Contacts of the helix formed by residues 73 - 94 (chain D) in PDB entry 5HZZ
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 LEU 73 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PRO* 4.5 2.7 - - + -
30B THR 3.8 37.7 - - - +
31B PRO* 4.0 5.8 - - + -
32B PRO* 3.8 23.1 - - + -
94B LEU* 4.3 12.3 - - + +
96B ILE* 4.0 25.5 - - + +
138B ILE* 4.9 0.9 - - + -
58D LEU* 4.1 20.4 - - + -
68D LEU* 5.4 2.5 - - + -
69D SER 4.1 6.7 - - - +
70D ALA* 3.5 17.5 - - - +
71D GLY 3.1 1.2 - - - -
72D ASP* 1.3 79.5 - - + +
74D ALA* 1.3 59.3 + - - +
75D PRO 3.4 0.9 - - - -
76D LEU* 3.3 9.0 + - + +
77D ALA* 2.8 28.9 + - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.5 6.1 - - + +
135B ARG* 3.7 37.9 - - + +
138B ILE* 4.0 18.6 - - + +
70D ALA 4.2 1.6 + - - -
71D GLY 3.2 14.3 + - - +
73D LEU* 1.3 76.2 - - - +
75D PRO* 1.3 66.4 - - + +
77D ALA* 3.2 1.0 + - - -
78D HIS* 2.9 30.0 + - - +
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Residues in contact with PRO 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLU* 3.5 27.8 - - - +
71D GLY 4.2 2.2 - - - +
72D ASP* 3.6 17.0 - - - +
74D ALA* 1.3 94.4 - - + +
76D LEU* 1.3 61.5 + - - +
78D HIS* 3.4 6.2 + - + +
79D GLU* 3.1 28.5 + - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 16.4 - - + -
94B LEU* 4.0 23.8 - - + -
51D VAL* 4.1 17.7 - - + +
54D GLU* 3.9 15.7 - - + +
55D ILE* 3.7 25.4 - - + -
58D LEU* 3.8 31.6 - - + -
72D ASP 5.1 0.4 + - - -
73D LEU* 3.3 9.8 + - + +
75D PRO* 1.3 78.4 - - - +
77D ALA* 1.3 58.8 + - - +
79D GLU* 3.2 1.3 + - - +
80D LEU* 2.9 48.1 + - + +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.1 17.6 - - + +
96B ILE* 4.0 24.6 - - + +
101B VAL* 3.7 7.4 - - + +
134B VAL* 4.1 11.2 - - + -
138B ILE* 4.3 7.6 - - + -
73D LEU 2.8 20.0 + - - +
74D ALA* 3.6 7.0 - - - +
76D LEU* 1.3 74.4 - - - +
78D HIS* 1.3 63.6 + - - +
80D LEU* 3.3 2.5 + - - +
81D ALA* 3.0 24.4 + - - +
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Residues in contact with HIS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.5 2.9 - - - -
105B VAL* 3.8 19.2 - - + +
129B TRP* 6.3 0.7 - + - -
131B PRO* 5.0 7.4 - - + -
132B ALA* 4.1 30.0 + - + +
134B VAL* 3.5 28.5 - - + +
74D ALA 2.9 16.2 + - - +
75D PRO* 3.5 8.5 - - + +
77D ALA* 1.3 75.6 - - - +
79D GLU* 1.3 64.8 + - + +
81D ALA* 3.2 4.2 + - - +
82D ASP* 3.0 41.8 + - - -
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA 4.6 1.4 - - - +
50D GLU* 3.2 19.6 - - + +
51D VAL* 3.3 31.1 - - + +
54D GLU* 3.7 23.2 - - + +
75D PRO* 3.1 17.7 + - + +
76D LEU* 3.9 2.5 - - - +
78D HIS* 1.3 80.5 - - - +
80D LEU* 1.3 61.9 + - - +
82D ASP* 3.2 7.0 + - - +
83D LEU* 3.0 22.2 + - - +
203D MN 2.5 34.9 + - - -
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Residues in contact with LEU 80 (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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44B LEU* 4.0 16.2 - - + -
87B THR* 3.5 24.2 - - + +
90B ALA* 4.2 15.9 - - + -
91B LEU* 3.8 33.9 - - + -
94B LEU* 4.1 12.6 - - + -
51D VAL* 3.9 26.0 - - + -
55D ILE* 5.9 0.4 - - + -
76D LEU* 2.9 40.3 + - + +
77D ALA 3.3 3.8 + - - +
79D GLU* 1.3 76.5 - - - +
81D ALA* 1.3 57.1 + - - +
83D LEU* 3.2 5.2 + - + +
84D LEU* 2.9 25.0 + - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.6 3.7 - - + +
98B ALA 5.5 0.4 - - - +
101B VAL* 3.6 22.2 - - + -
102B PHE* 4.0 17.3 - - + +
105B VAL* 3.9 14.5 - - + +
77D ALA 3.0 16.9 + - - +
78D HIS 3.2 4.7 + - - +
80D LEU* 1.3 75.0 - - - +
82D ASP* 1.3 59.5 + - - +
84D LEU* 3.3 15.1 + - + +
85D TYR* 2.8 28.8 + - - +
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Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.4 13.7 - - - +
47D ALA* 4.3 5.2 - - + -
78D HIS* 3.0 28.0 + - - +
79D GLU* 3.2 12.8 - - - +
81D ALA* 1.3 75.5 - - - +
83D LEU* 1.3 63.4 + - - +
85D TYR* 3.1 2.8 + - - +
86D VAL* 3.0 28.4 + - - +
201D UMP 2.6 40.8 + - - +
203D MN 2.4 35.5 + - - +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.3 18.8 - - + -
48B SER* 5.4 0.4 - - - +
83B LEU* 4.5 10.1 - - + -
87B THR* 3.7 26.7 - - + +
44D LEU* 4.2 14.6 - - + +
47D ALA* 3.9 20.3 - - + +
48D SER* 3.8 25.1 - - - +
51D VAL* 4.3 16.6 - - + -
79D GLU 3.0 14.0 + - - +
80D LEU* 3.2 8.9 + - + +
82D ASP* 1.3 73.5 - - - +
84D LEU* 1.3 65.7 + - - +
86D VAL* 3.4 2.5 + - + +
87D THR* 2.8 39.1 + - - +
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.9 16.6 - - + +
87B THR* 3.5 28.0 - - + -
88B TYR* 3.8 47.3 - - + +
91B LEU* 4.0 20.9 - - + -
98B ALA* 4.4 4.0 - - + +
102B PHE* 3.8 24.5 - - + -
10D ASN* 5.0 0.4 - - - +
80D LEU 2.9 15.5 + - - +
81D ALA* 3.5 12.1 - - + +
83D LEU* 1.3 75.0 - - - +
85D TYR* 1.3 58.8 + - - +
87D THR* 3.2 1.7 + - - -
88D TYR* 2.8 37.6 + - + -
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Residues in contact with TYR 85 (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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102B PHE* 3.4 32.8 - + - -
105B VAL* 4.2 8.7 - - + -
106B HIS* 2.7 44.6 + - + -
109B ASN* 3.4 34.0 - - - +
14D LEU* 3.6 30.6 - - + +
17D PHE* 3.2 28.7 - + - +
81D ALA 2.8 15.7 + - - +
82D ASP 3.1 8.9 + - - +
84D LEU* 1.3 73.7 - - - +
86D VAL* 1.3 57.9 + - - +
88D TYR 3.7 0.2 + - - -
89D GLY* 2.9 24.1 + - - -
201D UMP 3.4 34.5 - - + +
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Residues in contact with VAL 86 (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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40D ARG* 3.2 16.2 + - - +
43D LEU* 3.8 40.6 - - + +
44D LEU* 4.0 21.1 - - + +
47D ALA* 4.0 12.1 - - + -
82D ASP 3.0 11.6 + - - +
83D LEU* 3.5 10.1 - - + +
85D TYR* 1.3 74.2 - - - +
87D THR* 1.3 63.4 + - - +
89D GLY 3.6 0.4 - - - -
90D ALA* 3.1 24.4 + - - +
201D UMP 3.5 35.2 - - + +
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Residues in contact with THR 87 (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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80B LEU* 3.3 43.9 - - + +
83B LEU* 3.5 16.2 - - + +
84B LEU* 3.6 21.8 - - + +
87B THR* 5.5 0.3 + - - -
44D LEU* 3.5 18.5 - - - +
83D LEU* 2.8 21.9 + - - +
84D LEU* 3.2 3.6 + - - -
86D VAL* 1.3 74.0 - - - +
88D TYR* 1.3 64.2 + - - +
90D ALA* 3.2 12.5 + - - +
91D LEU* 3.3 14.5 + - + +
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Residues in contact with TYR 88 (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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10B ASN* 2.9 25.1 + - - -
84B LEU* 3.8 21.9 - - + +
88B TYR* 2.4 42.0 + + - -
102B PHE* 3.9 17.7 - + - -
10D ASN* 3.5 17.4 + - + +
11D ALA* 3.7 27.5 - - + -
14D LEU* 3.7 19.9 - - + +
84D LEU* 2.8 29.3 + - + +
87D THR* 1.3 72.6 - - - +
89D GLY* 1.3 58.0 + - - +
91D LEU* 3.2 7.6 + - - +
92D ASP* 2.9 29.3 + - - +
98D ALA* 3.5 26.0 - - + +
99D ASP* 4.4 0.5 + - - -
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Residues in contact with GLY 89 (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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14D LEU* 3.5 23.6 - - - -
18D HIS* 3.4 5.1 - - - -
40D ARG* 3.5 16.2 - - - -
85D TYR 2.9 13.8 + - - -
86D VAL 3.5 0.2 + - - -
87D THR 3.1 0.8 - - - -
88D TYR* 1.3 76.8 - - - +
90D ALA* 1.3 57.7 + - - +
92D ASP* 3.4 0.6 + - - -
93D GLN* 3.0 34.5 + - - +
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Residues in contact with ALA 90 (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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55B ILE* 6.3 0.4 - - + -
76B LEU* 6.3 0.2 - - + -
80B LEU* 4.0 23.6 - - + -
40D ARG* 3.5 34.4 - - + +
44D LEU* 5.1 3.1 - - + -
86D VAL 3.1 14.0 + - - +
87D THR 3.2 8.7 + - - +
89D GLY* 1.3 73.8 - - - +
91D LEU* 1.3 65.2 + - - +
93D GLN* 3.4 2.4 + - - +
94D LEU* 3.1 30.2 + - + +
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Residues in contact with LEU 91 (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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77B ALA* 3.7 37.0 - - + +
80B LEU* 3.8 26.7 - - + -
81B ALA* 4.6 7.2 - - + +
84B LEU* 4.2 17.0 - - + -
87D THR 3.3 9.1 + - - +
88D TYR* 3.2 7.6 + - - +
90D ALA* 1.3 75.5 - - - +
92D ASP* 1.3 64.0 + - - +
94D LEU* 3.2 13.0 + - + +
96D ILE* 3.0 47.8 + - + +
98D ALA* 3.5 29.8 - - + +
101D VAL* 5.1 3.1 - - + -
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA 4.5 4.2 - - - +
14D LEU* 3.9 9.7 - - + +
15D HIS* 3.5 27.0 + - - +
18D HIS* 2.8 27.1 + - - +
25D THR* 2.6 30.9 + - - -
26D PRO* 3.6 10.2 - - - +
88D TYR 2.9 16.3 + - - +
89D GLY 3.8 4.7 - - - +
91D LEU* 1.3 77.7 - - - +
93D GLN* 1.3 57.8 + - - +
95D GLY* 2.9 19.1 + - - -
96D ILE 4.3 5.6 - - - +
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Residues in contact with GLN 93 (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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18D HIS* 3.5 15.0 - - + -
23D ALA* 3.8 10.4 - - - +
24D ALA* 2.9 48.5 + - - +
26D PRO* 3.4 14.6 - - - +
30D THR* 4.9 1.9 - - - +
32D PRO* 5.3 0.2 - - - +
36D LEU* 3.6 39.2 - - + +
39D LEU* 4.5 8.7 - - - +
40D ARG* 3.0 32.2 + - - +
89D GLY 3.0 20.3 + - - +
90D ALA 4.0 3.1 - - - +
92D ASP* 1.3 75.3 - - - +
94D LEU* 1.3 60.0 + - - +
95D GLY 3.1 0.7 - - - -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.3 12.5 - - + +
76B LEU* 3.9 24.7 - - + -
77B ALA 5.2 0.7 - - - +
80B LEU* 4.2 13.9 - - + -
26D PRO* 4.6 1.6 - - - -
29D PRO* 3.4 2.1 - - - +
30D THR 2.9 30.4 + - - +
32D PRO* 3.6 39.3 - - + -
36D LEU* 4.4 8.3 - - + -
37D LEU* 4.5 7.6 - - + -
40D ARG* 6.3 0.2 - - + -
90D ALA* 3.1 21.1 + - + +
91D LEU* 3.2 10.5 + - + +
93D GLN* 1.3 75.1 - - - +
95D GLY* 1.3 60.9 + - - +
96D ILE* 3.4 25.8 + - + +
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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