Contacts of the helix formed by residues 88 - 112 (chain A) in PDB entry 3W5D
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 PHE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.7 33.9 - + - -
76A ALA* 3.1 37.5 - - + -
77A TRP* 3.7 30.7 - + - -
84A THR* 3.5 27.9 + - - +
87A ALA* 1.3 78.0 - - + +
89A VAL* 1.3 67.7 + - - +
90A GLU 3.4 1.6 - - - -
91A PRO* 3.4 13.9 - - + +
92A PHE* 3.2 22.7 + - - +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR 5.0 0.6 + - - +
85A ILE 3.5 25.8 - - - +
86A THR* 4.1 11.9 - - - +
87A ALA 3.3 0.6 - - - -
88A PHE* 1.3 79.2 - - - +
90A GLU* 1.3 67.4 + - - +
92A PHE* 3.2 4.6 + - - +
93A VAL* 2.8 42.0 + - + +
790A VAL* 4.6 9.0 - - + -
956A ILE* 3.9 37.0 - - + +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 2.8 25.9 + - - +
87A ALA 4.2 5.5 + - - +
89A VAL* 1.3 77.2 - - - +
91A PRO* 1.4 69.8 - - + +
93A VAL* 2.9 15.3 + - - +
94A ILE* 3.1 20.3 + - + +
300A VAL* 3.7 11.8 - - - +
788A ILE* 5.1 2.1 - - - +
789A PRO* 3.3 42.9 - - + +
790A VAL* 3.7 23.8 - - + +
793A LEU* 6.2 0.7 - - + -
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Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 4.0 8.5 - - - +
72A SER* 3.2 32.5 - - - +
73A PHE* 3.7 26.2 - - + +
76A ALA* 4.0 1.6 - - + -
87A ALA 3.7 7.0 - - - +
88A PHE* 3.4 37.0 - - + +
90A GLU* 1.4 95.4 - - + +
92A PHE* 1.3 59.5 + - - +
94A ILE* 3.5 6.0 + - + +
95A LEU* 3.1 24.4 + - - +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE 3.2 17.7 + - - +
89A VAL* 3.2 5.6 + - - +
90A GLU 3.1 0.6 - - - -
91A PRO* 1.3 76.4 - - - +
93A VAL* 1.3 59.0 + - + +
95A LEU* 3.1 14.7 + - + +
96A LEU* 2.8 60.1 + - + +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 2.8 39.8 + - + +
90A GLU* 2.9 9.4 + - - +
92A PHE* 1.3 75.3 - - + +
94A ILE* 1.3 62.7 + - - +
96A LEU* 3.4 7.8 + - - +
97A ILE* 3.1 29.9 + - + +
790A VAL* 4.7 14.6 - - + -
793A LEU* 3.6 26.7 - - + -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.6 27.8 - - + +
68A ALA* 4.5 6.1 - - + +
69A ALA* 3.6 34.3 - - + +
72A SER* 4.5 4.3 - - - -
90A GLU* 3.1 28.5 + - + +
91A PRO 3.8 6.3 - - - +
93A VAL* 1.3 75.0 - - - +
95A LEU* 1.3 63.0 + - - +
97A ILE* 3.4 7.9 + - + +
98A LEU* 3.2 23.4 + - + +
300A VAL* 4.6 3.6 - - + -
304A VAL* 4.2 21.8 - - + -
789A PRO* 5.2 0.7 - - + -
793A LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 6.5 0.9 - - + -
66A LEU* 5.6 9.9 - - + -
69A ALA* 4.7 8.7 - - + +
91A PRO 3.1 14.2 + - - +
92A PHE* 3.1 17.6 + - + +
94A ILE* 1.3 79.1 - - - +
96A LEU* 1.3 57.2 + - - +
98A LEU* 3.0 11.9 + - + +
99A ILE* 2.9 51.8 + - + +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 2.8 46.5 + - + +
93A VAL* 3.7 7.9 - - + +
95A LEU* 1.3 72.5 - - - +
97A ILE* 1.3 62.0 + - + +
99A ILE* 3.7 10.9 - - + +
100A ALA* 2.9 36.7 + - + +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 5.5 8.5 - - + -
93A VAL* 3.1 22.4 + - + +
94A ILE* 3.7 8.3 - - + +
95A LEU 3.3 0.2 - - - -
96A LEU* 1.3 80.8 - - + +
98A LEU* 1.3 65.1 + - + +
100A ALA* 3.8 6.2 - - - +
101A ASN* 2.9 28.5 + - + +
309A GLU* 5.4 9.9 - - + +
793A LEU* 3.8 34.3 - - + -
797A LEU* 3.7 31.9 - - + -
1002A PTY 4.0 18.8 - - + +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 4.1 19.4 - - + -
62A VAL* 3.9 34.1 - - + +
65A LEU* 4.1 22.0 - - + -
66A LEU* 3.6 47.1 - - + +
69A ALA* 5.4 0.7 - - + -
94A ILE* 3.2 15.0 + - + +
95A LEU* 3.0 14.1 + - + +
97A ILE* 1.3 82.6 - - + +
99A ILE* 1.3 58.1 + - - +
101A ASN* 3.4 10.8 + - + +
102A ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 5.5 4.5 - - + -
95A LEU* 2.9 40.4 + - + +
96A LEU* 3.7 10.3 - - + +
98A LEU* 1.3 73.2 - - - +
100A ALA* 1.3 55.2 + - - +
102A ALA* 3.3 5.1 + - - +
103A ILE* 2.6 59.1 + - + +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 2.9 24.1 + - + +
97A ILE* 3.8 6.3 - - - +
99A ILE* 1.3 76.2 - - - +
101A ASN* 1.3 57.6 + - - +
103A ILE* 3.5 10.7 - - - +
104A VAL* 2.9 38.0 + - + +
1002A PTY 4.9 15.7 - - + -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 3.9 16.9 + - - +
57A PHE* 6.2 0.2 - - - -
62A VAL* 3.5 29.6 - - - +
97A ILE* 2.9 21.1 + - + +
98A LEU* 3.4 14.4 + - + +
100A ALA* 1.3 78.6 - - - +
102A ALA* 1.3 57.2 + - - +
104A VAL* 3.4 2.6 + - - +
105A GLY* 3.0 24.6 + - - -
312A PRO* 5.7 4.2 - - - +
1002A PTY 4.3 37.4 + - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 4.9 7.0 - - + +
56A GLN* 3.5 32.2 - - + +
57A PHE* 4.0 17.9 - - + -
98A LEU 2.9 18.7 + - - +
99A ILE* 3.8 4.5 - - - +
101A ASN* 1.3 73.9 - - - +
103A ILE* 1.3 67.7 + - - +
105A GLY 3.3 0.5 + - - -
106A VAL* 3.1 26.3 + - + +
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 2.6 47.1 + - + +
100A ALA* 3.5 9.6 - - - +
102A ALA* 1.3 74.4 - - - +
104A VAL* 1.3 72.2 + - + +
106A VAL* 3.0 7.6 + - - +
107A TRP* 3.0 22.6 + - + +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA* 2.9 22.2 + - + +
101A ASN 3.8 3.8 - - - +
103A ILE* 1.3 79.6 - - + +
105A GLY* 1.3 65.4 + - - +
107A TRP* 2.9 24.6 + - + +
108A GLN* 2.9 23.9 + - + +
1002A PTY 3.9 60.6 - - + +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 2.9 29.9 + - - -
101A ASN 3.0 11.8 + - - -
103A ILE 3.3 0.4 - - - -
104A VAL* 1.3 78.0 - - - +
106A VAL* 1.3 60.4 + - - +
108A GLN* 3.4 19.3 - - - +
109A GLU* 3.4 13.5 + - - +
1002A PTY 4.6 8.5 + - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.8 22.9 - - + -
52A LEU* 3.7 30.8 - - + +
53A VAL* 4.1 26.0 - - + +
56A GLN* 4.3 5.4 - - + -
102A ALA 3.1 13.3 + - - +
103A ILE* 3.0 11.2 + - - +
105A GLY* 1.3 74.1 - - - +
107A TRP* 1.3 65.3 + - - +
108A GLN 3.2 0.4 - - - -
109A GLU* 3.2 4.0 + - - +
110A ARG* 3.1 24.6 + - + +
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Residues in contact with TRP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE* 3.0 15.5 + - + +
104A VAL* 2.9 18.5 + - + +
106A VAL* 1.3 77.3 - - - +
108A GLN* 1.3 77.3 + - + +
110A ARG* 3.8 12.8 + - - +
111A ASN* 3.3 45.3 + - + +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 2.9 23.3 + - + +
105A GLY* 3.4 12.4 - - - +
107A TRP* 1.3 89.7 - - + +
109A GLU* 1.3 57.9 + - + +
111A ASN* 3.3 5.4 + - - +
112A ALA* 3.1 26.9 + - - +
316A THR* 6.2 0.8 - - - +
1002A PTY 2.9 40.0 + - - -
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.4 36.0 + - + +
52A LEU* 3.5 39.4 - - + +
55A GLU* 4.3 2.9 - - - +
56A GLN* 5.5 0.7 - - - +
105A GLY 3.4 7.1 + - - +
106A VAL 3.2 2.0 + - - +
108A GLN* 1.3 75.2 - - + +
110A ARG* 1.3 65.4 + - - +
111A ASN 3.0 3.2 + - - -
112A ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 5.1 1.2 - - - +
106A VAL* 3.1 18.7 + - + +
107A TRP* 4.2 11.9 - - - +
108A GLN 3.5 0.2 - - - -
109A GLU* 1.3 75.5 - - - +
111A ASN* 1.3 73.7 + - - +
112A ALA 3.9 1.9 + - - +
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Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TRP* 3.3 57.8 + - + +
108A GLN* 3.3 6.8 + - - +
109A GLU 3.0 0.6 - - - -
110A ARG* 1.3 98.0 + - - +
112A ALA* 1.3 58.9 + - - +
113A GLU* 3.7 13.1 + - - +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLN 3.1 13.7 + - - +
109A GLU* 3.0 25.9 + - - +
110A ARG 4.7 2.1 - - - +
111A ASN* 1.3 78.1 - - - +
113A GLU* 1.3 61.8 + - - +
114A ASN 4.3 0.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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