Contacts of the helix formed by residues 81 - 104 (chain l) 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 LEU 81 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10k PHE* 4.3 13.9 - - + -
14k GLY 5.5 1.1 - - - +
16k LEU* 4.1 26.9 - - + -
30l ALA* 4.8 12.6 - - + +
33l LEU* 6.5 0.7 - - - +
79l SER 4.1 0.6 + - - -
80l GLY* 1.3 76.5 - - - +
82l ILE* 1.3 63.9 + - - +
83l ALA* 3.2 3.6 - - + +
84l ASP* 3.0 29.3 + - - +
85l ALA* 3.2 10.3 + - - +
138l GLY* 4.0 29.1 - - - -
139l VAL* 4.1 6.2 - - - +
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Residues in contact with ILE 82 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152k THR* 4.5 22.4 - - + +
153k TYR* 6.4 2.9 - - + -
65l GLU 6.1 4.3 - - - -
66l LYS* 4.1 35.0 - - + +
78l MET* 4.9 19.1 - - + +
80l GLY 3.8 13.5 - - - +
81l LEU* 1.3 71.4 - - - +
83l ALA* 1.3 59.4 + - - +
85l ALA* 2.9 25.5 + - + +
86l LYS* 3.0 14.6 + - - +
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Residues in contact with ALA 83 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116k GLN* 3.3 28.4 - - + +
150k SER* 3.4 27.6 - - - +
151k GLY 4.1 18.4 - - - -
152k THR* 4.3 6.9 - - + +
81l LEU* 3.2 2.8 - - + -
82l ILE* 1.3 82.4 - - - +
84l ASP* 1.3 66.0 + - - +
86l LYS* 3.5 16.9 + - - +
87l THR* 3.9 2.6 + - - -
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Residues in contact with ASP 84 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16k LEU* 5.2 0.9 - - - +
116k GLN* 4.1 13.4 + - - +
119k THR* 5.1 1.0 + - - -
120k GLN* 3.7 9.2 + - - -
81l LEU* 3.0 23.5 + - + +
83l ALA* 1.3 79.8 - - - +
85l ALA* 1.3 63.0 + - - +
87l THR* 3.8 5.1 + - - -
88l LEU* 3.6 6.9 - - - +
135l ARG* 2.4 36.1 + - - -
137l PHE* 3.3 41.4 - - + -
138l GLY 4.0 17.0 - - - +
139l VAL* 4.7 2.2 - - + -
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Residues in contact with ALA 85 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78l MET* 3.6 30.5 - - + -
81l LEU 3.2 4.0 + - - +
82l ILE* 2.9 16.2 + - - +
84l ASP* 1.3 76.0 - - - +
86l LYS* 1.3 66.2 + - - +
87l THR 3.2 0.4 - - - -
88l LEU* 3.1 7.9 + - - +
89l ILE* 2.9 27.0 + - + +
139l VAL* 3.8 27.3 - - + +
141l LEU* 4.8 2.2 - - + -
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Residues in contact with LYS 86 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113k SER* 6.3 3.1 - - - -
78l MET* 5.5 1.1 - - - +
82l ILE* 3.0 10.9 + - - +
83l ALA* 3.7 13.7 - - - +
84l ASP 3.4 0.6 - - - -
85l ALA* 1.3 76.7 - - - +
87l THR* 1.3 61.3 + - - +
89l ILE* 3.9 11.4 - - - -
90l ASP* 4.1 10.1 - - - -
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Residues in contact with THR 87 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116k GLN* 3.5 28.7 + - - +
120k GLN* 4.3 1.4 + - - -
83l ALA 3.9 1.0 + - - -
84l ASP 3.8 9.0 + - - -
85l ALA 3.2 0.2 - - - -
86l LYS* 1.3 77.2 + - - +
88l LEU* 1.3 59.2 + - + +
90l ASP* 3.2 7.1 + - - +
91l LYS* 3.0 28.7 + - + +
119l LEU* 6.3 1.8 - - + -
133l MET* 4.6 13.5 - - + -
137l PHE* 4.2 14.6 - - + -
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Residues in contact with LEU 88 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84l ASP 3.6 10.3 - - - +
85l ALA* 3.1 6.6 + - - +
87l THR* 1.3 73.1 - - + +
89l ILE* 1.3 61.8 + - + +
91l LYS* 3.4 6.2 + - - +
92l ALA* 2.9 28.9 + - - +
116l VAL* 4.0 25.9 - - + +
119l LEU* 4.0 20.2 - - + +
137l PHE* 3.5 39.5 - - + -
139l VAL* 3.5 31.9 - - + -
141l LEU* 4.0 20.4 - - + -
143l PHE* 6.2 0.2 - - - -
156l MET* 4.7 5.2 - - - -
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Residues in contact with ILE 89 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68l VAL* 3.8 19.3 - - + -
70l ILE* 3.9 11.8 - - + +
76l CYS* 3.5 32.5 - - - -
78l MET* 4.0 18.2 - - + -
85l ALA 2.9 24.6 + - - +
86l LYS* 4.2 7.0 - - - -
88l LEU* 1.3 78.4 - - + +
90l ASP* 1.3 59.3 + - - +
92l ALA* 3.1 5.4 + - - +
93l ARG* 2.9 56.6 + - - +
141l LEU* 4.5 6.3 - - + -
143l PHE* 4.9 4.0 - - + -
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Residues in contact with ASP 90 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86l LYS 4.1 6.1 - - - -
87l THR* 3.2 12.4 + - - +
89l ILE* 1.3 80.8 - - - +
91l LYS* 1.3 62.4 + - - +
93l ARG* 3.2 15.7 + - - +
94l VAL* 3.0 38.5 + - - +
65s ILE* 5.2 2.1 - - - +
69s ARG* 3.6 42.6 + - - +
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Residues in contact with LYS 91 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87l THR* 3.0 17.5 + - + +
88l LEU 3.6 5.4 - - - +
90l ASP* 1.3 76.8 - - - +
92l ALA* 1.3 58.4 + - - +
94l VAL* 3.9 6.2 - - - +
95l GLU* 2.9 65.2 + - + +
115l ALA* 3.8 24.8 + - - +
116l VAL* 5.2 2.5 - - + +
118l ASN* 5.6 1.4 - - - +
119l LEU* 3.5 45.4 - - + +
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Residues in contact with ALA 92 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70l ILE* 3.9 26.5 - - + -
88l LEU 2.9 18.7 + - - +
89l ILE* 3.1 5.8 + - - +
91l LYS* 1.3 75.2 - - - +
93l ARG* 1.3 60.2 + - - +
95l GLU* 3.2 7.8 + - - +
96l THR* 2.9 32.7 + - - +
112l VAL* 4.2 6.9 - - + +
115l ALA* 6.1 0.2 - - - -
116l VAL* 3.8 22.7 - - + -
143l PHE* 4.7 1.8 - - + -
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Residues in contact with ARG 93 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68l VAL* 3.7 26.1 - - - +
69l GLU* 3.0 26.8 + - - +
70l ILE* 3.5 12.8 - - - +
89l ILE* 2.9 32.5 + - - +
90l ASP* 3.2 18.8 + - - +
92l ALA* 1.3 76.1 - - - +
94l VAL* 1.3 63.4 + - + +
96l THR* 2.5 25.8 + - - -
97l GLN* 3.0 13.9 + - + +
65s ILE* 5.3 9.9 - - + -
68s LEU* 3.2 58.2 + - + +
69s ARG* 3.6 12.6 - - - +
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Residues in contact with VAL 94 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90l ASP* 3.0 30.0 + - - +
91l LYS* 3.9 5.8 - - - +
93l ARG* 1.3 75.8 - - + +
95l GLU* 1.3 58.3 + - + +
97l GLN* 3.3 1.8 + - - +
98l ASN* 2.9 38.3 + - - +
61s ARG* 3.5 25.4 - - - +
65s ILE* 3.8 28.5 - - + -
69s ARG* 5.3 3.1 - - - +
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Residues in contact with GLU 95 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91l LYS* 2.9 54.4 + - + +
92l ALA* 3.3 8.1 - - - +
94l VAL* 1.3 76.7 - - + +
96l THR* 1.3 63.8 + - - +
98l ASN* 3.3 12.6 + - - +
99l HIS* 3.0 24.3 + - - +
107l MET* 4.0 20.0 - - + +
112l VAL* 6.0 0.7 - - - -
115l ALA* 4.1 15.4 - - + +
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Residues in contact with THR 96 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70l ILE* 3.7 19.9 + - + -
71l ASP* 4.2 18.5 - - + +
73l HIS* 5.5 0.7 - - + -
74l ILE* 5.3 2.0 - - + -
92l ALA 2.9 17.2 + - - +
93l ARG* 2.5 25.3 + - - -
95l GLU* 1.3 73.9 - - - +
97l GLN* 1.3 69.8 + - - +
99l HIS* 3.2 4.5 + - - +
100l TRP* 2.9 27.4 + - - +
106l THR* 5.4 0.2 - - - -
107l MET* 3.8 18.9 + - + +
112l VAL* 3.5 29.6 - - + -
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Residues in contact with GLN 97 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70l ILE 4.9 2.4 + - - -
71l ASP* 3.6 22.7 + - - +
93l ARG* 3.0 14.8 + - + +
94l VAL* 3.7 5.6 - - - +
96l THR* 1.3 94.8 + - - +
98l ASN* 1.3 57.6 + - - +
100l TRP* 3.4 26.7 + - - +
101l PHE* 2.9 27.9 + - - +
61s ARG* 4.1 19.9 - - + +
64s ARG* 3.2 36.2 - - + +
65s ILE* 3.9 21.8 - - + +
68s LEU* 5.0 5.8 - - + +
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Residues in contact with ASN 98 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94l VAL* 2.9 34.8 + - - +
95l GLU* 3.3 14.2 + - - +
97l GLN* 1.3 73.2 - - - +
99l HIS* 1.3 65.6 + - - +
101l PHE* 3.2 8.8 + - + +
102l THR* 3.0 30.8 + - - +
61s ARG* 2.4 39.7 + - - +
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Residues in contact with HIS 99 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95l GLU* 3.0 9.9 + - - +
96l THR 3.5 1.3 - - - +
98l ASN* 1.3 76.0 - - - +
100l TRP* 1.3 59.6 + - - +
102l THR* 4.8 0.4 - - - -
103l TYR* 2.8 54.1 + + - -
105l GLU* 3.3 40.1 + - + -
106l THR 3.9 6.9 + - - -
107l MET* 3.4 42.9 - - + +
108l THR* 5.4 2.5 - - + -
75t TYR* 3.6 20.4 - + - -
79t ASN* 3.8 15.2 + - - -
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Residues in contact with TRP 100 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71l ASP* 6.1 1.1 - - - +
96l THR 2.9 13.9 + - - +
97l GLN* 3.5 26.5 - - - +
98l ASN 3.3 0.2 - - - -
99l HIS* 1.3 79.1 + - - +
101l PHE* 1.3 72.6 + - - +
104l ASN* 2.8 36.8 + - - +
105l GLU* 3.6 30.0 + - - +
106l THR* 4.8 11.2 - - + -
37s ILE 5.3 4.0 - - - -
57s ARG* 3.0 30.1 + - + -
60s ALA* 3.5 30.7 - - + -
61s ARG* 3.7 27.8 - - + -
64s ARG* 5.7 1.3 - - + -
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Residues in contact with PHE 101 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97l GLN 2.9 17.7 + - - +
98l ASN* 3.4 10.5 - - + +
100l TRP* 1.3 87.2 - + - +
102l THR* 1.3 71.1 + - - +
54s PHE* 4.1 28.0 - + - -
57s ARG* 3.1 47.8 - - + +
58s LEU* 3.6 43.7 - - + -
61s ARG* 4.3 13.0 - - + -
94t THR* 4.0 20.2 - - + -
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Residues in contact with THR 102 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98l ASN* 3.0 18.1 + - - +
99l HIS* 4.8 0.2 - - - -
101l PHE* 1.3 87.3 - - - +
103l TYR* 1.3 93.1 + - + +
104l ASN 3.6 0.4 - - - -
57s ARG* 4.2 1.3 + - - -
71t ARG* 4.0 11.2 - - - +
90t ALA* 3.4 21.1 - - - +
91t MET* 3.4 10.9 + - - -
94t THR* 4.2 23.2 - - - +
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Residues in contact with TYR 103 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99l HIS* 2.8 44.3 + + + +
102l THR* 1.3 86.6 - - + +
104l ASN* 1.3 74.2 + - - +
105l GLU* 3.1 16.6 + - + +
71t ARG* 2.1 34.9 + - - -
75t TYR* 3.7 26.3 - + + +
83t MET* 3.2 37.9 - - + -
87t ALA* 3.4 33.4 + - + +
90t ALA* 4.5 0.4 - - - -
91t MET* 3.6 17.1 - - + -
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Residues in contact with ASN 104 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100l TRP* 2.8 27.5 + - - -
102l THR 3.6 1.0 - - - -
103l TYR* 1.3 82.0 - - - +
105l GLU* 1.3 59.8 + - - +
57s ARG* 3.0 31.9 + - - +
86t GLY 5.2 4.6 + - - +
90t ALA* 4.2 9.9 - - + -
130t TYR* 4.5 10.9 + - - -
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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