Contacts of the helix formed by residues 48 - 71 (chain s) in PDB entry 5GJQ
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 GLY 48 (chain s).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45s MET* 5.2 0.2 - - - -
46s ALA 5.1 0.2 - - - -
47s GLY* 1.3 71.6 - - - -
49s ALA* 1.3 67.6 - - - -
50s ALA 3.3 2.5 - - - -
51s ASP* 3.3 9.0 + - - -
52s CYS* 3.1 26.3 + - - -
96s SER* 2.9 23.0 + - - +
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Residues in contact with ALA 49 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31s VAL* 5.7 2.9 - - + -
45s MET* 3.6 30.1 - - + +
47s GLY 3.8 3.2 + - - -
48s GLY* 1.3 73.2 - - - +
50s ALA* 1.3 58.7 + - - +
52s CYS* 3.9 1.7 - - - +
53s SER* 2.9 34.1 + - - -
125t ASP* 5.8 0.4 - - - +
129t SER* 3.6 20.2 - - - +
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Residues in contact with ALA 50 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48s GLY* 3.3 0.4 - - - -
49s ALA* 1.3 80.2 - - - +
51s ASP* 1.3 60.0 + - - +
53s SER* 3.8 3.0 - - - -
54s PHE* 2.9 34.0 + - - +
97t TYR* 4.3 4.5 - - + -
125t ASP* 4.2 1.3 + - - +
127t VAL* 3.3 41.3 - - + +
128t GLY 4.3 1.1 - - - -
129t SER* 3.5 29.2 - - - +
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Residues in contact with ASP 51 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48s GLY* 3.3 7.4 + - - +
49s ALA 3.3 0.8 - - - -
50s ALA* 1.3 77.0 - - - +
52s CYS* 1.3 64.3 + - - +
55s TRP* 2.9 39.9 + - + +
95s LEU* 3.8 9.6 - - + -
96s SER* 3.2 34.0 + - - +
97s MET* 4.3 5.1 - - + +
97t TYR* 2.8 19.5 + - - +
100t ARG* 2.7 46.8 + - - -
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Residues in contact with CYS 52 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35s ILE* 4.3 3.1 - - + -
44s THR 4.2 8.1 - - - +
45s MET* 3.9 20.6 - - + -
46s ALA 3.3 36.3 - - - -
48s GLY 3.1 13.6 + - - +
49s ALA 3.9 2.7 - - - +
51s ASP* 1.3 77.7 - - - +
53s SER* 1.3 63.4 + - - +
56s GLU* 2.9 35.1 + - - +
97s MET* 3.8 27.6 - - - -
98s GLY 4.2 2.5 - - - -
99s THR* 5.2 0.2 - - - -
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Residues in contact with SER 53 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35s ILE* 4.5 11.4 - - - +
45s MET* 3.4 18.9 - - - +
49s ALA* 2.9 21.7 + - - +
50s ALA* 3.8 6.3 - - - -
52s CYS* 1.3 76.0 - - - +
54s PHE* 1.3 58.3 + - - +
56s GLU* 3.9 0.9 - - - +
57s ARG* 3.0 32.0 + - - +
128t GLY 5.9 0.9 - - - -
129t SER* 5.4 7.4 + - - -
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Residues in contact with PHE 54 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101l PHE* 4.1 28.5 - + - -
50s ALA 2.9 19.7 + - - +
51s ASP 3.9 2.2 - - - +
53s SER* 1.3 77.8 - - - +
55s TRP* 1.3 81.5 + + - +
57s ARG* 3.1 6.2 + - - +
58s LEU* 3.0 34.3 + - + +
93t SER* 5.4 5.2 - - - -
94t THR* 4.9 13.7 - - + -
97t TYR* 2.9 65.1 - + + -
98t SER* 6.1 0.7 - - - -
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Residues in contact with TRP 55 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51s ASP* 2.9 29.9 + - + +
52s CYS 4.4 0.4 - - - +
54s PHE* 1.3 96.8 - + - +
56s GLU* 1.3 60.1 + - - +
58s LEU* 3.4 35.7 - - + +
59s LEU* 3.0 23.4 + - - +
83s LEU* 3.9 15.5 - - + +
86s MET* 3.9 36.5 - - + +
87s VAL* 4.0 13.2 - - + -
90s TYR* 3.4 46.4 - + - -
95s LEU* 3.7 16.8 - - + +
97s MET* 4.2 9.0 - - - -
97t TYR* 3.0 27.1 + + - -
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Residues in contact with GLU 56 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35s ILE* 3.6 27.7 - - + +
37s ILE* 3.5 17.4 - - + +
43s GLY* 3.2 25.2 - - - -
44s THR 3.0 7.3 - - - +
52s CYS* 2.9 18.2 + - - +
53s SER 4.3 1.1 - - - +
55s TRP* 1.3 75.9 - - - +
57s ARG* 1.3 60.8 + - - +
59s LEU* 3.2 10.2 - - + +
60s ALA* 2.9 24.1 + - - +
83s LEU* 4.1 17.0 - - + -
97s MET* 4.6 3.2 - - + +
99s THR* 2.4 36.4 + - - -
101s ILE* 4.3 6.1 - - - -
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Residues in contact with ARG 57 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100l TRP* 3.0 48.0 + - + -
101l PHE* 3.1 39.4 - - + -
102l THR 4.2 4.4 + - - -
104l ASN* 3.0 37.9 + - - +
35s ILE* 5.7 0.6 - - - +
53s SER 3.0 20.0 + - - +
54s PHE* 3.1 6.5 + - + +
56s GLU* 1.3 74.5 - - - +
58s LEU* 1.3 67.9 + - - +
60s ALA* 3.0 16.9 + - + +
61s ARG* 3.1 13.3 + - - +
90t ALA* 4.4 6.4 - - - +
130t TYR* 5.9 2.4 - - - -
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Residues in contact with LEU 58 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101l PHE* 3.6 29.5 - - + -
54s PHE* 3.0 22.4 + - + +
55s TRP* 3.4 42.0 - - + +
57s ARG* 1.3 78.3 - - - +
59s LEU* 1.3 60.5 + - - +
61s ARG* 3.3 24.9 + - - +
62s GLN* 3.0 24.7 + - - +
86s MET* 4.1 16.4 - - - -
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Residues in contact with LEU 59 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37s ILE* 3.9 26.7 - - + -
41s LEU* 5.2 0.2 - - + -
55s TRP 3.0 14.7 + - - +
56s GLU* 3.2 10.1 - - - +
57s ARG 3.1 0.2 - - - -
58s LEU* 1.3 76.0 - - - +
60s ALA* 1.3 63.2 - - - +
62s GLN* 3.1 3.6 + - + +
63s CYS* 2.9 45.3 + - - -
79s ALA* 3.6 30.5 - - + +
82s LEU* 4.1 18.2 - - + -
83s LEU* 4.2 18.4 - - + +
86s MET* 4.0 9.4 - - + +
101s ILE* 4.2 15.9 - - + -
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Residues in contact with ALA 60 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100l TRP* 3.5 21.7 - - + -
37s ILE* 3.7 37.0 - - + +
38s ASN* 4.2 7.8 - - - +
56s GLU 2.9 11.0 + - - +
57s ARG* 3.0 12.1 + - + +
59s LEU* 1.3 77.4 - - - +
61s ARG* 1.3 63.4 + - - +
63s CYS* 3.3 4.4 + - - +
64s ARG* 3.0 24.1 + - - +
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Residues in contact with ARG 61 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94l VAL* 3.5 21.4 + - - +
97l GLN* 4.1 20.7 - - + +
98l ASN* 2.4 32.0 + - - +
100l TRP* 3.7 18.6 - - + -
101l PHE* 4.3 12.6 - - + -
57s ARG 3.1 9.0 + - - +
58s LEU* 3.4 27.3 - - - +
60s ALA* 1.3 79.1 - - - +
62s GLN* 1.3 90.5 + - - +
64s ARG* 3.2 6.0 + - - +
65s ILE* 3.1 35.6 + - + +
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Residues in contact with GLN 62 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58s LEU* 3.0 14.7 + - - +
59s LEU* 3.6 11.7 - - + +
61s ARG* 1.3 104.5 + - - +
63s CYS* 1.3 58.2 + - - +
65s ILE* 3.5 18.7 + - - +
66s TYR* 3.0 27.1 + - - +
69s ARG* 5.2 6.3 - - - +
82s LEU* 3.9 37.3 - - + +
86s MET* 4.8 11.6 - - - +
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Residues in contact with CYS 63 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38s ASN* 3.8 18.2 - - - +
40s TYR* 4.4 4.3 + - - -
41s LEU* 3.9 16.8 - - - -
59s LEU* 2.9 42.8 + - - +
60s ALA* 3.6 6.7 - - - +
62s GLN* 1.3 79.8 - - - +
64s ARG* 1.3 57.1 + - - +
66s TYR* 3.2 9.3 + - - +
67s GLU* 2.9 27.2 + - - +
74s ILE* 3.7 35.0 - - + +
79s ALA* 4.2 1.1 - - - -
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Residues in contact with ARG 64 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69l GLU* 2.8 24.4 + - - -
71l ASP* 2.7 26.8 + - - -
72l ALA* 3.2 14.6 - - - +
97l GLN* 3.2 33.1 + - - +
100l TRP* 5.7 1.1 - - + -
38s ASN* 5.2 3.1 - - - +
40s TYR* 5.7 0.2 - - - -
60s ALA 3.0 13.8 + - - +
61s ARG 3.2 7.6 + - - +
63s CYS* 1.3 74.1 - - - +
65s ILE* 1.3 65.0 + - - +
67s GLU* 3.1 37.8 + - - +
68s LEU* 3.0 49.3 + - + +
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Residues in contact with ILE 65 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90l ASP* 5.2 2.7 - - - +
93l ARG* 5.3 6.7 - - + -
94l VAL* 3.8 32.8 - - + +
97l GLN* 3.9 15.9 - - + -
61s ARG* 3.1 42.9 + - + +
62s GLN* 3.7 18.6 - - - +
64s ARG* 1.3 74.7 - - - +
66s TYR* 1.3 64.0 + - - +
68s LEU* 3.3 7.6 + - - +
69s ARG* 3.0 60.0 + - + +
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Residues in contact with TYR 66 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94k HIS* 4.9 12.6 + + - -
98k VAL* 4.5 27.3 - - + +
100k ASP* 6.1 0.5 - - - +
62s GLN 3.0 14.3 + - - +
63s CYS* 3.3 12.3 - - - +
64s ARG 3.2 0.2 - - - -
65s ILE* 1.3 76.9 - - - +
67s GLU* 1.3 64.6 + - - +
69s ARG* 3.3 5.0 + - - +
70s ASN* 2.9 58.2 + - + +
72s GLU* 3.9 16.5 + - + +
73s ARG 4.2 3.4 + - - -
74s ILE* 3.6 50.2 - - + -
75s SER 5.4 1.3 + - - -
78s ALA* 5.9 0.2 - - + -
82s LEU* 6.0 2.7 - - + -
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Residues in contact with GLU 67 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38s ASN* 5.6 0.2 + - - -
40s TYR* 4.3 15.2 + - - +
63s CYS 2.9 14.2 + - - +
64s ARG* 3.3 37.3 + - - +
66s TYR* 1.3 76.7 - - + +
68s LEU* 1.3 59.0 + - + +
71s LYS* 3.0 27.5 + - - -
72s GLU 3.3 25.1 - - - +
73s ARG* 3.2 32.0 + - + +
74s ILE 5.4 0.2 - - - +
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Residues in contact with LEU 68 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69l GLU* 3.5 41.5 - - + +
70l ILE 3.0 28.7 - - - +
71l ASP* 4.4 4.0 - - - +
93l ARG* 3.2 42.2 + - + +
97l GLN* 5.0 5.8 - - + +
64s ARG* 3.0 45.8 + - + +
65s ILE* 3.8 6.3 - - - +
67s GLU* 1.3 79.4 - - + +
69s ARG* 1.3 66.3 + - - +
71s LYS* 3.9 10.7 + - - +
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Residues in contact with ARG 69 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105k GLU* 5.3 1.0 - - - +
106k TYR* 6.3 1.8 - - - -
109k ARG* 3.4 37.6 + - - +
90l ASP* 3.6 36.4 + - - +
93l ARG* 3.8 10.3 - - - +
94l VAL* 5.3 3.4 - - - +
62s GLN* 5.2 6.9 - - - +
65s ILE* 3.0 41.1 + - + +
66s TYR* 3.8 6.4 - - - +
68s LEU* 1.3 80.1 - - - +
70s ASN* 1.3 67.6 + - - +
71s LYS* 3.7 6.4 + - - +
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Residues in contact with ASN 70 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94k HIS* 5.4 1.5 + - - -
103k THR* 5.8 2.3 - - - +
105k GLU* 5.4 2.7 - - - +
106k TYR* 3.6 21.1 - - - +
109k ARG* 2.8 28.0 + - - +
66s TYR* 2.9 59.9 + - + +
69s ARG* 1.3 82.9 - - - +
71s LYS* 1.3 74.6 + - - +
72s GLU* 3.0 11.2 + - + +
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Residues in contact with LYS 71 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105k GLU* 4.4 16.2 - - - +
65l GLU* 4.0 29.9 - - - +
228l MET* 5.6 6.7 - - - +
67s GLU* 3.0 16.7 + - - -
68s LEU 4.1 11.2 - - - +
69s ARG 4.2 4.9 - - - +
70s ASN* 1.3 80.4 - - - +
72s GLU* 1.3 59.6 + - - +
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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