Contacts of the helix formed by residues 3939 - 3964 (chain D) 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 GLU3939 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3846D ASN* 5.8 2.7 - - - +
3932D TYR* 3.6 28.9 - - + +
3937D VAL* 4.2 1.6 + - - +
3938D ILE* 1.3 83.9 - - - +
3940D GLU* 1.3 64.6 + - - +
3941D GLN* 4.3 4.9 - - + +
3942D GLY* 3.4 9.0 + - - +
3943D LYS* 3.3 17.5 + - - +
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Residues in contact with GLU3940 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938D ILE 3.7 2.2 + - - -
3939D GLU* 1.3 71.7 - - - +
3941D GLN* 1.3 70.4 + - + +
3943D LYS* 3.3 15.6 + - - +
3944D ARG* 3.5 11.1 + - - +
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Residues in contact with GLN3941 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842D PHE* 4.5 2.2 - - + -
3846D ASN* 3.9 27.1 - - - +
3939D GLU* 3.3 4.4 - - + +
3940D GLU* 1.3 81.0 - - + +
3942D GLY* 1.3 62.2 + - - +
3944D ARG* 3.4 37.8 + - - +
3945D ASN* 3.1 20.8 + - - +
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Residues in contact with GLY3942 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842D PHE* 3.8 24.1 - - - -
3928D PHE* 3.5 19.9 - - - -
3932D TYR* 4.6 5.8 - - - -
3938D ILE* 5.4 1.1 - - - -
3939D GLU* 3.4 10.7 + - - +
3940D GLU 3.3 0.2 - - - -
3941D GLN* 1.3 76.4 - - - +
3943D LYS* 1.3 60.6 + - - +
3945D ASN* 3.6 0.9 + - - +
3946D PHE* 3.1 29.5 + - - +
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Residues in contact with LYS3943 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938D ILE* 4.9 6.0 - - + +
3939D GLU 3.3 12.8 + - - +
3940D GLU* 3.6 12.1 - - - +
3941D GLN 3.2 0.6 - - - -
3942D GLY* 1.3 76.0 - - - +
3944D ARG* 1.3 58.3 + - - +
3946D PHE* 4.0 2.0 - - - +
3947D SER* 3.1 28.1 + - - -
4004D GLN* 6.5 1.1 - - + -
4007D LEU* 3.8 29.6 - - + +
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Residues in contact with ARG3944 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3867D GLU* 4.9 17.8 - - - +
3869D VAL* 5.1 3.6 - - - +
3940D GLU 3.5 7.6 + - - +
3941D GLN* 3.4 29.9 + - - +
3942D GLY 3.3 0.8 - - - -
3943D LYS* 1.3 76.9 - - - +
3945D ASN* 1.3 92.5 + - - +
3947D SER* 3.4 7.0 + - - -
3948D LYS* 3.2 22.1 + - + +
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Residues in contact with ASN3945 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842D PHE* 3.2 21.6 - - + -
3867D GLU* 6.1 1.0 - - - +
3869D VAL* 3.4 45.0 - - + +
3870D MET* 4.8 10.2 - - + +
3928D PHE* 5.8 2.5 - - + -
3941D GLN* 3.1 18.5 + - - +
3942D GLY 3.6 4.9 + - - +
3944D ARG* 1.3 103.0 + - - +
3946D PHE* 1.3 58.4 + - - +
3948D LYS* 3.5 6.0 + - - +
3949D ALA* 3.1 27.2 + - - +
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Residues in contact with PHE3946 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925D ILE* 3.7 29.8 - - + -
3928D PHE* 3.9 30.0 - + + -
3942D GLY 3.1 19.1 + - - +
3943D LYS* 4.0 5.2 - - - +
3944D ARG 3.3 0.2 - - - -
3945D ASN* 1.3 75.9 - - - +
3947D SER* 1.3 62.8 + - - +
3949D ALA* 3.3 9.0 + - + +
3950D MET* 2.8 39.2 + - + +
3991D PHE* 5.4 4.3 - + - -
3994D MET* 3.5 27.1 - - + -
4007D LEU* 4.0 24.9 - - + -
4011D LEU* 3.5 27.8 - - + -
4014D LEU* 6.2 3.1 - - + -
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Residues in contact with SER3947 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3943D LYS 3.1 18.9 + - - -
3944D ARG* 3.7 6.7 - - - -
3945D ASN 3.4 0.2 - - - -
3946D PHE* 1.3 80.5 - - - +
3948D LYS* 1.3 59.4 + - - +
3950D MET* 3.4 8.1 + - - +
3951D SER* 3.0 25.8 + - - -
4007D LEU* 6.1 2.9 - - - -
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Residues in contact with LYS3948 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870D MET* 4.8 13.5 - - + -
3873D ASP* 5.6 10.5 - - + -
3944D ARG 3.2 13.2 + - - +
3945D ASN* 3.8 10.3 - - - +
3946D PHE 3.3 0.4 - - - -
3947D SER* 1.3 76.8 + - - +
3949D ALA* 1.3 61.7 + - - +
3951D SER* 3.3 16.7 + - - -
3952D VAL* 3.3 17.5 + - - +
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Residues in contact with ALA3949 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837D LEU* 5.3 9.0 - - + -
3870D MET* 4.7 18.5 - - + +
3921D LEU* 5.4 6.7 - - + +
3925D ILE* 5.1 15.1 - - + +
3945D ASN 3.1 17.7 + - - +
3946D PHE* 3.3 11.0 + - + +
3948D LYS* 1.3 74.0 - - - +
3950D MET* 1.3 60.4 + - - +
3952D VAL* 3.3 10.5 + - - +
3953D ALA* 2.9 28.1 + - - +
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Residues in contact with MET3950 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925D ILE* 6.3 0.4 - - - -
3946D PHE* 2.8 32.4 + - + +
3947D SER* 3.6 9.9 - - - +
3948D LYS 3.2 0.4 - - - -
3949D ALA* 1.3 75.2 - - - +
3951D SER* 1.3 59.9 + - - +
3953D ALA* 3.3 7.5 + - - +
3954D LYS* 2.9 30.7 + - - +
4010D GLU* 5.2 15.7 - - + +
4011D LEU* 5.9 2.2 - - - -
4014D LEU* 5.2 13.5 - - + +
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Residues in contact with SER3951 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3947D SER* 3.0 15.5 + - - -
3948D LYS* 3.3 9.9 + - - -
3949D ALA 3.3 0.4 - - - -
3950D MET* 1.3 79.7 - - - +
3952D VAL* 1.3 60.8 + - - +
3954D LYS* 3.4 10.3 + - - +
3955D GLN* 3.3 28.3 + - - +
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Residues in contact with VAL3952 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870D MET* 4.9 13.9 - - + -
3872D ASP 5.9 1.6 - - - +
3873D ASP* 6.0 5.2 - - - -
3876D THR* 3.7 29.4 - - + +
3877D GLN* 5.6 8.7 - - + +
3880D PHE* 5.3 3.3 - - + -
3917D TYR* 3.5 28.7 - - + +
3921D LEU* 4.9 4.9 - - + -
3948D LYS 3.3 16.8 - - - +
3949D ALA* 3.3 10.7 + - - +
3950D MET 3.3 0.2 - - - -
3951D SER* 1.3 77.0 - - - +
3953D ALA* 1.3 61.4 + - - +
3954D LYS 3.4 0.5 + - - -
3955D GLN* 3.5 4.1 + - - +
3956D VAL* 3.3 23.3 + - - +
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Residues in contact with ALA3953 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3921D LEU* 4.1 16.5 - - + +
3925D ILE* 4.4 13.5 - - + -
3949D ALA 2.9 17.4 + - - +
3950D MET* 3.3 6.7 + - - +
3952D VAL* 1.3 76.1 - - - +
3954D LYS* 1.3 58.5 + - - +
3956D VAL* 3.3 11.8 - - - +
3957D PHE* 3.1 31.4 - - + -
3987D PHE* 5.8 2.2 - - + -
4014D LEU* 3.4 22.1 - - + +
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Residues in contact with LYS3954 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3950D MET 2.9 17.2 + - - +
3951D SER* 3.7 9.9 - - - +
3952D VAL 3.2 0.4 - - - -
3953D ALA* 1.3 77.9 - - - +
3955D GLN* 1.3 71.7 + - + +
3956D VAL 3.5 0.2 + - - -
3957D PHE* 3.6 4.9 + - - +
3958D ASN* 3.0 35.1 + - - +
4013D ASP* 5.2 14.5 - - + +
4014D LEU* 4.2 12.3 - - + -
4016D LYS* 5.6 4.0 - - - +
4017D ASP* 3.5 28.4 - - - +
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Residues in contact with GLN3955 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3877D GLN* 5.0 19.5 - - + +
3880D PHE* 4.6 14.0 - - + +
3881D ARG* 3.6 36.7 + - - +
3884D GLN* 5.4 1.6 - - - +
3951D SER 3.3 16.1 + - - +
3952D VAL* 3.5 4.2 + - - +
3954D LYS* 1.3 86.0 - - + +
3956D VAL* 1.3 63.9 + - - +
3958D ASN* 2.8 42.0 + - - +
3959D SER* 3.5 11.3 + - - -
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Residues in contact with VAL3956 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880D PHE* 4.4 21.2 - - + +
3914D THR* 5.2 2.2 - - + +
3917D TYR* 4.3 16.6 - - + -
3918D LEU* 3.8 35.9 - - + -
3921D LEU* 4.3 9.9 - - + -
3952D VAL 3.3 14.6 + - - +
3953D ALA* 3.3 22.9 - - - +
3955D GLN* 1.3 77.6 - - - +
3957D PHE* 1.3 69.9 + - + +
3959D SER* 2.3 37.7 + - - +
3960D LEU* 3.1 9.1 - - + +
----------------------------------------------------------
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Residues in contact with PHE3957 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918D LEU* 3.9 20.6 - - + -
3921D LEU* 6.3 0.2 - - + -
3953D ALA* 3.1 26.2 - - + +
3954D LYS 3.6 7.3 + - - +
3955D GLN 3.4 0.4 - - - -
3956D VAL* 1.3 84.7 - - + +
3958D ASN* 1.3 61.4 + - - +
3959D SER 3.1 0.7 + - - -
3960D LEU* 3.6 13.4 + - + +
3961D THR* 3.3 22.2 + - - +
3983D ALA* 5.7 1.8 - - + -
3984D VAL* 4.6 12.8 - - + -
3987D PHE* 3.6 38.6 - + - -
4014D LEU* 3.9 16.6 - - + -
4017D ASP* 4.3 20.8 - - + +
4018D MET* 3.7 31.6 - - + -
4021D MET* 5.3 9.2 - - + +
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Residues in contact with ASN3958 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3881D ARG* 5.3 4.1 - - - +
3884D GLN* 4.3 6.8 - - + +
3954D LYS* 3.0 29.1 + - - +
3955D GLN* 2.8 38.2 + - - +
3956D VAL 3.1 0.8 - - - -
3957D PHE* 1.3 77.4 - - - +
3959D SER* 1.3 57.0 + - - +
3961D THR* 3.3 13.5 - - + +
3962D GLU* 3.2 26.7 - - - +
4017D ASP* 4.1 18.9 - - - +
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Residues in contact with SER3959 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880D PHE* 4.5 17.0 - - - -
3883D LEU* 5.8 0.7 - - - -
3884D GLN* 4.1 18.6 - - - +
3914D THR* 4.7 5.9 - - - +
3955D GLN 3.5 8.1 + - - -
3956D VAL* 2.3 33.2 + - - +
3958D ASN* 1.3 78.4 - - - +
3960D LEU* 1.3 68.8 + - - +
3961D THR 3.3 0.4 - - - -
3962D GLU* 3.5 2.1 + - - +
3963D TYR* 3.2 44.7 + - - -
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Residues in contact with LEU3960 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914D THR* 5.0 9.2 - - + -
3915D VAL* 3.7 30.3 - - + -
3918D LEU* 4.1 26.9 - - + -
3956D VAL* 3.1 28.9 - - + +
3957D PHE* 3.6 19.5 + - + +
3959D SER* 1.3 83.7 + - - +
3961D THR* 1.3 63.2 + - - +
3963D TYR* 3.3 20.8 + - + +
3964D ILE* 3.5 12.8 + - - +
3975D LEU* 4.1 27.3 - - + +
3980D LEU* 4.9 5.8 - - + -
4021D MET* 5.9 5.4 - - + -
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Residues in contact with THR3961 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957D PHE 3.3 18.6 + - - +
3958D ASN* 3.3 20.4 - - + +
3960D LEU* 1.3 78.3 - - - +
3962D GLU* 1.3 63.1 + - + +
3964D ILE* 3.1 5.4 + - - +
3965D GLN* 2.8 49.1 + - - +
4017D ASP 5.5 3.1 - - - +
4020D VAL* 4.9 10.5 + - + +
4021D MET* 4.7 16.1 - - - +
4024D SER* 3.5 17.7 + - - -
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Residues in contact with GLU3962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3884D GLN* 4.0 25.8 - - + +
3887D CYS* 3.2 34.7 - - + +
3888D GLU* 3.9 10.5 - - - +
3890D HIS* 4.0 7.5 + - - -
3895D GLN* 6.0 0.3 - - - +
3958D ASN 3.2 20.9 - - - +
3959D SER* 3.5 6.4 + - - +
3960D LEU 3.3 0.8 - - - -
3961D THR* 1.3 80.1 - - + +
3963D TYR* 1.3 66.1 + - + +
3964D ILE 3.5 0.5 + - - -
3965D GLN* 3.6 32.1 + - - +
4999D THR* 4.6 14.0 + - - +
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Residues in contact with TYR3963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3883D LEU* 3.4 47.3 + - - +
3884D GLN* 5.0 2.5 - - - -
3887D CYS* 5.1 12.8 - - + -
3895D GLN* 4.8 9.6 - - + +
3898D LEU* 4.2 23.3 - - + +
3910D ILE* 5.5 2.0 - - + +
3911D ILE* 3.7 24.9 - - + -
3914D THR* 4.3 21.4 + - + +
3959D SER* 3.2 29.8 - - - -
3960D LEU* 3.3 13.0 + - + +
3961D THR 3.2 0.6 - - - -
3962D GLU* 1.3 81.2 - - + +
3964D ILE* 1.3 57.7 + - + +
3965D GLN 3.6 0.8 + - - -
3968D CYS* 3.7 5.2 - - - +
3971D ASN* 3.1 40.9 - - + +
----------------------------------------------------------
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Residues in contact with ILE3964 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3960D LEU 3.5 9.3 + - - +
3961D THR* 3.1 8.0 + - - +
3963D TYR* 1.3 76.8 - - + +
3965D GLN* 1.3 66.1 + - - +
3966D GLY 3.6 6.2 - - - +
3968D CYS* 3.6 18.1 - - - -
3971D ASN* 4.6 8.7 - - + +
3972D GLN* 5.2 5.6 - - + -
3975D LEU* 5.5 8.1 - - + -
4021D MET 6.0 0.7 - - - +
4024D SER* 3.2 25.9 - - - +
4025D LEU* 5.1 9.2 - - + -
----------------------------------------------------------
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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