Contacts of the helix formed by residues 422 - 448 (chain I) in PDB entry 1MKD
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 PRO 422 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I TRP* 4.9 2.9 - - + -
200I GLY* 3.8 23.8 - - - +
420I THR 4.7 0.9 - - - +
421I LYS* 1.3 88.5 - - + +
423I LEU* 1.3 65.9 + - - +
424I GLN* 3.2 5.4 - - + +
425I LEU* 2.9 33.4 + - + +
426I TYR 3.1 9.9 + - - -
495I THR* 4.5 8.0 - - + -
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Residues in contact with LEU 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I LYS 3.3 2.9 + - - -
422I PRO* 1.3 72.0 - - - +
424I GLN* 1.3 63.3 + - - +
426I TYR* 4.2 11.7 - - + -
427I ARG* 2.9 54.2 + - + +
495I THR* 5.4 0.4 - - - +
499I ASN* 3.5 30.6 + - + +
502I TRP* 3.6 52.9 - - + +
503I TYR* 4.6 0.9 - - + -
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Residues in contact with GLN 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I HIS* 3.1 35.0 + - - -
205I ARG* 4.5 7.4 + - - +
422I PRO* 3.1 4.9 + - + +
423I LEU* 1.3 77.9 - - - +
425I LEU* 1.3 63.1 + - + +
427I ARG* 4.1 6.8 - - - +
428I GLN* 3.2 37.6 + - + +
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Residues in contact with LEU 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200I GLY* 3.6 26.9 - - - +
201I LEU 3.9 10.5 - - - +
202I HIS* 4.0 28.9 - - + +
203I VAL* 4.7 4.9 - - + +
204I PHE* 3.8 25.8 - - + -
421I LYS* 4.2 13.2 - - + +
422I PRO* 2.9 31.6 + - + +
424I GLN* 1.3 78.2 - - + +
426I TYR* 1.3 67.6 + - - +
428I GLN* 2.9 20.2 + - - +
429I TRP* 3.1 23.7 + - + +
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Residues in contact with TYR 426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418I ASN* 3.5 21.4 + - + +
419I PRO* 3.5 30.0 - - + +
421I LYS* 4.1 3.8 - - - +
422I PRO 3.1 9.1 + - - +
423I LEU* 3.7 9.4 - - + +
425I LEU* 1.3 77.2 - - - +
427I ARG* 1.3 58.5 + - - +
429I TRP* 3.0 9.6 + - - +
430I THR* 2.9 40.7 + - - -
466I GLN* 2.7 29.9 + - - +
470I ILE* 3.4 21.4 - - + +
499I ASN* 3.7 28.7 - - + -
503I TYR* 3.5 27.8 - + - -
3009I ZAR 3.6 14.8 - - - -
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Residues in contact with ARG 427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I LEU* 2.9 47.3 + - + +
424I GLN* 4.1 6.7 - - - +
426I TYR* 1.3 75.4 - - - +
428I GLN* 1.3 58.3 + - + +
430I THR* 3.3 2.4 + - - -
431I ASP* 3.0 36.2 + - - +
502I TRP* 3.2 36.0 - - + -
503I TYR* 3.6 19.8 + - + +
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Residues in contact with GLN 428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I HIS* 3.8 12.1 + - - -
204I PHE* 3.4 38.9 - - + +
424I GLN* 3.2 45.5 + - + +
425I LEU* 2.9 8.5 + - - +
427I ARG* 1.3 77.3 - - + +
429I TRP* 1.3 63.5 + - - +
431I ASP* 3.3 11.2 + - - +
432I ARG* 3.1 29.6 + - - +
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Residues in contact with TRP 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I VAL* 4.0 11.3 - - + +
204I PHE* 3.5 31.8 - + - -
255I ALA 5.6 0.2 - - - -
256I TYR* 3.6 26.0 - + - -
258I ASN* 5.3 0.7 - - - -
260I ILE* 3.8 11.2 - - + -
261I HIS* 3.7 40.6 - - + -
264I ASP* 3.5 30.3 + - + -
418I ASN* 3.5 40.7 - - + +
421I LYS* 5.4 4.3 - - + +
425I LEU* 3.1 33.5 + - + +
426I TYR* 3.0 7.5 + - - +
428I GLN* 1.3 73.9 - - - +
430I THR* 1.3 60.7 + - - +
432I ARG* 3.0 13.8 + - - +
433I ILE* 2.8 27.4 + - - +
3009I ZAR 3.3 8.8 - - - -
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Residues in contact with THR 430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426I TYR* 2.9 36.0 + - - -
427I ARG 3.3 4.5 + - - -
429I TRP* 1.3 75.9 - - - +
431I ASP* 1.3 65.7 + - - +
433I ILE* 3.1 4.2 - - - +
434I MET* 3.1 24.1 + - + +
462I VAL* 3.8 20.6 - - + -
466I GLN* 3.4 28.1 - - + +
503I TYR* 3.2 26.1 + - - +
3009I ZAR 3.3 10.8 - - - -
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Residues in contact with ASP 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427I ARG* 3.0 23.1 + - - +
428I GLN* 3.6 11.4 - - - +
429I TRP 3.1 0.2 - - - -
430I THR* 1.3 80.8 - - - +
432I ARG* 1.3 59.7 + - + +
434I MET* 3.8 4.0 - - - +
435I GLU* 2.9 30.7 + - - +
462I VAL* 5.7 2.9 - - - +
503I TYR* 5.5 0.7 + - - -
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Residues in contact with ARG 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I PHE* 3.0 33.9 - - - -
255I ALA* 2.8 56.9 + - + +
256I TYR* 4.0 7.2 - - + -
258I ASN* 4.0 9.1 - - - +
260I ILE* 3.7 21.0 - - - +
428I GLN* 3.1 19.3 + - - +
429I TRP* 3.0 20.5 + - - +
431I ASP* 1.3 76.3 - - + +
433I ILE* 1.3 64.7 + - - +
435I GLU* 3.1 10.5 + - - +
436I GLU* 2.9 19.8 + - - +
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Residues in contact with ILE 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I TYR* 3.6 37.8 - - + -
257I HIS* 3.8 12.8 - - + -
429I TRP 2.8 13.1 + - - +
430I THR* 3.1 14.4 - - - +
432I ARG* 1.3 73.9 - - - +
434I MET* 1.3 70.9 + - + +
436I GLU* 3.2 3.6 + - + +
437I PHE* 2.9 66.3 + - + -
466I GLN* 4.6 0.9 - - - +
3009I ZAR 3.5 47.3 - - + +
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Residues in contact with MET 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430I THR* 3.1 20.2 + - + +
431I ASP* 3.9 4.5 - - - +
433I ILE* 1.3 86.0 - - + +
435I GLU* 1.3 65.1 + - - +
437I PHE* 3.8 6.9 - - - +
438I PHE* 3.1 64.4 + - + -
454I MET* 3.5 47.8 - - + +
460I ALA* 4.1 6.7 - - + -
462I VAL* 3.8 39.5 - - + +
465I SER* 5.2 0.9 - - - +
466I GLN* 4.8 4.5 - - - -
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Residues in contact with GLU 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I ALA* 3.7 19.6 - - + +
431I ASP 2.9 19.2 + - - +
432I ARG* 3.1 12.1 + - - +
434I MET* 1.3 79.7 - - - +
436I GLU* 1.3 51.1 + - - +
438I PHE* 4.4 6.2 - - - +
439I PRO* 2.6 33.4 - - + +
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Residues in contact with GLU 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I VAL* 3.2 14.4 - - + +
255I ALA* 4.1 9.2 - - + +
256I TYR* 2.8 32.8 + - + +
257I HIS* 2.7 38.3 + - - -
301I HIS* 4.1 0.5 - - - -
303I GLY* 3.2 36.8 - - - +
432I ARG 2.9 14.1 + - - +
433I ILE* 3.7 5.4 - - - +
434I MET 3.1 0.2 - - - -
435I GLU* 1.3 76.7 - - - +
437I PHE* 1.3 69.8 + - + +
438I PHE 3.3 0.4 - - - -
439I PRO* 3.0 14.6 - - - +
440I GLN* 3.5 11.3 + - - +
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Residues in contact with PHE 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257I HIS* 5.2 5.4 - + - -
433I ILE* 2.9 51.5 + - + +
434I MET* 3.3 11.0 + - - +
436I GLU* 1.3 81.5 - - + +
438I PHE* 1.3 56.9 + - - +
440I GLN* 3.1 14.5 + - - +
441I GLY 2.9 22.0 + - - -
454I MET* 3.7 48.9 - - + +
455I CYS* 3.3 32.0 - - - +
3009I ZAR 3.9 31.0 - + - -
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Residues in contact with PHE 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434I MET* 3.1 43.6 + - + +
435I GLU* 4.4 4.5 - - - +
437I PHE* 1.3 76.4 - - - +
439I PRO* 1.3 57.3 - - + +
441I GLY* 2.8 4.0 + - - -
442I ASP* 2.7 40.1 + - - +
454I MET 3.4 19.7 - - - -
455I CYS 3.5 8.8 - - - +
457I LYS* 3.5 49.8 - - + +
460I ALA* 3.6 21.8 - - + -
462I VAL* 4.8 5.6 - - + -
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Residues in contact with PRO 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435I GLU* 2.6 31.4 - - + +
436I GLU* 3.0 12.3 - - - +
438I PHE* 1.3 88.3 - - + +
440I GLN* 1.3 56.0 + - - +
442I ASP* 3.5 14.6 - - + +
443I ARG* 2.8 35.2 + - + +
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Residues in contact with GLN 440 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I GLY 4.0 3.4 - - - +
304I VAL* 3.2 18.9 - - + -
305I SER* 3.0 45.0 + - - -
308I PHE* 3.8 20.8 - - + +
436I GLU 3.5 8.9 + - - +
437I PHE* 3.1 17.1 + - - +
438I PHE 3.1 0.4 - - - -
439I PRO* 1.3 77.6 - - - +
441I GLY* 1.3 54.6 + - - +
443I ARG* 3.0 9.3 + - - +
444I GLU* 2.8 58.0 + - - +
452I SER* 3.8 9.3 + - - -
455I CYS* 4.0 14.6 - - - -
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Residues in contact with GLY 441 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437I PHE 2.9 7.9 + - - -
438I PHE 2.8 3.6 + - - -
440I GLN* 1.3 78.4 - - - +
442I ASP* 1.3 55.9 + - - +
444I GLU* 3.3 14.4 + - - -
445I ARG* 2.9 27.7 + - - +
451I ILE* 3.1 16.9 - - - +
455I CYS* 3.2 25.5 - - - +
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Residues in contact with ASP 442 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438I PHE* 2.7 21.4 + - - +
439I PRO* 3.5 16.8 - - + +
440I GLN 3.1 0.2 - - - -
441I GLY* 1.3 70.9 - - - +
443I ARG* 1.3 66.2 + - - +
445I ARG* 2.8 44.9 + - - +
446I GLU* 2.9 26.1 + - + +
457I LYS* 3.1 36.5 + - - +
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Residues in contact with ARG 443 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I PRO 5.4 3.6 + - - -
304I VAL* 3.7 19.0 - - - +
308I PHE* 3.3 34.5 - - + -
439I PRO* 2.8 25.4 + - + +
440I GLN* 3.2 11.9 - - - +
442I ASP* 1.3 76.2 - - - +
444I GLU* 1.3 56.3 + - - +
446I GLU* 3.3 19.5 + - - +
447I ARG* 3.0 61.4 + - - +
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Residues in contact with GLU 444 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I PHE* 3.6 23.8 - - + +
311I ASN* 5.7 1.6 + - - -
440I GLN* 2.8 35.9 + - - +
441I GLY* 3.5 14.3 - - - +
443I ARG* 1.3 72.5 - - - +
445I ARG* 1.3 61.9 + - - +
447I ARG 3.4 0.5 + - - -
448I GLY 3.0 3.1 + - - -
449I MET* 2.8 55.7 + - + +
450I GLU 4.1 5.8 - - - +
451I ILE* 3.6 9.7 - - + -
452I SER* 2.6 50.7 + - - -
455I CYS* 4.2 0.5 - - - +
----------------------------------------------------------
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Residues in contact with ARG 445 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441I GLY 2.9 15.3 + - - +
442I ASP* 2.8 39.5 + - - +
444I GLU* 1.3 76.8 - - - +
446I GLU* 1.3 63.3 + - + +
448I GLY* 3.1 12.6 + - - -
449I MET 4.6 1.6 - - - -
451I ILE* 3.3 17.3 - - + +
456I ASP* 3.0 28.3 + - - +
457I LYS* 3.8 16.0 - - - +
458I HIS* 3.8 26.1 + - - -
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Residues in contact with GLU 446 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442I ASP* 2.9 28.0 + - - +
443I ARG* 3.3 26.1 + - - +
445I ARG* 1.3 74.9 - - + +
447I ARG* 1.3 71.1 + - - +
448I GLY* 2.9 6.2 + - - -
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Residues in contact with ARG 447 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I PHE* 4.0 8.0 - - + -
312I THR* 4.1 17.8 - - + +
443I ARG* 3.0 64.4 + - - +
444I GLU 3.7 0.9 - - - +
446I GLU* 1.3 82.6 + - - +
448I GLY* 1.3 58.3 + - - +
449I MET* 3.1 38.2 + - + +
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Residues in contact with GLY 448 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444I GLU 3.0 2.8 + - - -
445I ARG 3.1 10.7 + - - -
446I GLU 2.9 6.3 - - - -
447I ARG* 1.3 79.5 - - - +
449I MET* 1.3 63.9 + - - +
450I GLU 4.1 0.2 + - - -
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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