Contacts of the helix formed by residues 376 - 400 (chain A) in PDB entry 1SL1
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 ASP 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ALA* 5.2 2.3 + - + +
374A VAL* 3.5 5.7 - - + +
375A ASP* 1.3 77.5 - - - +
377A PRO* 1.3 69.9 - - - +
378A GLU* 2.6 40.6 + - - +
379A LYS* 2.9 44.4 + - + +
380A GLN* 3.1 21.5 + - - +
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Residues in contact with PRO 377 (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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375A ASP 3.0 10.3 - - - +
376A ASP* 1.3 87.1 - - - +
378A GLU* 1.3 59.9 + - + +
380A GLN* 3.3 8.1 + - + +
381A ALA* 3.0 28.2 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 5.2 4.5 - - - +
260A THR* 3.4 34.8 + - + +
376A ASP* 2.6 16.8 + - - +
377A PRO* 1.3 78.0 - - + +
379A LYS* 1.3 56.6 + - + +
381A ALA* 3.3 6.3 + - - +
382A ALA* 2.9 26.0 + - + +
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A THR* 4.0 17.2 + - + +
261A PHE* 3.7 37.9 - - + -
345A LYS* 5.4 2.3 + - - +
346A LEU* 4.8 3.6 - - + +
348A GLU 5.6 2.0 - - - -
349A ALA* 3.9 24.9 - - + +
374A VAL* 4.0 8.5 - - + +
376A ASP* 2.9 39.5 + - + +
378A GLU* 1.3 75.0 - - + +
380A GLN* 1.3 65.1 + - - +
382A ALA* 3.4 14.6 + - - +
383A ILE* 3.4 18.9 + - - +
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Residues in contact with GLN 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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369A LEU 5.6 0.2 + - - -
372A VAL 3.0 22.5 + - - -
373A ARG* 3.0 17.3 - - - +
374A VAL* 2.5 46.5 + - + +
376A ASP 3.1 14.6 + - - +
377A PRO* 3.4 12.8 - - + +
378A GLU 3.2 0.2 - - - -
379A LYS* 1.3 79.3 - - - +
381A ALA* 1.3 59.6 + - - +
383A ILE* 3.5 26.7 - - - +
384A ASP* 4.4 4.5 + - - +
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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
----------------------------------------------------------
377A PRO 3.0 15.3 + - - +
378A GLU* 3.8 7.6 - - - +
380A GLN* 1.3 72.9 - - - +
382A ALA* 1.3 65.9 + - - +
383A ILE 3.1 2.9 - - - -
384A ASP* 3.2 24.7 + - - +
385A LEU* 3.7 10.1 + - - +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.9 8.3 - - + -
260A THR* 4.3 9.6 - - + +
261A PHE* 3.9 27.4 - - + -
378A GLU 2.9 16.7 + - - +
379A LYS* 3.6 8.7 - - - +
380A GLN 3.3 0.4 - - - -
381A ALA* 1.3 74.6 - - - +
383A ILE* 1.3 60.7 + - - +
385A LEU* 3.0 17.9 + - + +
386A ILE* 2.9 31.5 + - - +
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.3 22.0 - - + -
369A LEU* 3.2 40.4 - - + +
372A VAL* 3.6 32.1 - - + +
374A VAL* 4.9 2.9 - - + -
379A LYS 3.4 14.8 - - - +
380A GLN* 3.5 31.4 - - - +
381A ALA 3.1 0.8 - - - -
382A ALA* 1.3 78.4 - - - +
384A ASP* 1.3 61.5 + - - +
386A ILE* 3.1 10.8 + - + +
387A LYS* 2.9 30.9 + - + +
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLU* 4.6 8.0 - - - +
380A GLN 4.9 5.6 - - - +
381A ALA* 3.2 14.6 + - - +
383A ILE* 1.3 80.2 - - - +
385A LEU* 1.3 61.3 + - + +
387A LYS* 3.4 18.5 + - - +
388A GLU* 2.9 28.9 + - - +
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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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249A ARG* 4.7 5.4 - - - +
253A LEU* 4.1 22.7 - - + +
256A LYS* 4.2 32.3 - - + -
257A LEU* 3.8 21.1 - - + +
260A THR* 5.9 2.0 - - - +
381A ALA 3.8 12.6 - - - +
382A ALA* 3.0 18.3 + - + +
384A ASP* 1.3 77.3 - - + +
386A ILE* 1.3 61.7 + - - +
388A GLU* 3.4 10.9 + - - +
389A TYR* 2.9 28.9 + - - +
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.7 22.9 - - + -
261A PHE* 3.9 25.6 - - + -
334A PHE* 4.2 12.6 - - + -
336A PRO* 4.2 6.1 - - + +
342A ILE* 3.7 43.3 - - + -
346A LEU* 5.1 6.1 - - + -
369A LEU* 4.5 7.2 - - + -
382A ALA 2.9 18.2 + - - +
383A ILE* 3.1 16.4 + - + +
385A LEU* 1.3 75.0 - - - +
387A LYS* 1.3 66.7 + - - +
389A TYR* 3.1 3.8 + - - +
390A LEU* 3.0 31.8 + - + +
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 3.2 34.0 - - - +
369A LEU* 4.1 28.5 - - + -
370A GLU* 4.6 12.8 - - + +
383A ILE* 2.9 21.2 + - + +
384A ASP* 3.6 23.3 - - - +
386A ILE* 1.3 77.8 - - - +
388A GLU* 1.3 61.9 + - - +
390A LEU* 3.3 8.8 + - - +
391A MET* 3.2 22.2 + - - +
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Residues in contact with GLU 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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249A ARG* 2.7 45.2 + - - +
253A LEU* 3.3 16.9 - - + +
384A ASP 2.9 17.0 + - - +
385A LEU* 3.8 8.1 - - - +
387A LYS* 1.3 76.4 - - - +
389A TYR* 1.3 62.9 + - - +
391A MET* 3.5 16.7 + - + +
392A ILE* 3.0 34.1 + - + +
447A TYR* 5.0 4.2 + - - -
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Residues in contact with TYR 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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250A ARG* 3.6 39.8 - - + +
253A LEU* 3.8 28.7 - - + -
254A LEU* 4.1 17.9 - - + +
257A LEU* 4.5 1.8 - - + -
335A ASN* 4.6 2.8 + - - -
336A PRO* 3.2 51.4 - - + +
337A SER* 3.3 26.4 + - - -
385A LEU 2.9 18.1 + - - +
386A ILE* 3.1 6.2 + - - +
388A GLU* 1.3 78.5 - - - +
390A LEU* 1.3 58.3 + - - +
392A ILE* 3.4 4.4 + - + +
393A GLN* 2.9 40.9 + - - +
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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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336A PRO 3.3 22.7 - - - +
337A SER* 3.8 22.2 - - - +
339A ARG* 3.7 39.0 - - - +
342A ILE* 4.3 5.8 - - + -
366A ASP* 6.1 1.3 - - + +
369A LEU* 4.2 13.2 - - + -
386A ILE* 3.0 32.5 + - + +
387A LYS* 3.7 5.4 - - - +
389A TYR* 1.3 77.4 - - - +
391A MET* 1.3 56.3 + - - +
393A GLN* 3.4 6.3 + - + +
394A LYS* 3.1 26.9 + - - +
18P G 5.9 6.5 - - - +
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Residues in contact with MET 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 LYS 3.2 15.4 + - - +
388A GLU* 3.8 17.9 - - + +
389A TYR 3.3 0.2 - - - -
390A LEU* 1.3 72.7 - - - +
392A ILE* 1.3 80.5 + - + +
394A LYS* 3.0 10.7 + - - +
395A ARG* 3.0 34.7 + - - +
446A PRO* 3.7 36.3 - - + -
447A TYR* 3.9 24.0 - - + -
18P G 6.4 0.9 - - - -
19P C 4.1 18.6 - - - +
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Residues in contact with ILE 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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246A LEU* 3.8 26.5 - - + +
249A ARG* 3.3 36.1 - - + -
250A ARG* 4.3 10.8 - - + -
253A LEU* 3.7 16.2 - - + -
388A GLU* 3.0 25.6 + - + +
389A TYR* 3.8 4.9 - - - +
391A MET* 1.3 87.7 - - + +
393A GLN* 1.3 65.7 + - - +
395A ARG* 3.3 6.7 + - - +
396A ILE* 3.0 34.6 + - + +
447A TYR* 4.3 15.7 - - + +
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Residues in contact with GLN 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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250A ARG* 2.7 38.9 + - - +
335A ASN* 5.6 0.2 + - - -
337A SER* 2.9 30.0 + - - +
389A TYR* 2.9 34.0 + - + +
390A LEU* 3.5 9.9 - - + +
391A MET 3.2 0.2 - - - -
392A ILE* 1.3 78.2 - - - +
394A LYS* 1.3 63.4 + - - +
396A ILE* 3.4 3.4 + - - +
397A GLY* 3.0 21.7 + - - -
11T C 5.2 1.2 - - - +
12T T 4.1 31.3 + - - +
13T G 5.1 2.4 + - - -
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Residues in contact with LYS 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 3.1 13.6 + - - +
391A MET* 3.0 16.5 + - - +
393A GLN* 1.3 78.6 - - - +
395A ARG* 1.3 65.7 + - - +
397A GLY* 4.0 0.6 - - - -
398A GLN* 3.2 27.0 + - + +
17P T 5.3 3.6 - - - -
18P G 2.9 71.9 + - - +
19P C 3.1 23.8 + - - -
10T A 5.4 3.4 - - - -
11T C 5.2 18.0 - - - +
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Residues in contact with ARG 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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242A LEU* 6.0 0.9 - - + -
246A LEU* 3.9 17.5 - - + -
391A MET* 3.0 32.9 + - - +
392A ILE* 3.3 8.2 + - - +
394A LYS* 1.3 84.6 - - - +
396A ILE* 1.3 57.7 + - - +
398A GLN* 3.6 6.1 + - - +
399A SER* 2.9 33.1 + - - -
406A TRP* 5.8 0.2 - - - -
441A PRO* 3.8 30.0 - - - +
445A SER* 3.6 22.4 - - - -
446A PRO* 2.9 36.1 + - - +
447A TYR* 4.3 13.5 - - + -
451A CYS* 4.4 6.7 - - - -
19P C 3.4 38.5 + - - -
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Residues in contact with ILE 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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243A TYR* 3.8 11.7 - - + -
246A LEU* 3.6 39.7 - - + +
247A ALA* 4.0 4.7 - - + +
250A ARG* 3.7 29.8 - - - +
392A ILE* 3.0 27.9 + - + +
393A GLN* 3.8 5.8 - - - +
395A ARG* 1.3 75.2 - - - +
397A GLY* 1.3 60.4 + - - +
399A SER* 4.0 5.2 - - - -
400A ALA* 2.8 26.7 + - - -
401A GLU* 2.9 45.6 + - + +
12T T 5.6 0.4 - - - +
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Residues in contact with GLY 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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393A GLN 3.0 14.6 + - - -
394A LYS 4.0 1.3 - - - -
396A ILE* 1.3 77.0 - - - +
398A GLN* 1.3 62.5 + - - +
399A SER 3.6 0.2 + - - -
401A GLU 4.4 0.2 - - - -
402A GLY* 2.7 37.4 + - - -
405A ALA* 3.7 4.7 - - - +
11T C 4.2 13.6 + - - -
12T T 3.7 18.4 + - - -
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Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 3.2 19.8 + - - +
395A ARG* 4.0 6.9 + - - +
396A ILE 3.3 0.2 - - - -
397A GLY* 1.3 77.2 - - - +
399A SER* 1.3 57.6 + - - +
404A LYS 4.3 1.7 - - - +
405A ALA* 3.3 5.1 - - - +
406A TRP* 3.1 58.2 + - + +
436A ASN 4.8 1.6 + - - -
439A GLN* 3.2 44.5 + - - +
440A ILE* 4.0 0.6 - - - +
441A PRO* 3.2 23.8 - - - +
19P C 4.9 6.8 - - - +
11T C 4.7 7.4 - - - -
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.9 14.6 + - - +
242A LEU* 5.0 5.4 - - - +
243A TYR* 5.2 2.8 - - - +
246A LEU* 4.5 8.5 - - - +
395A ARG 2.9 22.7 + - - -
396A ILE* 3.8 4.3 + - - -
398A GLN* 1.3 78.0 - - - +
400A ALA* 1.3 63.8 + - - +
405A ALA* 3.8 2.7 - - - -
406A TRP* 3.3 34.1 - - - +
407A LEU* 3.1 32.4 + - - +
451A CYS* 5.7 0.4 - - - -
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR* 3.7 37.5 - - + -
396A ILE 2.8 13.5 + - - +
399A SER* 1.3 79.9 + - - +
401A GLU* 1.3 57.7 + - - +
405A ALA* 3.3 15.7 - - - +
407A LEU* 3.6 26.3 - - + +
408A ARG* 3.8 14.9 + - - +
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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