SER 3.8 3.8 - - - +
410A TYR* 1.3 73.5 - - - +
412A LEU* 1.3 64.4 + - - +
413A GLY* 3.4 0.9 + - - -
24D LEU* 6.1 0.3 - - - +
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASN* 3.6 16.6 + - - +
262A TYR* 3.9 31.2 - - + -
293A GLU* 3.8 42.0 - - + +
298A LYS* 4.4 13.0 + - + +
299A GLY* 4.2 12.6 - - - +
408A SER 3.0 16.9 + - - +
409A GLY 3.2 5.3 + - - +
411A LEU* 1.3 77.1 - - - +
413A GLY* 1.3 58.2 + - - +
414A VAL* 4.0 16.8 - - + +
24D LEU* 5.4 0.9 - - - +
263D ASN* 3.6 27.7 - - + +
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP* 4.9 1.9 - - - +
298A LYS* 4.3 10.9 + - - -
409A GLY 3.1 3.0 + - - -
410A TYR 3.2 9.4 + - - -
411A LEU 3.2 3.6 - - - -
412A LEU* 1.3 80.9 - - - +
414A VAL* 1.3 62.9 + - - +
20D GLU* 4.8 4.9 - - - +
23D TYR* 3.6 21.9 - - - +
24D LEU* 3.8 26.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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