Contacts of the helix formed by residues 443 - 466 (chain A) in PDB entry 2WWB
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 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TRP* 3.1 45.9 + - - -
67A VAL* 4.4 9.3 - - - +
68A ILE* 3.7 11.7 - - - +
351A PHE* 4.9 1.8 - - - -
436A ASP* 4.7 0.4 - - - -
440A ALA* 4.0 4.8 - - - +
441A ILE* 3.7 7.7 - - - +
442A GLY* 1.4 82.1 + - - +
444A GLY* 1.4 61.6 + - - +
445A THR 4.2 0.4 - - - +
446A GLY* 3.4 21.0 + - - -
447A ILE* 3.5 14.4 + - - +
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Residues in contact with GLY 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ALA* 3.4 23.8 - - - +
436A ASP* 3.1 27.0 + - - -
440A ALA* 3.8 9.3 - - - +
443A SER* 1.4 69.0 - - - +
445A THR* 1.4 62.8 + - - +
446A GLY 3.3 0.4 - - - -
447A ILE* 3.5 20.8 + - - +
448A LEU* 3.5 15.1 + - - +
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Residues in contact with THR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 4.2 24.0 - - + -
68A ILE* 5.6 2.0 - - + -
291A ILE* 5.5 2.7 - - + -
295A SER* 3.4 26.7 - - - +
364A TYR* 5.0 0.5 + - - -
368A MET* 4.7 10.1 - - + +
432A SER* 3.4 35.9 + - - +
433A VAL* 4.5 0.5 + - - -
436A ASP* 3.0 18.0 + - - -
443A SER* 4.8 1.3 - - - -
444A GLY* 1.4 76.3 - - - +
446A GLY* 1.4 60.9 + - - +
448A LEU* 3.4 6.7 + - - +
449A LEU* 3.2 24.7 + - + +
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Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 5.3 2.9 - - - -
68A ILE* 4.7 12.1 - - - +
187A ILE* 3.3 28.8 - - - +
443A SER* 3.4 17.2 + - - -
444A GLY 3.3 0.8 - - - -
445A THR* 1.4 77.5 - - - +
447A ILE* 1.4 61.2 + - - +
449A LEU* 3.3 6.9 + - - +
450A ALA* 3.1 18.0 + - - +
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Residues in contact with ILE 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE* 4.4 6.7 - - - -
191A ILE* 4.3 20.4 - - + -
247A ALA* 3.6 36.3 - - + +
248A THR* 4.5 14.6 - - + +
251A VAL* 4.3 20.9 - - + -
439A GLY 4.4 1.1 - - - +
440A ALA* 4.4 0.9 - - - -
441A ILE* 3.8 27.4 - - + +
443A SER 3.5 12.7 + - - +
444A GLY* 3.8 19.5 - - - +
445A THR 3.4 0.6 - - - -
446A GLY* 1.4 73.7 - - - +
448A LEU* 1.4 61.0 + - - +
450A ALA* 3.3 10.8 + - + +
451A VAL* 3.3 19.9 + - + +
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Residues in contact with LEU 448 (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 VAL* 4.0 24.3 - - + +
254A VAL* 5.1 7.2 - - + -
255A VAL* 5.2 5.8 - - + -
258A PHE* 5.9 1.3 - - + -
428A ILE* 3.8 21.5 - - + +
431A LEU* 3.9 31.6 - - + -
432A SER* 3.4 31.6 - - - +
435A ALA* 5.2 2.9 - - + -
444A GLY 3.5 8.3 + - - +
445A THR* 3.4 10.5 + - - +
446A GLY 3.3 0.6 - - - -
447A ILE* 1.4 75.8 - - - +
449A LEU* 1.4 62.4 + - + +
451A VAL* 3.3 13.2 - - + +
452A THR* 2.9 28.3 + - - +
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Residues in contact with LEU 449 (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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68A ILE* 3.9 22.7 - - + -
183A ILE* 5.3 5.6 - - + -
187A ILE* 4.8 5.4 - - + -
288A ASN* 4.7 7.6 - - - +
291A ILE* 3.9 28.0 - - + -
292A ILE* 3.9 35.0 - - + -
295A SER* 3.9 21.1 - - - +
428A ILE* 5.8 2.5 - - + -
445A THR* 3.2 14.3 + - + +
446A GLY* 3.3 9.2 + - - +
448A LEU* 1.4 78.4 - - + +
450A ALA* 1.4 62.5 + - - +
452A THR* 3.5 5.0 + - - -
453A ILE* 3.3 35.8 + - + +
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Residues in contact with ALA 450 (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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184A ALA* 4.8 10.5 - - - +
187A ILE* 3.6 33.2 - - + +
188A CYS* 5.2 4.0 - - - +
191A ILE* 5.4 5.2 - - + -
446A GLY 3.1 13.9 + - - +
447A ILE* 3.3 9.6 + - - +
449A LEU* 1.4 76.2 - - - +
451A VAL* 1.4 59.5 + - + +
453A ILE* 4.1 0.7 - - - +
454A ILE* 3.1 39.7 + - + +
44B PHE* 5.6 3.4 - - + -
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 5.9 4.7 - - + -
251A VAL* 3.7 23.8 - - + -
252A PHE* 5.8 6.3 - - + -
255A VAL* 3.8 32.0 - - + +
447A ILE* 3.3 16.8 + - + +
448A LEU* 3.3 13.7 - - + +
450A ALA* 1.4 77.0 - - + +
452A THR* 1.4 67.1 + - - +
454A ILE* 4.7 1.3 - - - +
455A TYR* 3.3 45.6 + - + +
44B PHE* 5.0 15.9 - - + -
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Residues in contact with THR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.5 12.4 - - + +
259A GLN* 5.3 5.3 + - + +
284A PHE* 5.5 8.3 - - + +
285A TYR* 3.4 22.0 - - + -
288A ASN* 4.0 15.7 - - + +
428A ILE* 5.6 9.0 - - + +
448A LEU* 2.9 24.7 + - - +
449A LEU* 3.8 6.9 - - - -
450A ALA 3.4 0.6 - - - -
451A VAL* 1.4 82.6 - - - +
453A ILE* 1.4 60.4 + - - +
455A TYR* 5.1 0.2 - - - +
456A GLN* 3.4 22.5 + - - +
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Residues in contact with ILE 453 (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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180A SER* 4.6 22.9 - - - +
181A LEU* 6.0 3.1 - - + -
183A ILE* 5.2 7.0 - - + -
184A ALA* 4.0 25.8 - - + +
285A TYR* 3.7 12.7 + - - +
288A ASN* 3.6 23.3 - - - +
292A ILE* 3.9 28.7 - - + -
449A LEU* 3.3 22.3 + - + +
450A ALA 4.2 2.0 - - - +
452A THR* 1.4 75.9 - - - +
454A ILE* 1.4 59.4 + - + +
457A TYR* 3.0 37.2 + - + +
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Residues in contact with ILE 454 (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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181A LEU* 5.9 5.6 - - + -
184A ALA* 3.8 27.6 - - + +
185A THR* 5.2 1.8 - - - +
188A CYS* 4.1 22.7 - - - -
450A ALA 3.1 23.0 + - - +
451A VAL* 4.6 2.7 - - - +
452A THR 3.6 0.2 - - - -
453A ILE* 1.4 74.4 - - + +
455A TYR* 1.4 70.4 + - + +
457A TYR* 3.8 6.7 + - - +
458A PHE* 3.8 13.2 + - - +
40B THR* 4.0 23.5 + - + +
43B GLY 5.3 3.1 - - - +
44B PHE* 4.7 16.6 - - + -
47B MET* 5.0 13.9 - - + -
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Residues in contact with TYR 455 (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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252A PHE* 4.2 23.1 - + - -
255A VAL* 5.8 2.0 - - + -
256A ILE* 5.2 10.1 - - + -
259A GLN* 3.4 26.0 - - - +
451A VAL* 3.3 37.2 + - + +
454A ILE* 1.4 82.1 - - + +
456A GLN* 1.4 62.1 + - - +
457A TYR 3.7 0.2 + - - -
458A PHE* 4.0 7.4 + - - +
459A GLU* 3.1 20.3 - - - +
36B ILE* 3.5 38.1 - - + -
37B ALA* 4.4 8.7 - - - +
40B THR* 3.3 36.9 + - + -
41B ALA* 4.2 14.4 + - - +
44B PHE* 5.0 12.9 - + + +
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Residues in contact with GLN 456 (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 GLN* 3.7 30.5 + - + +
262A ARG* 6.3 1.2 - - - +
282A LYS* 3.2 28.6 + - - +
285A TYR* 3.7 40.8 - - + +
452A THR 3.4 20.0 + - - +
453A ILE 3.6 0.6 + - - -
454A ILE 3.4 0.4 - - - -
455A TYR* 1.4 77.6 - - - +
457A TYR* 1.4 63.7 + - - +
459A GLU* 3.2 35.7 + - - +
460A ILE* 3.4 11.9 + - + +
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Residues in contact with TYR 457 (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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35A THR* 6.5 0.4 - - + -
175A LEU 3.0 25.1 + - - -
176A GLY* 3.7 14.4 - - - -
177A SER* 4.6 6.0 + - - -
181A LEU* 4.8 22.0 - - + -
285A TYR* 4.2 12.5 + + - +
453A ILE* 3.0 27.5 + - + +
454A ILE* 4.5 2.9 - - - +
455A TYR 3.5 0.2 - - - -
456A GLN* 1.4 75.0 - - - +
458A PHE* 1.4 57.5 + - - +
460A ILE* 3.2 25.8 + - + +
461A PHE* 3.0 53.0 + + + +
464A GLU* 4.0 4.4 + - - -
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Residues in contact with PHE 458 (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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454A ILE 3.8 14.7 + - - +
455A TYR 4.1 5.6 - - - +
456A GLN 3.3 0.6 - - - -
457A TYR* 1.4 77.3 - - - +
459A GLU* 1.4 64.2 + - + +
461A PHE* 3.6 13.8 + + + +
462A VAL* 3.7 21.5 - - + +
470A SER* 3.9 31.2 + - - -
471A MET 4.5 11.9 - - - -
472A GLY* 6.2 0.4 - - - -
474A LEU* 6.2 5.6 - - + -
39B ALA* 3.5 38.8 - - + -
40B THR* 5.0 7.6 - - + +
43B GLY* 6.6 0.2 - - - -
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Residues in contact with GLU 459 (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 GLN* 3.4 21.1 + - - -
455A TYR* 3.1 22.4 - - - +
456A GLN* 3.2 22.6 + - - +
458A PHE* 1.4 78.7 - - + +
460A ILE* 1.4 61.2 + - + +
462A VAL 4.3 1.6 + - - -
463A LYS* 3.5 27.2 + - - +
470A SER* 4.0 14.3 + - - +
36B ILE* 4.8 18.1 - - + +
39B ALA* 6.1 4.3 - - + -
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Residues in contact with ILE 460 (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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282A LYS* 4.4 15.9 - - - +
285A TYR* 3.9 28.5 - - + -
456A GLN* 3.4 24.4 + - + +
457A TYR* 3.2 23.0 + - + +
459A GLU* 1.4 74.3 - - + +
461A PHE* 1.4 64.0 - - - +
463A LYS* 3.2 18.2 + - - +
464A GLU* 3.3 34.4 + - + +
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Residues in contact with PHE 461 (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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32A VAL* 4.0 20.0 - - + -
35A THR* 4.5 17.7 - - + -
175A LEU* 4.0 23.7 - - + +
176A GLY* 4.2 8.5 - - - -
457A TYR* 3.0 47.5 + + + +
458A PHE* 4.0 11.7 - + + +
459A GLU 3.5 0.8 - - - -
460A ILE* 1.4 75.6 - - - +
462A VAL* 1.4 64.4 + - + +
464A GLU* 3.4 17.2 + - - +
465A GLN* 3.3 22.0 + - + +
473A ALA* 3.9 33.0 - - + -
474A LEU* 5.9 0.7 - - - -
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PHE* 3.7 23.1 + - + +
459A GLU 4.3 0.4 + - - +
460A ILE 3.4 0.2 - - - -
461A PHE* 1.4 79.6 - - + +
463A LYS* 1.4 64.3 + - - +
465A GLN* 3.3 15.6 + - - +
467A GLU* 3.0 45.7 + - + +
468A VAL* 4.1 2.7 - - - +
470A SER* 3.8 30.5 - - - +
471A MET* 3.5 29.2 - - + +
472A GLY 4.6 2.7 - - - +
473A ALA* 4.7 8.5 - - + -
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Residues in contact with LYS 463 (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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459A GLU* 3.5 16.9 + - - +
460A ILE* 3.2 9.3 + - - +
462A VAL* 1.4 74.5 - - - +
464A GLU* 1.4 61.9 + - + +
465A GLN 3.5 0.2 + - - -
466A SER* 3.8 8.1 + - - -
467A GLU 3.5 9.8 - - - +
468A VAL* 3.9 28.6 - - + +
469A GLY 3.5 15.9 - - - +
470A SER* 3.4 27.1 + - - +
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Residues in contact with GLU 464 (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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28A PHE* 4.4 10.0 - - - -
175A LEU* 3.9 43.6 - - + +
457A TYR* 4.0 5.8 + - - -
460A ILE* 3.3 29.5 + - + +
461A PHE* 3.5 31.9 - - - +
463A LYS* 1.4 75.7 - - + +
465A GLN* 1.4 63.3 + - - +
466A SER* 3.4 1.2 + - - -
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Residues in contact with GLN 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.2 46.2 + - - +
32A VAL* 3.7 17.0 - - + +
175A LEU* 3.9 12.7 - - + +
461A PHE* 3.3 10.9 + - + +
462A VAL* 3.3 16.1 + - - +
464A GLU* 1.4 78.7 - - - +
466A SER* 1.4 68.7 + - - +
467A GLU* 3.3 19.5 - - - +
473A ALA* 3.9 20.9 - - + -
476A PHE* 3.2 28.2 + - - +
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.3 35.0 - - - -
462A VAL 3.7 0.4 + - - -
463A LYS 3.8 5.3 + - - -
464A GLU 3.3 3.9 - - - -
465A GLN* 1.4 81.4 + - - +
467A GLU* 1.4 64.4 + - - +
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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