Contacts of the helix formed by residues 408 - 432 (chain B) in PDB entry 2R8K
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 SER 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ASN* 1.3 85.0 + - - +
409B ILE* 1.3 67.3 + - - +
410B VAL* 2.9 21.0 + - - +
411B ASP* 2.6 34.5 + - - +
412B CYS* 3.3 9.4 + - - -
494B TYR* 3.5 19.1 - - - -
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 1.3 75.3 - - - +
410B VAL* 1.3 72.1 + - + +
412B CYS* 3.8 2.3 - - - +
413B ILE* 2.8 42.0 + - + +
481B VAL* 3.4 27.8 - - + +
482B THR* 3.8 17.7 - - + +
485B ASP* 3.9 17.0 - - + +
494B TYR* 3.6 21.8 + - + +
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 2.9 20.5 - - - +
409B ILE* 1.3 88.2 - - + +
411B ASP* 1.3 72.4 + - - +
412B CYS 3.1 2.0 + - - -
413B ILE* 3.2 9.8 + - - +
414B SER* 2.8 33.1 + - - +
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Residues in contact with ASP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS* 3.1 20.2 + - + +
405B SER 2.7 24.0 - - - +
406B CYS* 3.5 22.7 - - - -
407B ASN* 3.7 7.9 - - - +
408B SER* 2.6 29.4 + - - +
410B VAL* 1.3 88.6 - - - +
412B CYS* 1.3 63.6 + - - +
414B SER* 3.3 9.6 - - - -
415B TRP* 2.9 29.7 + - + -
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Residues in contact with CYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B CYS* 3.5 8.9 - - - -
408B SER 3.3 12.8 + - - -
409B ILE* 3.8 8.7 - - - +
410B VAL 3.1 0.2 - - - -
411B ASP* 1.3 76.3 - - - +
413B ILE* 1.3 65.8 + - + +
415B TRP* 2.8 6.6 + - - +
416B LEU* 2.7 26.2 + - - +
447B LEU* 5.4 1.1 - - - -
481B VAL* 3.2 33.7 - - + -
493B TYR* 5.7 0.7 - - - -
494B TYR* 4.0 13.7 - - - -
496B LEU* 3.4 33.2 - - - -
499B LEU* 4.0 8.0 - - + +
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Residues in contact with ILE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 2.8 33.7 - - + +
410B VAL* 3.2 10.1 + - - +
412B CYS* 1.3 78.9 - - + +
414B SER* 1.3 59.6 + - - +
416B LEU* 3.1 12.2 + - - +
417B GLU* 2.8 40.2 + - + +
474B LEU* 4.5 1.9 - - + +
478B ILE* 3.3 30.3 - - + -
481B VAL* 3.5 27.1 - - + -
482B THR* 5.0 0.7 - - - +
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Residues in contact with SER 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS* 4.3 8.5 - - - -
98B GLY* 3.6 25.2 + - - -
410B VAL* 2.8 24.8 + - - +
411B ASP* 3.3 14.1 - - - -
413B ILE* 1.3 77.8 - - - +
415B TRP* 1.3 63.7 + - - +
417B GLU* 3.0 31.2 + - - +
418B VAL* 3.2 9.4 + - - +
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Residues in contact with TRP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE 6.1 0.4 - - - -
97B LYS* 3.1 41.0 - - + +
122B GLU 3.8 11.0 - - - -
123B ASP 4.2 9.2 - - - -
124B HIS 4.3 1.3 - - - -
125B LYS* 4.5 15.9 - - + -
399B LYS* 3.5 48.2 - - + -
401B LEU* 3.4 22.5 - - + +
405B SER* 3.6 16.4 + - - -
406B CYS* 3.9 13.3 - - + +
411B ASP 2.9 24.0 + - - -
412B CYS 2.8 10.1 + - - +
414B SER* 1.3 72.7 - - - +
416B LEU* 1.3 51.0 + - - +
418B VAL* 2.7 25.1 + - + +
419B PHE* 2.7 48.5 + + + -
499B LEU* 3.6 16.8 - - + -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B CYS 2.7 20.3 + - - +
413B ILE* 3.2 11.4 - - - +
415B TRP* 1.3 72.5 - - - +
417B GLU* 1.3 51.8 + - - +
419B PHE* 3.9 11.4 - - + -
420B CYS* 2.7 38.5 + - - -
445B ILE* 4.7 10.5 - - + -
474B LEU* 3.6 13.5 - - + -
477B GLY* 3.7 16.8 - - - +
478B ILE* 3.8 15.7 - - + -
481B VAL* 3.5 32.5 - - + -
499B LEU* 4.1 24.2 - - + -
500B SER 5.6 0.2 - - - +
501B MET* 4.0 19.3 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 2.6 34.4 - - - +
99B GLU 4.3 3.4 - - - +
100B ASP* 4.2 22.9 - - + +
413B ILE* 2.8 27.1 + - + +
414B SER* 3.0 11.9 + - - +
416B LEU* 1.3 75.5 - - - +
418B VAL* 1.3 62.3 + - - +
420B CYS* 4.1 2.2 - - - +
421B ALA* 3.1 24.3 + - - +
474B LEU* 4.0 25.1 - - + +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.5 29.5 - - + -
96B LYS 3.5 17.7 - - - +
97B LYS* 4.0 6.5 - - - -
98B GLY 3.7 5.6 - - - +
99B GLU 3.5 20.2 - - - +
125B LYS* 4.4 21.1 - - + -
414B SER 3.6 11.9 - - - +
415B TRP* 2.7 23.4 + - + +
417B GLU* 1.3 77.2 - - - +
419B PHE* 1.3 63.2 + - + +
421B ALA* 3.3 6.5 - - - +
422B GLU* 3.1 20.7 + - + +
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Residues in contact with PHE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 4.1 16.6 - - + -
397B SER* 3.0 32.3 - - - +
398B ASN* 3.2 24.9 - - - -
399B LYS* 3.1 33.9 - - + -
415B TRP* 2.7 47.6 + + + -
416B LEU* 3.6 17.0 - - + +
418B VAL* 1.3 69.6 - - + +
420B CYS* 1.3 67.7 + - - +
422B GLU* 2.9 15.0 + - - +
423B LEU* 3.0 17.8 + - - +
499B LEU* 3.7 22.0 - - + -
501B MET* 4.4 16.8 - - + -
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Residues in contact with CYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU 2.7 27.1 + - - +
417B GLU* 4.1 3.4 - - - +
419B PHE* 1.3 73.4 - - - +
421B ALA* 1.3 55.3 + - - +
423B LEU* 3.3 7.6 + - - +
424B THR* 2.9 36.1 + - - +
470B SER* 5.2 6.1 - - - +
473B LEU* 4.6 7.1 - - + +
474B LEU* 3.2 47.3 - - + +
501B MET* 3.3 30.7 - - - -
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Residues in contact with ALA 421 (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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95B PHE* 3.6 22.3 - - + -
100B ASP* 4.0 20.2 - - + +
417B GLU 3.1 19.2 + - - +
418B VAL 3.3 6.3 - - - +
419B PHE 3.0 0.6 - - - -
420B CYS* 1.3 78.2 - - - +
422B GLU* 1.3 56.8 + - - +
424B THR* 3.3 7.2 + - - -
425B SER* 3.0 27.5 + - - -
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.1 20.8 - - + -
125B LYS* 3.1 37.5 + - + +
126B VAL 3.7 14.9 - - - +
127B SER* 4.9 2.4 - - - -
128B LEU 6.3 0.2 - - - -
132B ARG* 4.8 8.3 - - - +
397B SER* 3.6 11.0 + - - +
418B VAL 3.1 8.2 + - - +
419B PHE 2.9 7.4 + - - +
421B ALA* 1.3 79.3 - - - +
423B LEU* 1.3 61.4 + - - +
425B SER* 3.3 8.2 - - - -
426B ARG* 2.6 53.5 + - - +
7T T 4.0 7.1 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B MET* 4.5 3.1 - - + -
396B MET 3.9 18.6 - - - +
397B SER* 3.7 22.2 - - - -
419B PHE 3.0 15.6 + - - +
420B CYS* 3.7 6.3 - - - +
422B GLU* 1.3 74.9 - - - +
424B THR* 1.3 66.6 + - - +
425B SER 3.0 1.6 - - - -
426B ARG* 3.0 15.9 + - - +
427B ILE* 2.9 28.0 + - - +
473B LEU* 4.5 7.6 - - + -
501B MET* 3.8 41.3 - - + +
503B ILE* 3.9 38.8 - - + -
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Residues in contact with THR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B CYS* 2.9 23.0 + - - +
421B ALA* 3.7 7.4 - - - -
423B LEU* 1.3 75.5 - - - +
425B SER* 1.3 61.5 + - - +
427B ILE* 3.3 2.3 + - - +
428B GLN* 3.2 39.1 + - - +
469B GLN* 3.4 27.5 + - + +
470B SER* 3.5 34.3 + - - +
473B LEU* 5.5 3.7 - - - +
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Residues in contact with SER 425 (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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95B PHE* 5.6 4.5 - - - -
102B TRP* 5.9 1.2 - - - -
129B GLU* 2.9 31.5 + - - +
132B ARG* 3.4 20.9 + - - -
421B ALA 3.0 13.5 + - - -
422B GLU* 3.3 15.3 - - - -
424B THR* 1.3 77.7 - - - +
426B ARG* 1.3 62.3 + - - +
428B GLN* 3.3 10.2 + - - +
429B ASP* 3.2 18.7 + - - +
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Residues in contact with ARG 426 (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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132B ARG* 3.5 37.9 - - - +
395B MET* 3.2 24.9 - - + +
396B MET 2.7 26.6 + - - +
422B GLU* 2.6 47.3 + - - +
423B LEU* 3.0 14.6 + - - +
425B SER* 1.3 76.5 - - - +
427B ILE* 1.3 65.6 + - - +
429B ASP* 3.5 9.3 + - + +
430B LEU* 3.2 26.2 + - - +
7T T 3.3 17.3 + - - -
8T C 2.5 30.2 + - - -
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Residues in contact with ILE 427 (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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395B MET* 3.8 12.8 - - - -
423B LEU 2.9 19.9 + - - +
424B THR 3.5 1.8 - - - +
426B ARG* 1.3 76.4 - - - +
428B GLN* 1.3 67.2 + - - +
430B LEU* 2.9 17.6 + - + +
431B GLU* 3.0 22.9 + - + +
438B VAL* 3.7 26.7 - - + +
440B PRO* 4.6 7.9 - - + -
469B GLN* 2.8 46.0 - - - +
473B LEU* 6.4 0.4 - - + -
503B ILE* 3.6 28.0 - - + -
506B PHE* 4.1 10.8 - - + -
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR 5.6 6.3 - - - +
200A ASP* 4.3 14.3 + - - +
129B GLU* 6.1 0.2 - - - +
424B THR* 3.2 27.6 + - - +
425B SER* 3.4 11.7 - - - +
427B ILE* 1.3 83.2 - - - +
429B ASP* 1.3 63.0 + - - +
431B GLU* 2.8 45.5 + - + +
432B GLN* 3.2 17.9 + - + +
469B GLN* 5.2 1.9 + - - -
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Residues in contact with ASP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG* 3.0 40.6 - - - +
136B ARG* 2.6 39.4 + - - -
151B ARG* 5.0 4.6 + - - -
425B SER 3.2 9.3 + - - +
426B ARG* 3.5 15.7 - - + +
428B GLN* 1.3 78.6 - - - +
430B LEU* 1.3 64.4 + - + +
432B GLN* 3.2 18.5 + - - +
433B GLU* 3.4 5.4 + - - +
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Residues in contact with LEU 430 (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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392B VAL* 3.3 32.1 - - + -
395B MET* 3.5 29.8 - - + -
426B ARG 3.3 9.4 - - - +
427B ILE* 2.9 10.6 + - + +
429B ASP* 1.3 75.9 - - + +
431B GLU* 1.3 57.7 + - - +
432B GLN 2.8 4.7 - - - -
433B GLU* 2.8 31.6 + - + +
434B TYR* 2.9 46.8 + - + +
438B VAL* 4.6 7.0 - - + -
506B PHE* 4.3 6.3 - - + -
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASP* 3.7 14.4 - - - +
201A ILE* 3.4 26.1 - - + +
202A ASN* 5.8 1.2 + - - -
427B ILE* 3.0 18.3 + - - +
428B GLN* 2.8 34.5 + - + +
430B LEU* 1.3 74.4 - - - +
432B GLN* 1.3 57.2 + - - +
433B GLU 3.5 0.2 - - - -
434B TYR* 5.0 0.2 - - - -
435B ASN* 3.2 22.8 + - - +
436B LYS 3.5 17.9 - - - +
437B ILE* 3.8 9.8 - - - +
438B VAL* 3.1 38.6 + - + +
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Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.9 5.8 - - - +
197A GLY* 4.1 6.2 - - - +
199A TYR* 3.2 56.0 + - - +
201A ILE* 3.8 12.8 - - + +
136B ARG* 3.4 28.2 + - - -
140B LYS* 4.1 14.0 - - - +
143B LYS* 5.2 3.8 + - - -
428B GLN* 3.2 17.0 + - + +
429B ASP* 3.4 8.3 - - - +
430B LEU 2.8 1.0 + - - -
431B GLU* 1.3 80.8 - - + +
433B GLU* 1.3 59.9 + - - +
434B TYR 3.5 0.4 - - - -
435B ASN* 4.1 6.5 + - - +
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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