Contacts of the helix formed by residues 414 - 447 (chain P) in PDB entry 6LTJ
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 GLN 414 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905N HIS* 4.8 5.8 - - + -
411P THR 3.3 22.4 - - - +
412P ALA* 2.7 26.4 + - - +
413P SER* 1.3 73.8 - - - +
415P GLN* 1.3 75.4 + - - +
416P GLU* 3.1 7.0 - - - -
417P ILE* 2.7 39.4 + - + +
418P ALA* 3.1 13.7 + - - +
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Residues in contact with GLN 415 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412P ALA 4.7 5.5 + - - +
413P SER* 6.1 0.2 - - - -
414P GLN* 1.3 93.5 - - - +
416P GLU* 1.3 60.1 + - - +
418P ALA* 3.1 10.9 + - + +
419P THR* 2.9 33.9 + - + +
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Residues in contact with GLU 416 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901N ILE* 3.6 32.3 - - + +
904N ARG* 5.3 4.9 + - - +
413P SER* 2.9 29.8 - - - +
414P GLN* 3.4 4.0 + - - -
415P GLN* 1.3 83.3 + - - +
417P ILE* 1.3 58.0 + - - +
419P THR* 2.5 25.7 + - - +
420P LEU* 2.9 19.9 + - + +
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Residues in contact with ILE 417 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898N LYS* 3.6 46.9 - - + +
901N ILE* 3.6 46.2 - - + -
902N LYS* 4.6 15.9 - - + +
905N HIS* 5.4 2.0 - - + -
414P GLN* 2.7 32.2 + - + +
416P GLU* 1.3 70.1 - - - +
418P ALA* 1.3 57.8 + - - +
420P LEU* 3.7 3.3 - - + +
421P ASP* 2.9 36.4 + - - +
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Residues in contact with ALA 418 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414P GLN* 3.1 13.1 + - - +
415P GLN* 3.1 17.9 + - + +
417P ILE* 1.3 77.0 - - - +
419P THR* 1.3 57.1 + - + +
421P ASP* 2.7 31.3 - - - +
422P ASN* 2.9 19.2 + - - +
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Residues in contact with THR 419 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415P GLN* 2.9 20.6 + - + +
416P GLU* 2.5 28.1 + - - +
418P ALA* 1.3 76.9 - - + +
420P LEU* 1.3 67.2 + - - +
422P ASN* 2.7 32.3 - - - +
423P LYS* 2.9 9.3 + - - +
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Residues in contact with LEU 420 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894N THR* 3.6 25.8 - - + +
897N LYS* 3.8 22.9 - - + -
898N LYS* 3.4 42.8 - - + +
901N ILE* 4.1 17.3 - - + -
416P GLU* 2.9 14.6 + - + +
417P ILE* 3.7 6.5 - - + +
418P ALA 3.3 0.2 - - - -
419P THR* 1.3 87.2 + - - +
421P ASP* 1.3 58.2 + - - +
423P LYS* 3.2 17.8 - - + +
424P ILE* 2.9 24.0 + - - +
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Residues in contact with ASP 421 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898N LYS* 3.8 23.8 + - - +
131P LYS* 5.3 2.7 - - + -
417P ILE* 2.9 27.0 + - - +
418P ALA* 2.7 17.1 - - - +
420P LEU* 1.3 74.1 - - - +
422P ASN* 1.3 83.0 + - - +
424P ILE* 3.2 10.9 + - + +
425P HIS* 2.9 46.7 + - + +
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Residues in contact with ASN 422 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418P ALA* 2.9 17.3 + - - +
419P THR* 2.7 23.5 - - - +
421P ASP* 1.3 82.4 + - - +
423P LYS* 1.3 80.8 + - - +
425P HIS* 3.3 9.2 + - - +
426P GLU* 2.9 30.4 + - - +
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Residues in contact with LYS 423 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890N LEU* 4.5 19.5 - - + +
893N GLU* 5.9 1.0 + - - -
894N THR* 4.2 26.6 + - + +
897N LYS* 5.8 4.0 - - - +
419P THR 2.9 9.3 + - - +
420P LEU* 3.2 20.0 - - + +
422P ASN* 1.3 87.5 + - - +
424P ILE* 1.3 56.2 + - - +
426P GLU* 3.4 15.9 + - - +
427P THR* 2.9 38.2 + - - +
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Residues in contact with ILE 424 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890N LEU* 6.3 0.4 - - - -
891N LEU* 3.9 22.2 - - + +
894N THR* 3.7 25.6 - - + +
895N GLN* 3.1 36.6 - - + +
898N LYS* 4.8 8.3 - - + +
131P LYS* 4.7 7.9 - - + -
147P TYR* 3.7 22.2 - - + +
420P LEU 2.9 14.5 + - - +
421P ASP* 3.5 14.8 - - - +
422P ASN 3.2 0.4 - - - -
423P LYS* 1.3 76.1 - - - +
425P HIS* 1.3 67.9 + - + +
427P THR* 3.3 1.8 + - - -
428P ILE* 2.9 35.6 + - + +
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Residues in contact with HIS 425 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LYS* 4.2 26.0 - - + +
127P LYS 4.8 1.1 - - - -
130P ASP* 3.8 29.0 + - + +
131P LYS* 3.3 38.6 - - + +
421P ASP* 2.9 39.3 + - - +
422P ASN* 3.7 8.9 - - - +
423P LYS 3.3 0.2 - - - -
424P ILE* 1.3 78.7 - - + +
426P GLU* 1.3 62.8 + - - +
428P ILE* 3.2 2.1 + - - +
429P GLU* 3.0 34.2 + - + +
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Residues in contact with GLU 426 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422P ASN* 2.9 15.7 + - - +
423P LYS* 3.6 17.6 - - - +
425P HIS* 1.3 75.1 - - - +
427P THR* 1.3 69.0 + - - +
429P GLU* 3.2 13.6 + - - +
430P THR* 3.0 33.6 + - + +
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Residues in contact with THR 427 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887N LEU* 3.8 32.8 - - + +
890N LEU* 3.3 20.8 - - + +
891N LEU* 3.6 30.7 - - + -
423P LYS* 2.9 21.4 + - - +
424P ILE* 3.7 4.0 - - - -
426P GLU* 1.3 82.2 - - - +
428P ILE* 1.3 58.0 + - - +
430P THR* 2.6 22.4 + - - -
431P ILE* 2.9 14.8 + - + +
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Residues in contact with ILE 428 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891N LEU* 3.6 21.1 - - + -
130P ASP* 4.2 13.5 - - - +
131P LYS* 3.4 37.7 - - - +
132P ILE 4.0 13.0 - - - +
133P LEU* 3.7 20.6 - - + -
134P PRO* 5.2 0.4 - - + -
147P TYR* 3.7 10.3 - - - +
424P ILE* 2.9 20.8 + - + +
425P HIS 3.9 3.1 - - - +
427P THR* 1.3 73.2 - - - +
429P GLU* 1.3 62.1 + - + +
431P ILE* 3.6 6.4 - - - +
432P ASN* 2.9 46.2 + - - +
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Residues in contact with GLU 429 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ASP* 6.1 0.7 - - - -
425P HIS* 3.0 22.5 + - + +
426P GLU* 3.6 11.7 - - - +
428P ILE* 1.3 78.2 - - + +
430P THR* 1.3 61.0 + - + +
432P ASN* 3.1 11.8 + - - +
433P GLN* 3.0 35.8 + - - +
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Residues in contact with THR 430 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887N LEU* 3.8 19.4 - - - +
426P GLU* 3.0 24.1 + - + +
427P THR* 2.6 26.4 + - - -
429P GLU* 1.3 77.0 - - + +
431P ILE* 1.3 55.5 + - - +
433P GLN* 3.4 20.7 + - - +
434P LEU* 2.9 37.7 + - - +
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Residues in contact with ILE 431 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884N ILE* 4.5 6.7 - - + +
887N LEU* 3.6 36.1 - - + -
888N VAL* 4.0 15.9 - - + -
891N LEU* 3.5 31.9 - - + -
133P LEU* 4.5 9.0 - - + -
134P PRO* 4.9 0.4 - - + -
137P ILE* 3.7 34.4 - - + +
427P THR* 2.9 20.0 + - + +
428P ILE* 3.6 6.3 - - - +
429P GLU 3.2 0.2 - - - -
430P THR* 1.3 73.2 - - - +
432P ASN* 1.3 64.3 + - - +
434P LEU* 3.7 3.5 - - - +
435P LYS* 2.8 27.2 + - - +
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Residues in contact with ASN 432 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P PRO* 3.2 38.4 - - - +
428P ILE* 2.9 31.4 + - - +
429P GLU* 3.1 12.1 + - - +
431P ILE* 1.3 73.2 - - - +
433P GLN* 1.3 67.4 + - + +
435P LYS* 3.2 9.3 + - - +
436P THR* 3.0 31.3 + - + +
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Residues in contact with GLN 433 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429P GLU* 3.0 25.1 + - - +
430P THR* 3.6 21.3 - - - +
432P ASN* 1.3 75.9 - - + +
434P LEU* 1.3 66.5 + - + +
436P THR* 2.9 25.3 + - - -
437P GLN* 3.0 24.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 434 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880N GLU* 4.2 14.4 - - + +
883N LYS* 3.5 45.5 - - + +
884N ILE* 3.6 19.3 - - + +
887N LEU* 3.8 19.7 - - + -
430P THR* 2.9 20.3 + - - +
431P ILE* 4.0 1.1 - - - +
433P GLN* 1.3 80.4 - - + +
435P LYS* 1.3 57.0 + - - +
437P GLN* 3.7 25.2 - - - +
438P ARG* 2.9 30.5 + - - +
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Residues in contact with LYS 435 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1963L ASP 4.2 12.7 + - - -
1964L GLU* 3.3 26.1 + - - +
884N ILE* 3.7 8.7 - - - +
134P PRO* 3.6 25.6 - - + -
136P ARG* 3.7 17.9 - - + -
137P ILE* 3.6 31.2 - - + -
140P LEU* 5.2 1.1 - - + -
431P ILE 2.8 18.5 + - - +
432P ASN* 3.5 13.7 - - - +
434P LEU* 1.3 77.0 - - - +
436P THR* 1.3 68.0 + - - +
438P ARG* 3.1 4.0 + - - +
439P GLU* 2.5 55.1 + - - +
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Residues in contact with THR 436 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964L GLU* 3.2 31.6 - - - +
1966L PRO* 4.0 18.7 - - - +
432P ASN* 3.0 16.9 + - + +
433P GLN* 2.9 17.4 + - - -
435P LYS* 1.3 82.6 - - - +
437P GLN* 1.3 61.0 + - - +
439P GLU* 3.4 7.0 + - - -
440P PHE* 2.9 28.5 + - - +
198Q ARG* 4.3 22.7 - - - +
202Q LEU* 5.1 1.7 - - - +
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Residues in contact with GLN 437 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880N GLU* 4.0 20.5 - - + +
883N LYS* 5.5 1.2 + - - -
433P GLN* 3.0 26.6 + - - +
434P LEU* 3.7 24.9 - - - +
436P THR* 1.3 85.5 + - - +
438P ARG* 1.3 62.2 + - - +
440P PHE* 3.2 8.3 + - - +
441P MET* 3.0 30.3 + - + +
198Q ARG* 5.8 0.9 - - - -
201Q ARG* 4.2 20.6 - - - +
202Q LEU* 3.7 28.7 - - + +
205Q GLU* 4.5 7.1 - - - +
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Residues in contact with ARG 438 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877N ALA* 3.8 22.4 + - + +
880N GLU* 4.1 15.2 + - + -
881N GLU* 3.4 43.7 + - + +
884N ILE* 4.6 4.7 - - + -
136P ARG* 5.9 2.0 - - - +
140P LEU* 3.6 40.3 - - - +
434P LEU 2.9 18.7 + - - +
435P LYS* 3.1 8.3 + - - +
437P GLN* 1.3 76.6 - - - +
439P GLU* 1.3 65.6 + - - +
441P MET* 3.2 3.9 + - - +
442P LEU* 2.9 63.1 + - - +
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Residues in contact with GLU 439 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1963L ASP 5.7 1.1 - - - -
1964L GLU 5.0 3.1 - - - +
1965L THR* 6.4 0.2 - - - -
1966L PRO* 4.2 16.8 - - + +
136P ARG* 3.5 41.6 + - - +
140P LEU* 4.4 9.9 - - - +
435P LYS* 2.5 61.8 + - - +
436P THR* 3.7 6.6 - - - +
438P ARG* 1.3 82.3 + - - +
440P PHE* 1.3 56.9 + - - +
442P LEU* 4.0 8.2 - - + +
443P SER* 2.6 36.6 + - - -
446P ARG* 5.0 1.7 + - - +
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Residues in contact with PHE 440 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966L PRO* 3.9 15.8 - - + +
1967L LEU* 4.2 2.2 - - + -
436P THR 2.9 14.4 + - - +
437P GLN 3.2 9.9 - - - +
439P GLU* 1.3 75.0 - - - +
441P MET* 1.3 64.0 + - + +
443P SER* 2.4 21.1 + - - -
444P PHE* 3.0 9.4 + - - +
451P PHE* 3.4 29.2 - + - -
455P TRP* 3.7 24.0 - + - -
199Q ASN* 3.2 28.7 - - - -
202Q LEU* 3.6 35.7 - - + -
203Q ILE* 4.0 11.2 - - + -
206Q ILE* 3.5 29.2 - - + -
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Residues in contact with MET 441 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873N ALA* 3.4 24.6 - - - +
876N LEU* 3.9 15.7 - - + -
877N ALA* 3.6 12.1 - - + +
880N GLU* 3.5 28.5 - - - +
437P GLN* 3.0 17.8 + - + +
438P ARG 3.8 0.2 - - - +
440P PHE* 1.3 77.2 - - + +
442P LEU* 1.3 58.4 + - - +
444P PHE* 3.4 4.9 + - - +
445P ALA* 2.9 30.4 + - - +
202Q LEU* 4.1 22.4 - - + +
205Q GLU* 4.0 25.1 - - - +
206Q ILE* 3.5 31.0 - - + -
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Residues in contact with LEU 442 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874N LYS* 4.6 21.5 - - + -
877N ALA* 3.9 17.7 - - + -
438P ARG* 2.9 61.1 + - - +
439P GLU* 4.0 8.5 - - + +
441P MET* 1.3 74.1 - - - +
443P SER* 1.3 66.3 + - - +
445P ALA* 3.2 4.2 + - + +
446P ARG* 2.9 51.6 + - + +
----------------------------------------------------------
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Residues in contact with SER 443 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966L PRO* 4.7 4.9 - - - +
1967L LEU* 5.9 0.4 - - - -
439P GLU 2.6 16.6 + - - -
440P PHE* 2.4 26.3 + - - -
442P LEU* 1.3 73.9 - - - +
444P PHE* 1.3 61.6 + - - +
446P ARG* 3.5 30.1 + - - +
447P ASP* 3.8 4.2 + - - +
451P PHE* 3.2 35.2 - - - +
----------------------------------------------------------
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Residues in contact with PHE 444 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866N LEU* 5.4 1.6 - - + -
869N ALA* 3.4 42.8 - - + -
870N ALA* 3.6 2.5 - - - -
873N ALA* 3.6 13.9 - - + -
677O VAL* 6.0 0.9 - - + -
440P PHE 3.0 14.4 + - - +
441P MET 3.5 7.6 - - - +
443P SER* 1.3 79.3 + - - +
445P ALA* 1.3 65.2 + - - +
446P ARG 3.0 1.9 + - - -
447P ASP 3.1 0.2 - - - -
448P PRO* 3.0 52.0 - - + +
451P PHE* 3.3 35.6 - + + -
452P ILE* 4.2 18.2 - - + -
203Q ILE* 4.0 15.9 - - + -
206Q ILE* 3.9 23.6 - - + -
207Q LEU* 5.3 4.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 445 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870N ALA* 3.3 40.7 - - - +
873N ALA* 4.2 0.7 - - + -
874N LYS* 3.9 23.3 - - + +
693O ALA* 5.3 0.9 - - - +
697O LEU* 4.2 18.3 - - + +
441P MET 2.9 19.9 + - - +
442P LEU* 3.9 5.8 - - + +
444P PHE* 1.3 73.2 - - - +
446P ARG* 1.3 64.7 + - - +
448P PRO* 4.4 1.8 - - - +
----------------------------------------------------------
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Residues in contact with ARG 446 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693O ALA* 4.8 7.6 - - - +
136P ARG* 5.4 7.3 - - - +
439P GLU* 5.0 1.6 + - - +
442P LEU* 2.9 37.7 + - + +
443P SER* 3.6 32.7 - - - +
444P PHE 3.0 0.2 + - - -
445P ALA* 1.3 81.2 - - - +
447P ASP* 1.3 67.7 + - - +
448P PRO* 4.3 1.4 - - - +
----------------------------------------------------------
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Residues in contact with ASP 447 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690O SER* 5.3 9.9 - - - +
693O ALA* 5.6 0.9 - - - -
443P SER 3.8 4.7 + - - +
444P PHE 3.1 3.1 + - - -
446P ARG* 1.3 85.5 - - - +
448P PRO* 1.3 68.9 - - - +
449P GLN* 3.1 3.3 + - + +
450P GLY* 4.2 18.0 + - - +
451P PHE* 3.0 19.1 + - - +
----------------------------------------------------------
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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