Contacts of the helix formed by residues 3979 - 4001 (chain H) in PDB entry 6X34
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 ARG3979 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3915H VAL* 5.0 10.1 - - + +
3919H LEU* 4.0 33.1 - - + +
3978H SER* 1.3 75.1 - - - +
3980H LEU* 1.3 62.5 + - - +
3981H TRP 3.4 2.2 - - - -
3982H ASP* 3.2 16.9 + - + +
3983H ALA* 3.1 21.5 + - - +
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Residues in contact with LEU3980 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3915H VAL* 4.6 12.2 - - + +
3960H LEU* 4.9 5.8 - - + -
3975H LEU* 3.7 42.6 - - + +
3978H SER* 3.3 7.9 + - - +
3979H ARG* 1.3 77.9 - - - +
3981H TRP* 1.3 60.2 - - - +
3983H ALA* 3.2 16.2 + - - +
3984H VAL* 3.6 15.6 + - - +
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Residues in contact with TRP3981 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3975H LEU 5.0 1.4 + - - -
3976H ALA 5.9 2.5 - - - +
3978H SER 4.7 3.0 + - - +
3979H ARG* 4.4 0.2 - - - +
3980H LEU* 1.3 80.0 - - - +
3982H ASP* 1.3 58.4 + - - +
3984H VAL* 3.2 24.8 - - + +
3985H VAL* 3.4 11.4 + - - +
4038H GLN* 5.6 5.2 - - + +
4042H MET* 5.0 17.8 - - + +
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Residues in contact with ASP3982 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3919H LEU* 5.2 7.3 - - + +
3978H SER 5.5 0.2 + - - -
3979H ARG* 3.2 26.2 + - + +
3980H LEU 3.2 1.0 - - - -
3981H TRP* 1.3 77.9 - - - +
3983H ALA* 1.3 58.1 + - - +
3985H VAL* 3.3 21.7 - - + +
3986H GLY* 3.8 5.4 + - - -
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Residues in contact with ALA3983 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3918H LEU* 4.7 23.8 - - + +
3919H LEU* 5.2 6.5 - - + +
3922H GLN* 5.1 6.7 - - + +
3957H PHE* 5.7 1.8 - - + -
3979H ARG 3.1 10.4 + - - +
3980H LEU* 3.2 12.5 + - - +
3982H ASP* 1.3 77.7 - - - +
3984H VAL* 1.3 62.8 + - + +
3985H VAL 3.3 0.4 - - - -
3986H GLY* 3.4 1.8 + - - -
3987H PHE* 2.9 47.1 + - + -
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Residues in contact with VAL3984 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957H PHE* 4.6 22.7 - - + -
3980H LEU 3.6 11.6 + - - +
3981H TRP* 3.2 24.0 - - + +
3983H ALA* 1.3 75.0 - - + +
3985H VAL* 1.3 57.4 + - + +
3987H PHE* 3.6 6.2 - - + +
3988H LEU* 2.7 46.7 + - + +
4018H MET* 5.1 12.3 - - + +
4022H LEU* 5.7 13.9 - - + -
4042H MET* 5.8 5.6 - - + -
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Residues in contact with VAL3985 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3981H TRP 3.4 14.1 - - - +
3982H ASP* 3.3 22.2 - - + +
3984H VAL* 1.3 82.3 - - + +
3986H GLY* 1.3 61.9 + - - +
3988H LEU* 3.8 5.9 + - - +
3989H HIS* 3.3 22.2 + - - +
4042H MET* 5.4 4.9 - - + +
4045H GLU* 4.8 17.9 - - + +
4046H SER* 4.3 31.2 - - - +
4049H ASN* 4.8 9.0 - - + +
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Residues in contact with GLY3986 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3922H GLN* 5.8 4.7 - - - -
3982H ASP 3.8 5.4 + - - -
3983H ALA* 3.4 5.7 + - - -
3985H VAL* 1.3 81.6 - - - +
3987H PHE* 1.3 68.1 + - - +
3989H HIS* 3.6 6.5 + - - +
3990H VAL* 3.5 25.1 + - - +
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Residues in contact with PHE3987 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3918H LEU* 4.5 9.0 - - + -
3921H LEU* 4.9 7.0 - - + -
3922H GLN* 3.6 39.9 - - + -
3925H ILE* 4.3 23.6 - - + -
3953H ALA* 5.8 1.8 - - + -
3957H PHE* 3.6 39.0 - + - -
3983H ALA* 2.9 32.7 + - + +
3984H VAL* 3.1 8.9 + - + +
3986H GLY* 1.3 74.6 - - - +
3988H LEU* 1.3 62.8 + - + +
3989H HIS 3.1 2.1 + - - -
3990H VAL* 3.2 10.3 + - + +
3991H PHE* 2.9 61.2 + + + -
4014H LEU* 6.3 1.8 - - + -
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Residues in contact with LEU3988 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3984H VAL* 2.7 30.1 + - + +
3985H VAL* 4.3 6.5 - - - +
3987H PHE* 1.3 72.7 - - + +
3989H HIS* 1.3 61.1 + - - +
3991H PHE* 3.8 19.6 - - + +
3992H ALA* 3.2 24.8 + - - +
4015H GLN* 4.8 9.6 - - + -
4046H SER* 5.5 5.4 - - - -
4049H ASN* 4.7 14.1 - - + +
4050H VAL* 4.9 17.5 - - + -
4053H ILE* 5.6 12.3 - - + -
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Residues in contact with HIS3989 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3930H TRP* 4.1 31.0 + + - -
3985H VAL 3.3 18.2 + - - +
3986H GLY* 3.8 7.6 - - - +
3987H PHE 3.1 0.8 - - - -
3988H LEU* 1.3 79.5 - - - +
3990H VAL* 1.3 64.2 + - + +
3992H ALA* 3.7 7.5 + - - +
3993H HIS* 3.5 48.4 + + - -
4049H ASN* 3.2 25.4 + - - +
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Residues in contact with VAL3990 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925H ILE* 5.5 8.5 - - + -
3926H SER* 4.5 19.3 - - - +
3929H TYR* 4.5 16.1 - - + +
3930H TRP* 4.5 15.9 - - + -
3986H GLY 3.5 15.0 + - - +
3987H PHE* 3.2 17.5 - - + +
3989H HIS* 1.3 86.7 - - + +
3991H PHE* 1.3 85.0 + - + +
3992H ALA 3.3 0.2 - - - -
3993H HIS* 3.4 7.0 + - - +
3994H MET* 3.2 32.1 + - + +
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Residues in contact with PHE3991 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925H ILE* 5.5 8.3 - - + -
3946H PHE* 5.4 3.8 - + - -
3987H PHE* 2.9 53.4 + + + +
3988H LEU* 4.1 13.0 - - + +
3990H VAL* 1.3 86.8 - - + +
3992H ALA* 1.3 61.4 + - - +
3993H HIS 3.2 0.2 - - - -
3994H MET* 3.7 21.0 - - + +
3995H MET* 3.2 27.9 + - - +
4011H LEU* 4.1 12.7 - - + +
4014H LEU* 3.7 24.0 - - + -
4015H GLN* 3.1 44.9 - - + +
4053H ILE* 5.7 2.3 - - - +
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Residues in contact with ALA3992 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988H LEU 3.2 18.7 + - - +
3989H HIS* 4.0 6.3 - - - +
3990H VAL 3.3 0.8 - - - -
3991H PHE* 1.3 76.3 - - - +
3993H HIS* 1.3 65.4 + - + +
3995H MET* 5.0 1.5 - - - +
3996H MET* 3.3 27.2 - - - +
4049H ASN* 4.5 8.1 - - + +
4052H MET* 3.8 36.1 - - + +
4053H ILE* 5.0 10.3 - - + +
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Residues in contact with HIS3993 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3930H TRP* 5.7 6.8 + - - -
3933H SER* 6.0 2.2 - - - +
3989H HIS* 3.5 46.1 + + - -
3990H VAL* 3.4 9.9 + - - +
3991H PHE 3.2 0.2 - - - -
3992H ALA* 1.3 89.4 - - + +
3994H MET* 1.3 63.8 + - - +
3995H MET 3.3 1.6 - - - -
3996H MET* 3.5 9.0 + - - +
3997H LYS* 3.4 28.5 + - + +
4052H MET* 5.7 11.0 - - + +
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Residues in contact with MET3994 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925H ILE* 5.3 4.3 - - + +
3928H PHE* 5.6 5.4 - - + -
3929H TYR* 5.4 12.1 - - + -
3946H PHE* 3.5 37.5 - - + -
3990H VAL* 3.2 26.8 + - + +
3991H PHE* 3.7 27.6 - - + +
3993H HIS* 1.3 76.9 - - - +
3995H MET* 1.3 63.0 + - - +
3996H MET 3.2 0.9 - - - -
3997H LYS* 4.3 10.3 - - + +
3998H LEU* 2.9 44.0 + - + +
4007H LEU* 5.8 0.4 - - + -
4011H LEU* 3.7 18.2 - - + -
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Residues in contact with MET3995 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3991H PHE 3.2 18.1 + - - +
3992H ALA* 5.0 2.0 - - - -
3993H HIS 3.3 0.8 - - - -
3994H MET* 1.3 83.6 - - + +
3996H MET* 1.3 61.5 + - + +
3998H LEU* 4.3 3.4 - - - +
3999H ALA* 3.3 24.4 + - - +
4008H LEU* 5.8 3.6 - - - +
4011H LEU* 5.5 8.7 - - + -
4053H ILE* 5.6 4.5 - - + -
4056H PHE* 3.7 28.2 - - + -
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Residues in contact with MET3996 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3992H ALA 3.3 25.4 - - - +
3993H HIS* 3.5 8.0 + - - +
3994H MET 3.2 0.4 - - - -
3995H MET* 1.3 77.1 - - + +
3997H LYS* 1.3 63.7 + - + +
3999H ALA* 3.7 3.3 + - - +
4000H GLN* 3.6 19.1 + - - +
4052H MET* 4.6 27.4 - - + +
4056H PHE* 3.9 33.4 - - + -
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Residues in contact with LYS3997 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3932H TYR 3.4 20.9 - - - -
3933H SER* 3.8 19.6 + - - +
3935H LYS 3.2 19.9 + - - -
3936H ASP* 3.7 18.6 + - - +
3938H ILE* 4.5 15.3 - - + -
3993H HIS* 3.4 18.4 - - + +
3994H MET* 3.2 12.9 + - + +
3996H MET* 1.3 78.3 - - + +
3998H LEU* 1.3 69.0 + - + +
3999H ALA 3.4 0.7 + - - -
4000H GLN* 3.4 16.9 + - - +
4001H ASP* 4.0 1.7 + - - +
4004H GLN* 3.8 9.9 + - - -
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Residues in contact with LEU3998 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3938H ILE* 4.7 14.4 - - + -
3994H MET* 2.9 35.6 + - + +
3995H MET* 4.6 2.7 - - - +
3997H LYS* 1.3 83.4 - - + +
3999H ALA* 1.3 58.7 + - - +
4001H ASP 3.3 19.7 - - - +
4004H GLN* 3.4 52.4 - - + +
4005H ILE* 4.8 2.8 + - - +
4007H LEU* 3.6 39.0 - - + -
4008H LEU* 4.0 19.7 - - + +
4011H LEU* 5.5 2.2 - - + -
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Residues in contact with ALA3999 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995H MET 3.3 20.4 + - - +
3996H MET* 3.7 6.0 + - - +
3997H LYS 3.2 1.0 - - - -
3998H LEU* 1.3 76.4 - - - +
4000H GLN* 1.3 63.7 + - - +
4001H ASP 3.3 3.9 - - - +
4002H SER* 4.9 1.7 + - - -
4005H ILE* 5.6 7.6 - - + -
4008H LEU* 5.6 2.0 - - + -
4056H PHE* 4.6 12.6 - - + -
4060H PHE* 5.1 9.9 - - + -
4127H PHE* 6.0 6.9 - - + -
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Residues in contact with GLN4000 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3996H MET 3.6 11.1 + - - +
3997H LYS* 3.4 11.3 + - - +
3998H LEU 3.4 0.8 - - - -
3999H ALA* 1.3 80.9 - - - +
4001H ASP* 1.3 58.8 + - + +
4002H SER* 3.8 5.2 + - - -
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Residues in contact with ASP4001 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3997H LYS 4.0 2.3 + - - +
3998H LEU 3.3 16.3 + - - +
3999H ALA 3.3 3.0 - - - +
4000H GLN* 1.3 76.7 - - + +
4002H SER* 1.3 63.8 + - - +
4003H SER* 3.3 6.3 + - - +
4004H GLN* 3.5 39.1 + - + +
4005H ILE* 4.1 1.7 + - - +
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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) + - + + + + + -
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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