Contacts of the helix formed by residues 88 - 113 (chain D) in PDB entry 6WNX
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 88 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D MET* 4.1 3.6 - - + -
87D PRO* 1.4 95.1 - - + +
89D ASN* 1.3 65.7 + - - +
90D SER* 3.5 19.7 - - - +
91D PHE* 3.2 22.1 + - + +
92D TYR* 3.3 9.2 - - - -
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 4.3 2.6 + - - +
46D SER* 3.4 43.7 + - - +
49D MET* 3.5 38.8 - - + +
50D LEU 3.7 6.9 + - - -
51D TRP* 3.7 29.9 + - - +
52D LYS 4.6 1.2 + - - -
88D PRO* 1.3 68.8 - - - +
90D SER* 1.3 68.0 - - - +
91D PHE 2.8 2.3 + - - -
92D TYR* 2.8 17.8 + - - +
93D ARG* 3.1 13.6 + - - +
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D PRO* 3.5 20.8 - - - +
89D ASN* 1.3 78.2 - - - +
91D PHE* 1.3 59.8 + - - +
93D ARG* 3.5 15.3 - - - +
94D SER* 3.0 27.1 + - - -
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D TRP* 6.0 1.3 - - + -
77D TYR* 5.3 16.2 - + + -
87D PRO* 6.0 2.2 - - + -
88D PRO* 3.2 27.3 + - + +
89D ASN 2.8 5.3 + - - -
90D SER* 1.3 75.6 + - - +
92D TYR* 1.3 78.1 + + + +
94D SER* 3.1 13.4 + - - -
95D LEU* 3.0 49.6 + - + +
98D LYS* 6.5 1.6 - - - -
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Residues in contact with TYR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D MET* 4.7 3.1 - - - -
51D TRP* 3.6 22.8 - - + +
52D LYS* 3.6 47.5 - - + +
55D ILE* 4.0 8.2 - - + +
77D TYR* 2.6 39.7 + - + +
78D LEU* 4.2 7.2 - - + -
87D PRO* 3.3 37.7 - - + +
88D PRO 3.3 20.2 - - - -
89D ASN* 2.8 13.3 + - - +
91D PHE* 1.3 81.7 - + + +
93D ARG* 1.3 64.6 + - - +
95D LEU* 3.6 22.0 - - + +
96D TYR* 3.3 22.7 + - - +
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Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 2.5 34.6 + - - -
51D TRP* 3.5 40.3 - - + +
89D ASN* 3.1 12.9 + - - +
90D SER* 3.5 17.0 - - - +
91D PHE 3.3 0.2 - - - -
92D TYR* 1.3 76.6 - - - +
94D SER* 1.3 60.7 + - - +
96D TYR* 3.9 2.3 + - - +
97D PRO* 3.3 18.9 - - - +
135E VAL* 4.5 2.2 - - - +
138E GLU* 3.2 61.3 + - - +
139E ASN* 3.3 17.5 - - - +
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Residues in contact with SER 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D SER 3.0 13.0 + - - -
91D PHE* 3.1 15.9 + - - -
93D ARG* 1.3 76.5 - - - +
95D LEU* 1.3 62.9 + - - +
96D TYR 3.5 0.2 - - - -
97D PRO* 3.4 16.5 - - - +
98D LYS* 3.6 18.4 - - - +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE* 3.9 20.2 - - + -
74D TRP* 4.4 32.8 - - + +
77D TYR* 6.5 0.7 - - + -
78D LEU* 6.0 1.3 - - + -
91D PHE* 3.0 40.9 + - + +
92D TYR* 3.6 16.4 - - + +
93D ARG 3.3 0.2 - - - -
94D SER* 1.3 76.2 - - - +
96D TYR* 1.3 67.4 + - - +
98D LYS* 2.7 31.0 + - + +
99D ILE* 3.0 32.8 + - + +
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Residues in contact with TYR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA* 3.7 25.9 + - + +
51D TRP* 3.8 31.6 - + + -
54D LEU* 3.5 27.4 - - + +
55D ILE* 4.1 13.7 - - + +
58D MET* 4.7 7.3 - - + +
65D TRP* 3.5 31.5 - + - -
92D TYR 3.3 10.6 + - - +
93D ARG 4.1 0.7 - - - +
95D LEU* 1.3 77.9 - - - +
97D PRO* 1.4 72.3 - - + +
99D ILE* 3.1 11.9 + - - +
100D ILE* 3.0 45.1 + - + +
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Residues in contact with PRO 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ARG 3.3 15.5 - - - +
94D SER* 3.4 17.3 - - - +
96D TYR* 1.4 100.3 - - + +
98D LYS* 1.3 54.0 + - + +
100D ILE* 3.3 11.2 + - + +
101D GLN* 2.9 28.4 + - - +
138E GLU 6.1 0.7 - - - +
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Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PHE* 6.5 1.1 - - - -
94D SER* 3.6 19.7 - - - +
95D LEU* 2.7 28.5 + - + +
97D PRO* 1.3 70.7 - - + +
99D ILE* 1.3 57.4 + - - +
101D GLN* 3.7 15.0 + - - +
102D ASP* 3.0 26.5 + - - +
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ILE* 4.3 7.2 - - + -
65D TRP* 3.5 39.5 - - + -
68D LEU* 4.3 7.6 - - + -
74D TRP* 3.3 51.1 - - + +
95D LEU* 3.0 35.7 + - + +
96D TYR* 3.4 7.6 - - - +
98D LYS* 1.3 73.2 - - - +
100D ILE* 1.3 54.4 + - - +
102D ASP* 3.1 9.9 - - - +
103D ILE* 2.8 43.9 + - + +
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Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TRP* 4.8 10.3 - - + -
96D TYR* 3.0 44.0 + - + +
97D PRO* 3.3 10.7 + - + +
99D ILE* 1.3 76.1 - - - +
101D GLN* 1.3 57.5 + - - +
103D ILE* 3.1 12.9 + - + +
104D GLU* 2.8 54.7 + - - +
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Residues in contact with GLN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D PRO 2.9 17.1 + - - +
98D LYS* 3.7 14.5 - - - +
100D ILE* 1.3 72.7 - - - +
102D ASP* 1.3 70.9 + - - +
104D GLU* 3.0 18.3 + - + +
105D THR* 3.0 36.4 + - + +
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Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 2.9 33.1 - - + +
72D ARG* 3.0 38.0 + - - +
74D TRP* 5.3 1.2 + - - -
98D LYS 3.0 16.5 + - - +
99D ILE* 3.1 14.1 - - - +
101D GLN* 1.3 76.9 + - - +
103D ILE* 1.3 63.1 + - - +
105D THR* 2.7 28.4 + - - -
106D ILE* 3.2 10.7 + - - +
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU* 4.1 18.6 - - + -
65D TRP* 4.0 28.9 - - + +
68D LEU* 3.5 17.9 - - + -
99D ILE* 2.8 31.8 + - + +
100D ILE* 3.1 16.1 + - + +
102D ASP* 1.3 71.7 - - - +
104D GLU* 1.3 70.4 + - + +
106D ILE* 3.1 16.0 + - + +
107D GLU* 3.1 24.6 + - + +
341D LYS* 4.2 21.3 - - - +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ILE* 2.8 46.4 + - - +
101D GLN* 3.0 7.7 + - + +
103D ILE* 1.3 77.5 - - + +
105D THR* 1.3 58.1 + - + +
107D GLU* 3.3 15.2 + - + +
108D SER* 2.9 27.0 + - - -
111D ARG* 4.6 7.1 + - - +
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Residues in contact with THR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ARG* 5.8 1.0 + - - -
101D GLN* 3.0 34.9 + - + +
102D ASP* 2.7 22.6 + - - -
104D GLU* 1.3 72.6 - - - +
106D ILE* 1.3 66.4 + - - +
108D SER* 3.3 9.0 + - - -
109D ASN* 3.0 32.4 + - - +
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D LEU* 4.8 4.7 - - + -
68D LEU* 4.0 20.2 - - + -
72D ARG* 5.2 4.0 - - - +
102D ASP* 3.6 12.8 - - - +
103D ILE* 3.1 16.5 + - + +
105D THR* 1.3 78.9 + - - +
107D GLU* 1.3 59.3 + - + +
109D ASN* 2.8 29.6 + - - +
110D TRP* 3.1 24.0 + - + +
342D ARG* 5.7 0.2 - - - +
389D GLU* 3.6 26.2 - - + +
390D PHE* 3.9 29.6 - - + -
406D PHE 4.3 11.7 - - - +
407D LEU* 4.1 13.5 - - + +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ILE* 3.1 20.5 + - + +
104D GLU* 3.3 18.1 + - + +
106D ILE* 1.3 75.5 - - + +
108D SER* 1.3 56.9 + - - +
110D TRP* 3.2 8.6 + - - +
111D ARG* 3.0 57.6 + - - +
341D LYS* 2.9 37.5 + - - +
342D ARG* 2.5 33.2 + - - -
389D GLU* 5.0 0.9 - - - -
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Residues in contact with SER 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLU 2.9 14.2 + - - -
105D THR* 3.4 13.2 - - - -
106D ILE 3.1 0.2 - - - -
107D GLU* 1.3 74.8 - - - +
109D ASN* 1.3 53.2 + - - +
111D ARG* 3.2 14.5 + - - +
112D CYS* 2.9 49.0 + - - -
114D ARG* 3.5 15.8 + - - -
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Residues in contact with ASN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D THR* 3.0 20.9 + - - +
106D ILE* 2.8 15.6 + - - +
108D SER* 1.3 73.3 - - - +
110D TRP* 1.3 53.9 + - - +
113D GLY* 2.7 29.6 + - - -
114D ARG* 2.9 60.3 + - - +
406D PHE* 2.6 32.8 + - + +
407D LEU 4.5 8.1 + - - -
408D ASN* 4.9 7.1 + - - +
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Residues in contact with TRP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ILE* 3.1 32.4 + - + +
107D GLU* 3.5 8.3 - - - +
109D ASN* 1.3 75.1 - - - +
111D ARG* 1.3 62.5 + - - +
113D GLY* 3.2 11.8 + - - -
342D ARG* 3.7 47.0 - - - +
344D VAL* 4.5 1.6 - - + -
354D VAL* 4.0 19.2 - - + +
372D LEU* 5.1 6.8 - - + +
373D ARG* 4.0 13.7 - - - +
387D PHE* 3.8 12.8 - + - -
388D ASP 3.3 26.7 - - - -
389D GLU 3.1 17.8 + - - -
391D GLN 3.8 9.4 - - - -
392D ILE* 3.7 37.7 - - + -
406D PHE* 3.6 46.3 - + + +
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLU* 4.6 7.5 + - - +
107D GLU* 3.0 46.5 + - - +
108D SER* 3.2 16.2 + - - +
110D TRP* 1.3 75.2 - - - +
112D CYS* 1.3 62.6 + - - +
372D LEU* 3.5 49.0 - - + +
373D ARG* 3.5 9.2 + - - -
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D SER* 2.9 28.6 + - - +
109D ASN 4.3 0.9 - - - +
111D ARG* 1.3 81.1 - - - +
113D GLY* 1.3 62.9 + - - +
114D ARG* 3.3 33.5 + - + +
373D ARG* 3.4 22.9 + - - +
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Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ASN 2.7 11.9 + - - -
110D TRP 3.2 8.5 + - - -
111D ARG 3.3 0.6 - - - -
112D CYS* 1.3 78.5 - - - +
114D ARG* 1.3 57.7 + - - -
115D HIS* 3.2 21.9 + - - -
373D ARG* 3.6 25.8 + - - -
375D LEU* 4.7 2.9 - - - +
406D PHE* 4.2 7.4 - - - -
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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