Contacts of the helix formed by residues 396 - 419 (chain A) in PDB entry 3LMK
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 LYS 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 4.6 3.2 + - - +
68A ARG* 3.9 19.7 - - - +
172A TYR* 4.1 7.0 - - + +
173A SER* 3.2 32.1 - - - +
305A ASP* 2.7 40.8 + - - +
308A ALA* 5.8 1.4 - - - +
329A LEU* 4.1 23.1 - - + -
394A ASP* 3.1 7.8 + - - +
395A SER* 1.3 80.4 - - - +
397A MET* 1.3 63.2 + - - +
398A GLY 3.3 2.5 - - - -
399A PHE* 3.0 33.3 + - + +
400A VAL* 3.2 11.7 + - - +
506A GLU* 2.8 23.6 + - - +
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Residues in contact with MET 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 3.6 30.7 - - + +
68A ARG* 4.3 4.0 - - + +
71A ALA* 3.4 25.1 - - + -
332A PRO 5.9 0.2 - - - +
334A VAL* 4.0 3.8 - - + -
337A PHE* 3.8 20.9 - - + -
393A GLN* 3.4 26.0 - - + +
394A ASP* 3.3 44.4 + - + +
395A SER 3.3 2.6 - - - -
396A LYS* 1.3 77.3 - - - +
398A GLY* 1.3 62.7 + - - +
400A VAL* 3.3 6.9 + - - +
401A ILE* 3.2 36.1 + - + +
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Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A SER* 3.5 15.0 + - - -
332A PRO 4.7 4.3 + - - -
334A VAL* 3.8 19.7 - - - +
396A LYS 3.3 0.8 - - - -
397A MET* 1.3 79.0 - - - +
399A PHE* 1.3 58.4 + - - +
401A ILE* 3.4 1.8 + - - +
402A ASN* 2.9 38.7 + - - +
449A VAL* 4.1 8.0 - - - +
450A SER* 5.2 2.5 - - - -
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Residues in contact with PHE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 3.4 20.6 - - + +
191A VAL* 3.3 38.3 - - + +
192A VAL* 3.6 17.0 - - + -
193A PRO* 5.8 0.9 - - + -
329A LEU* 3.7 33.4 - - + -
330A GLN 3.4 24.7 - - - -
331A SER* 3.5 16.8 - - - -
396A LYS* 3.0 34.4 + - + +
398A GLY* 1.3 76.8 - - - +
400A VAL* 1.3 66.4 + - - +
402A ASN* 3.3 7.4 + - - -
403A ALA* 3.0 21.0 + - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.2 22.0 - - + -
68A ARG* 3.8 27.6 - - + +
71A ALA* 4.6 14.1 - - + -
147A ILE* 5.0 1.1 - - + -
172A TYR* 3.6 34.2 - - + +
394A ASP* 4.4 2.0 - - - +
396A LYS 3.2 10.7 + - - +
397A MET* 3.5 10.8 - - - +
399A PHE* 1.3 77.4 - - - +
401A ILE* 1.3 64.1 + - + +
403A ALA* 3.2 4.4 + - - +
404A ILE* 3.1 38.7 + - + +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 4.3 8.5 - - + -
75A THR* 3.7 14.4 - - - +
334A VAL* 3.8 20.9 - - + -
336A TRP* 3.5 40.2 - - + -
337A PHE* 4.7 1.3 - - + -
397A MET* 3.2 38.7 + - + +
398A GLY 3.9 4.7 - - - +
399A PHE 3.2 0.6 - - - -
400A VAL* 1.3 77.5 - - + +
402A ASN* 1.3 57.9 + - - +
404A ILE* 3.3 8.8 + - - +
405A TYR* 3.1 50.0 + - + -
449A VAL* 4.1 14.8 - - + -
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Residues in contact with ASN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 4.2 10.5 - - + +
398A GLY 2.9 24.2 + - - +
399A PHE* 3.9 11.1 - - - +
401A ILE* 1.3 75.0 - - - +
403A ALA* 1.3 59.0 + - - +
405A TYR* 3.3 5.3 + - - -
406A SER* 2.8 33.7 + - - -
446A PHE* 3.5 5.5 - - - -
448A GLY* 3.7 2.5 - - - -
449A VAL* 3.1 36.8 + - - +
450A SER* 5.4 3.6 + - - +
454A ILE* 3.5 35.8 - - + +
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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
----------------------------------------------------------
147A ILE* 3.6 26.7 - - + +
170A ILE* 3.9 20.8 - - + +
171A ALA 4.5 2.7 - - - +
172A TYR* 4.6 2.9 - - + -
191A VAL* 4.0 19.2 - - + +
399A PHE 3.0 13.5 + - - +
400A VAL* 3.2 11.6 + - - +
402A ASN* 1.3 77.2 - - - +
404A ILE* 1.3 60.8 + - - +
406A SER* 3.3 5.1 + - - -
407A MET* 3.1 17.3 + - - +
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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
----------------------------------------------------------
37A ILE* 6.0 1.1 - - + -
71A ALA 4.7 0.2 - - - -
72A MET* 3.8 45.8 - - + +
75A THR* 3.8 28.0 - - + +
76A LEU* 3.9 25.6 - - + -
79A ILE* 4.1 2.9 - - + -
147A ILE* 4.0 17.9 - - + -
400A VAL* 3.1 34.8 + - + +
401A ILE* 3.7 6.5 - - - +
402A ASN 3.3 0.4 - - - -
403A ALA* 1.3 75.9 - - - +
405A TYR* 1.3 57.5 + - - +
407A MET* 3.3 5.3 + - + +
408A ALA* 2.9 26.2 + - - +
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.8 17.3 - - + -
78A ARG* 4.4 24.8 + - - +
79A ILE* 3.7 26.9 + - + +
82A ASP* 5.4 6.2 + - - +
85A LEU* 4.0 16.2 - - + -
336A TRP* 4.9 5.4 - + - -
401A ILE* 3.1 39.8 + - + +
402A ASN* 3.7 7.9 - - - +
403A ALA 3.2 0.2 - - - -
404A ILE* 1.3 75.2 - - - +
406A SER* 1.3 60.0 + - - +
408A ALA* 3.5 3.4 - - - +
409A TYR* 2.8 60.3 + + - -
446A PHE* 3.8 17.3 - + + -
449A VAL* 5.3 8.1 - - + -
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 3.9 11.9 - - - -
191A VAL* 4.0 4.2 - - - +
402A ASN 2.8 16.9 + - - -
403A ALA* 3.4 11.4 - - - -
405A TYR* 1.3 74.0 - - - +
407A MET* 1.3 56.6 + - - +
409A TYR* 3.2 2.4 + - - +
410A GLY 2.8 30.8 + - - -
441A LEU* 3.1 9.3 - - - +
444A THR* 3.7 16.8 + - - +
446A PHE* 3.0 24.5 - - - -
454A ILE* 3.9 7.4 - - - +
456A PHE* 4.1 7.5 - - - -
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Residues in contact with MET 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.8 28.9 - - + -
144A VAL* 6.1 0.2 - - - -
145A GLY* 3.7 13.0 - - - -
146A VAL 3.4 35.4 - - - +
147A ILE* 3.9 11.7 - - + -
168A PRO 3.9 4.7 - - - +
170A ILE* 3.6 26.6 - - + +
403A ALA 3.1 8.4 + - - +
404A ILE* 3.3 9.6 + - + +
406A SER* 1.3 77.9 - - - +
408A ALA* 1.3 63.5 + - - +
410A GLY* 3.1 3.1 + - - -
411A LEU* 2.9 31.6 + - + +
437A LEU* 4.5 9.4 - - - +
441A LEU* 3.8 23.1 - - - +
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Residues in contact with ALA 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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79A ILE* 3.9 23.8 - - + -
85A LEU* 4.0 15.3 - - + -
86A LEU* 3.5 14.8 - - + +
91A LEU* 4.1 12.5 - - + +
404A ILE 2.9 16.2 + - - +
405A TYR* 3.5 6.7 - - - +
407A MET* 1.3 76.7 - - - +
409A TYR* 1.3 56.6 + - - +
411A LEU* 3.2 7.3 + - - +
412A HIS* 2.9 28.3 + - - +
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Residues in contact with TYR 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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82A ASP* 5.5 2.1 + - - -
85A LEU* 3.7 29.2 - - + +
405A TYR* 2.8 52.7 + + - +
406A SER 3.8 3.1 - - - +
408A ALA* 1.3 70.4 - - - +
410A GLY* 1.3 61.2 + - - +
412A HIS* 3.7 9.3 - + + +
413A ASN* 2.9 48.2 + - - +
444A THR* 5.9 2.5 - - + -
445A ASN 6.3 0.2 - - - +
446A PHE* 3.5 54.6 - + + +
447A THR 5.1 3.8 + - - -
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Residues in contact with GLY 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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406A SER 2.8 11.5 + - - -
407A MET 3.7 0.2 - - - -
409A TYR* 1.3 76.3 - - - +
411A LEU* 1.3 60.7 + - - +
413A ASN* 4.5 1.8 - - - -
414A MET* 3.2 13.7 + - - +
437A LEU* 3.8 7.0 - - - -
440A SER* 2.7 29.7 + - - -
441A LEU* 3.5 26.9 - - - -
444A THR* 5.6 0.8 + - - -
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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
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35A ILE* 4.0 18.6 - - + -
37A ILE* 3.8 28.3 - - + -
86A LEU* 3.9 13.1 - - + +
91A LEU* 4.0 14.1 - - + -
144A VAL* 3.8 27.8 - - + -
407A MET* 2.9 31.5 + - + +
408A ALA* 3.5 8.5 - - - +
410A GLY* 1.3 77.0 - - - +
412A HIS* 1.3 55.7 + - - +
414A MET* 3.4 6.7 - - - +
415A GLN* 3.0 28.1 + - - +
429A MET* 4.0 7.7 - - + +
432A ILE* 4.3 7.6 - - + -
437A LEU* 3.9 17.3 - - + -
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Residues in contact with HIS 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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84A THR 3.4 24.5 + - - -
85A LEU* 3.7 16.6 - - + -
86A LEU* 2.8 37.1 + - + +
87A PRO* 3.9 11.7 - - + -
408A ALA 2.9 16.6 + - - +
409A TYR* 3.7 9.4 - + - +
411A LEU* 1.3 74.3 - - - +
413A ASN* 1.3 66.7 + - - +
415A GLN* 3.1 9.5 + - - +
416A MET* 3.0 60.5 + - + +
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Residues in contact with ASN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR* 2.9 34.5 + - - +
410A GLY* 4.4 0.8 - - - +
412A HIS* 1.3 86.4 - - - +
414A MET* 1.3 62.7 + - - +
416A MET* 3.3 20.4 + - - +
417A SER* 3.3 14.0 + - - -
440A SER* 3.5 22.6 + - - +
443A LYS* 5.2 6.5 + - - +
444A THR* 5.8 2.6 - - - +
445A ASN 5.9 1.0 - - - +
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Residues in contact with MET 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLY 3.2 15.6 + - - +
411A LEU* 3.4 6.5 - - - +
413A ASN* 1.3 78.7 - - - +
415A GLN* 1.3 56.1 + - - +
417A SER* 3.3 8.2 + - - -
418A LEU* 3.0 57.7 + - + +
429A MET* 4.1 17.9 - - + -
432A ILE* 3.7 22.7 - - + -
433A ASP* 3.6 28.7 - - + +
436A LYS* 3.9 11.9 - - + +
437A LEU* 3.8 31.4 - - - -
440A SER* 3.7 8.8 + - - +
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Residues in contact with GLN 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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86A LEU* 4.7 3.1 - - + -
87A PRO* 5.0 10.0 + - - +
89A ILE* 3.9 23.6 - - + -
411A LEU 3.0 15.4 + - - +
412A HIS* 3.1 21.9 + - - +
414A MET* 1.3 76.3 - - - +
416A MET* 1.3 68.2 + - - +
419A CYS* 2.8 41.0 + - + +
422A TYR 3.0 26.5 + - - -
423A ALA* 4.3 0.8 - - - +
424A GLY 3.4 24.7 + - - +
429A MET* 3.5 20.6 - - + -
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Residues in contact with MET 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A HIS* 3.0 48.4 + - + +
413A ASN* 3.3 17.0 + - - +
415A GLN* 1.3 86.8 - - - +
417A SER* 1.3 60.2 + - - +
419A CYS 4.7 2.2 - - - -
420A PRO* 3.5 23.5 - - - +
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASN 3.3 10.4 + - - -
414A MET* 3.3 11.6 + - - -
416A MET* 1.3 81.6 - - - +
418A LEU* 1.3 68.4 + - - +
419A CYS 3.5 0.2 - - - -
420A PRO* 4.4 8.0 - - - +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A MET* 3.0 48.7 + - + +
417A SER* 1.3 85.1 + - - +
419A CYS* 1.3 58.9 + - - +
420A PRO* 3.7 6.6 - - - +
426A CYS* 3.3 12.3 - - - -
428A ALA* 3.9 29.4 - - + +
429A MET* 3.6 24.2 - - + -
433A ASP* 6.1 0.9 - - + -
436A LYS* 5.3 7.9 - - + -
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Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLN* 2.8 33.1 + - - +
416A MET* 4.7 1.4 - - - -
418A LEU* 1.3 79.8 - - - +
420A PRO* 1.4 65.5 - - - +
421A GLY 3.6 1.6 - - - -
422A TYR* 3.3 22.2 + - + +
424A GLY 4.1 5.2 - - - +
426A CYS* 2.1 60.6 - - + -
429A MET* 4.1 21.5 - - - -
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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