Contacts of the helix formed by residues 548 - 579 (chain E) in PDB entry 2SIV
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 ILE 548 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ILE* 3.6 29.6 - - + -
549A VAL* 3.9 18.6 - - + -
552A GLN* 3.7 21.1 - - + +
548C ILE* 3.5 28.3 - - + -
545E ACE 4.2 12.3 - - + +
547E GLY* 1.3 86.7 - - - +
549E VAL* 1.3 59.0 + - - +
550E GLN 3.3 1.8 - - - -
551E GLN* 3.4 4.4 + - - +
552E GLN* 2.8 27.5 + - - +
656F ASN* 3.3 26.7 - - + +
660F LEU* 4.8 9.9 - - + -
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Residues in contact with VAL 549 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ILE* 3.3 13.5 - - + -
653D GLN* 2.6 41.3 + - - +
656D ASN* 3.9 26.9 - - + +
657D MET* 3.7 26.5 - - + +
660D LEU* 3.1 37.7 - - + -
546E ALA* 3.6 12.8 - - - +
547E GLY 3.5 1.0 - - - +
548E ILE* 1.3 76.2 - - - +
550E GLN* 1.3 62.8 + - - +
552E GLN* 3.4 5.8 + - - +
553E GLN 3.2 6.2 + - - -
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Residues in contact with GLN 550 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657D MET* 4.5 13.7 - - + -
546E ALA 5.4 1.1 - - - -
547E GLY* 4.4 6.0 + - - +
548E ILE 3.3 0.4 - - - +
549E VAL* 1.3 77.2 - - - +
551E GLN* 1.3 62.9 + - - +
553E GLN* 2.7 28.7 + - - +
554E GLN* 2.9 37.3 + - - +
652F GLN* 3.7 27.0 + - - +
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Residues in contact with GLN 551 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A GLN* 3.0 24.6 + - + +
556A LEU* 4.0 6.1 - - - +
547E GLY 3.8 7.1 + - - +
548E ILE 3.6 6.9 - - - +
549E VAL 3.3 0.4 - - - -
550E GLN* 1.3 80.3 - - - +
552E GLN* 1.3 57.2 + - - +
554E GLN* 2.8 30.4 + - - +
555E LEU* 3.0 37.8 + - - +
649F ALA* 2.9 27.2 + - - +
652F GLN* 3.4 17.4 - - + +
653F GLN* 2.6 30.7 - - - +
656F ASN* 4.0 7.6 - - - +
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Residues in contact with GLN 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A GLN* 3.1 30.8 + - - +
548C ILE* 2.8 42.6 + - - +
551C GLN* 2.8 32.1 + - + +
552C GLN* 3.6 7.7 - - - +
555C LEU* 4.0 19.6 - - + +
653D GLN* 3.9 7.7 - - - +
656D ASN* 3.9 9.5 + - - -
548E ILE 2.8 18.7 + - - +
549E VAL* 3.6 7.3 - - - +
550E GLN 3.0 0.4 - - - -
551E GLN* 1.3 75.7 - - - +
553E GLN* 1.3 57.9 - - - +
555E LEU* 4.5 0.4 - - - -
556E LEU* 3.2 27.5 + - - +
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Residues in contact with GLN 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D GLN* 3.3 26.5 + - - +
653D GLN* 3.1 42.8 + - - +
657D MET* 5.6 4.0 - - + -
549E VAL 3.2 4.2 + - - +
550E GLN* 2.7 16.1 + - - +
552E GLN* 1.3 76.1 - - - +
554E GLN* 1.3 57.9 + - + +
556E LEU* 3.0 9.2 - - - +
557E ASP* 2.6 65.2 + - - +
560E LYS* 4.3 1.4 - - - +
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Residues in contact with GLN 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550E GLN* 2.9 34.8 + - - +
551E GLN* 2.8 35.6 + - - +
553E GLN* 1.3 79.1 - - + +
555E LEU* 1.3 57.8 + - - +
557E ASP* 3.2 12.4 + - - +
558E VAL* 2.9 32.7 + - + +
645F LEU* 5.5 3.5 - - + +
648F GLU* 4.3 17.5 + - + +
649F ALA* 3.6 17.0 - - + +
652F GLN* 3.2 19.5 + - - +
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Residues in contact with LEU 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A GLN* 3.3 45.1 - - - +
555A LEU* 4.3 11.7 - - + -
556A LEU* 3.5 42.4 - - + +
559A VAL* 4.2 13.0 - - + -
555C LEU* 4.4 15.5 - - + -
551E GLN* 3.0 23.5 + - - +
552E GLN* 4.0 4.9 - - - +
554E GLN* 1.3 76.2 - - - +
556E LEU* 1.3 62.0 + - - +
558E VAL* 3.4 6.3 + - + +
559E VAL* 3.1 31.4 + - + +
649F ALA* 4.5 5.8 - - + -
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Residues in contact with LEU 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C GLN* 4.3 4.9 - - - +
555C LEU* 3.7 20.2 - - + +
558C VAL* 5.6 0.2 - - + -
646D LEU* 3.9 22.0 - - + +
649D ALA* 3.7 39.9 - - + +
650D GLN* 3.3 28.7 - - - +
653D GLN* 4.2 12.1 - - + -
552E GLN 3.2 16.3 + - - +
553E GLN* 3.0 20.6 + - - +
555E LEU* 1.3 77.6 - - - +
557E ASP* 1.3 60.3 + - - +
559E VAL* 3.4 5.1 + - - +
560E LYS* 3.1 30.4 + - - +
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Residues in contact with ASP 557 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553E GLN* 2.6 51.5 + - - +
554E GLN* 3.5 10.8 - - - +
556E LEU* 1.3 76.4 - - - +
558E VAL* 1.3 58.1 + - - +
560E LYS* 3.4 19.0 + - - +
561E ARG* 3.0 32.3 + - + +
645F LEU* 4.6 11.2 - - + -
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Residues in contact with VAL 558 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A VAL* 4.1 11.4 - - + -
554E GLN* 2.9 19.8 + - + +
555E LEU* 3.6 9.6 - - + +
556E LEU 3.2 0.2 - - - -
557E ASP* 1.3 73.4 - - - +
559E VAL* 1.3 56.6 + - - +
560E LYS 3.0 1.6 - - - -
561E ARG* 3.0 4.4 + - - +
562E GLN* 2.8 60.1 + - + +
642F ILE* 4.5 4.7 - - + +
645F LEU* 3.6 39.0 - - + +
646F LEU* 3.9 28.3 - - + -
649F ALA* 5.2 4.3 - - + -
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Residues in contact with VAL 559 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A VAL* 3.9 24.2 - - + -
562A GLN* 5.8 0.2 - - - +
555C LEU* 5.0 4.7 - - + -
558C VAL* 4.2 20.2 - - + -
559C VAL* 3.9 16.8 - - + -
562C GLN* 3.2 21.4 + - + +
642D ILE* 5.2 0.7 - - + -
646D LEU* 4.0 21.3 - - + -
555E LEU* 3.1 19.0 + - + +
556E LEU* 3.8 5.6 - - - +
558E VAL* 1.3 75.7 - - - +
560E LYS* 1.3 56.9 + - - +
562E GLN* 3.7 9.0 - - - +
563E GLN* 2.9 26.5 + - - +
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Residues in contact with LYS 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646D LEU* 4.0 32.3 - - + +
650D GLN* 3.7 23.1 + - - +
553E GLN* 4.3 1.4 - - - +
556E LEU* 3.1 19.4 + - - +
557E ASP* 3.4 32.5 + - - +
558E VAL 3.0 0.4 - - - -
559E VAL* 1.3 75.2 - - - +
561E ARG* 1.3 65.6 + - + +
563E GLN* 3.3 3.9 + - + +
564E GLU* 3.1 39.8 + - - +
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Residues in contact with ARG 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557E ASP* 3.0 18.9 + - + +
558E VAL 3.5 4.9 - - - +
560E LYS* 1.3 77.0 - - - +
562E GLN* 1.3 63.5 + - - +
564E GLU* 3.2 30.0 + - - +
565E LEU* 3.0 23.0 + - - +
637F PHE* 4.2 13.1 - - - -
638F LEU* 3.7 19.4 - - + +
641F ASN* 3.6 28.2 - - - +
642F ILE* 3.4 23.0 - - + +
645F LEU* 3.7 18.6 - - + -
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Residues in contact with GLN 562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A VAL* 3.1 36.5 + - - +
562A GLN* 4.2 9.1 - - - +
563A GLN* 2.9 35.9 + - - +
566A LEU* 4.0 10.4 - - + +
562C GLN* 3.4 18.9 + - - +
558E VAL* 2.8 34.8 + - - +
559E VAL* 3.7 8.8 - - - +
561E ARG* 1.3 75.4 - - - +
563E GLN* 1.3 54.4 + - - +
565E LEU* 3.2 3.6 + - - +
566E LEU* 2.7 36.8 + - - +
642F ILE* 3.9 17.2 - - + +
646F LEU* 5.3 0.2 - - - +
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Residues in contact with GLN 563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C GLN* 2.6 33.3 + - - +
565C LEU* 3.8 18.2 - - - +
639D GLU* 3.2 30.0 - - - +
642D ILE* 3.6 22.9 - - + +
643D THR* 3.7 6.5 + - + +
646D LEU* 4.5 6.3 - - + -
559E VAL 2.9 18.8 + - - +
560E LYS* 3.3 8.9 + - + +
562E GLN* 1.3 76.5 - - - +
564E GLU* 1.3 59.5 + - + +
566E LEU* 3.2 2.8 + - - +
567E ARG* 2.8 58.2 + - - +
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Residues in contact with GLU 564 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560E LYS* 3.1 32.1 + - - +
561E ARG* 3.4 39.2 + - - +
562E GLN 3.2 0.2 - - - -
563E GLN* 1.3 78.3 - - + +
565E LEU* 1.3 61.9 + - - +
567E ARG* 3.3 14.4 + - - +
568E LEU* 3.1 26.4 + - + +
638F LEU* 3.6 21.4 - - + +
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Residues in contact with LEU 565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A GLN* 3.8 18.4 - - - +
566A LEU* 3.3 33.4 - - + -
567A ARG* 6.3 0.2 - - - -
570A VAL* 4.3 12.8 - - + -
561E ARG 3.0 12.8 + - - +
562E GLN 3.6 5.6 - - - +
564E GLU* 1.3 75.8 - - - +
566E LEU* 1.3 57.2 + - - +
568E LEU* 3.1 5.2 + - - +
569E THR* 2.9 32.5 + - - +
635F VAL* 3.7 45.3 - - + +
638F LEU* 3.6 16.3 - - + +
639F GLU* 4.4 9.0 - - + +
642F ILE* 3.8 9.6 - - + -
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Residues in contact with LEU 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LEU* 4.3 23.8 - - + -
562C GLN* 3.6 35.7 - - + +
565C LEU* 3.4 37.0 - - + +
566C LEU* 4.4 9.9 - - + +
569C THR* 3.7 28.0 - - + +
562E GLN 2.7 19.9 + - - +
563E GLN* 3.2 8.3 + - - +
565E LEU* 1.3 74.0 - - - +
567E ARG* 1.3 56.9 + - - +
569E THR* 3.1 4.5 + - - -
570E VAL* 2.9 34.2 + - + +
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Residues in contact with ARG 567 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C LEU* 5.7 0.4 - - + +
639D GLU* 3.7 52.2 + - + +
640D GLU* 4.3 4.2 - - - +
643D THR* 3.4 23.6 + - - +
563E GLN* 2.8 46.8 + - - +
564E GLU* 3.6 13.0 - - - +
566E LEU* 1.3 73.9 - - - +
568E LEU* 1.3 63.8 + - + +
570E VAL* 3.4 2.6 + - - +
571E TRP* 3.1 21.8 + - - +
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Residues in contact with LEU 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E GLU* 3.1 12.6 + - + +
565E LEU* 3.1 7.9 + - - +
567E ARG* 1.3 76.0 - - + +
569E THR* 1.3 65.4 + - - +
571E TRP* 3.2 8.6 + - + +
572E GLY 3.1 10.9 + - - -
631F TRP* 2.7 35.6 + - + +
634F LYS* 4.1 31.9 - - + +
635F VAL* 3.9 23.6 - - + -
638F LEU* 3.4 32.8 - - + -
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Residues in contact with THR 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LEU* 4.2 5.0 - - + +
569A THR* 3.6 33.0 - - + +
570A VAL* 3.3 24.4 - - + +
573A THR* 3.7 15.1 + - - +
569C THR* 3.6 12.8 - - + -
565E LEU* 2.9 17.0 + - - +
566E LEU* 3.4 12.8 - - + -
568E LEU* 1.3 77.5 - - - +
570E VAL* 1.3 55.7 + - - +
572E GLY* 3.1 4.7 + - - -
573E THR* 3.0 27.6 + - - -
631F TRP* 4.4 9.6 - - - +
635F VAL* 5.0 1.4 - - - +
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Residues in contact with VAL 570 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C LEU* 4.3 14.4 - - + -
569C THR* 3.5 26.7 - - + +
631D TRP* 4.5 5.4 - - + -
635D VAL* 4.2 12.8 - - + -
639D GLU* 3.4 26.9 - - - +
566E LEU* 2.9 19.8 + - + +
567E ARG 3.7 2.0 - - - +
569E THR* 1.3 73.9 - - - +
571E TRP* 1.3 60.6 + - - +
573E THR* 3.1 9.0 + - - -
574E LYS* 2.9 53.4 + - + +
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Residues in contact with TRP 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E ARG 3.1 13.5 + - - +
568E LEU* 3.2 13.0 + - + +
570E VAL* 1.3 76.3 - - - +
572E GLY* 1.3 76.7 + - - +
574E LYS* 3.4 12.1 + - + +
575E ASN* 2.9 45.0 + - + +
627F ACE 4.2 10.1 - - + -
628F TRP* 3.7 57.9 - + - -
631F TRP* 3.3 32.8 - + + -
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Residues in contact with GLY 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A THR* 4.3 5.6 - - - -
568E LEU 3.1 5.9 + - - -
569E THR 3.1 7.8 + - - -
571E TRP* 1.3 85.7 - - - +
573E THR* 1.3 56.9 + - - +
575E ASN 3.4 0.2 + - - -
576E LEU* 2.9 39.2 + - - +
628F TRP* 3.4 26.0 - - - -
631F TRP* 4.5 0.9 - - - -
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Residues in contact with THR 573 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A THR* 4.3 6.3 + - - +
569C THR* 3.7 16.7 - - - +
572C GLY* 4.1 12.6 - - - -
573C THR* 4.2 7.2 + - - +
576C LEU* 3.5 14.7 - - + +
628D TRP* 3.9 15.5 - - + -
631D TRP* 3.6 29.2 - - + -
569E THR 3.0 13.2 + - - -
570E VAL* 3.1 9.6 + - - -
572E GLY* 1.3 75.9 - - - +
574E LYS* 1.3 63.1 + - - +
576E LEU* 4.6 3.1 - - - -
577E GLN* 3.0 23.1 + - - +
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Residues in contact with LYS 574 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D TRP* 3.6 19.1 - - + -
632D GLU* 3.4 30.4 + - - +
635D VAL* 3.7 15.0 - - - -
636D ASP* 2.7 27.1 + - - -
639D GLU* 5.5 1.8 + - - -
570E VAL* 2.9 40.8 + - + +
571E TRP* 3.7 9.4 - - + +
573E THR* 1.3 73.2 - - - +
575E ASN* 1.3 66.4 + - - +
577E GLN* 3.2 8.9 + - - +
578E THR* 3.0 27.5 + - - -
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Residues in contact with ASN 575 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E TRP* 2.9 40.5 + - + +
572E GLY* 3.6 4.5 - - - +
574E LYS* 1.3 77.5 - - - +
576E LEU* 1.3 61.9 + - - +
578E THR* 3.4 8.7 + - - -
579E ARG* 3.0 41.6 + - - +
628F TRP* 2.6 38.5 + - + +
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Residues in contact with LEU 576 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A THR* 3.8 31.4 - - + +
576A LEU* 3.9 18.2 - - + -
577A GLN* 3.4 37.9 - - - +
580A VAL* 4.4 17.3 - - + -
576C LEU* 3.6 24.2 - - + -
572E GLY 2.9 27.0 + - - +
573E THR* 4.6 1.6 - - - -
575E ASN* 1.3 73.4 - - - +
577E GLN* 1.3 61.9 + - - +
579E ARG* 3.0 10.7 + - - +
580E VAL* 2.8 32.1 + - - +
628F TRP* 3.5 10.1 - - + -
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Residues in contact with GLN 577 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C LEU* 3.6 8.1 - - + +
579C ARG* 2.9 25.3 + - - +
628D TRP* 3.3 56.4 - - + +
573E THR 3.0 18.1 + - - +
574E LYS* 3.2 9.0 - - - +
576E LEU* 1.3 80.2 - - - +
578E THR* 1.3 65.6 + - - +
580E VAL* 3.2 1.6 + - - +
581E THR* 3.0 43.1 + - - +
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Residues in contact with THR 578 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574E LYS 3.0 14.4 + - - -
575E ASN* 3.7 9.7 - - - -
577E GLN* 1.3 79.7 - - - +
579E ARG* 1.3 58.2 + - - +
581E THR* 3.8 5.5 + - - -
582E NH2 3.0 21.7 + - - -
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Residues in contact with ARG 579 (chain E).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A VAL* 3.9 27.1 + - + +
581A THR* 3.4 26.9 - - - +
575E ASN* 3.0 33.7 + - - +
576E LEU* 3.0 12.9 + - - +
578E THR* 1.3 79.2 - - + +
580E VAL* 1.3 65.5 + - - +
582E NH2 3.8 4.7 + - - -
628F TRP* 3.9 19.7 - - - +
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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