Contacts of the helix formed by residues 100 - 121 (chain D) in PDB entry 5JTO
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 ALA 100 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 2.9 21.8 + - + +
98D LEU 3.3 0.4 - - - -
99D GLY* 1.3 79.0 - - - +
101D TYR* 1.3 61.9 + - + +
102D CYS 3.6 1.3 - - - -
103D PRO* 3.4 4.7 - - - +
104D ASN* 3.2 27.1 + - - +
133D PHE* 4.1 11.1 - - - -
134D ASP* 3.4 46.9 - - - +
137D PHE* 5.6 1.6 - - + -
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASN* 2.8 30.4 + - - -
11D PHE* 3.5 36.8 - + - -
96D HIS* 6.4 1.1 - - + -
97D CYS* 3.0 37.7 + - - +
100D ALA* 1.3 73.9 - - + +
102D CYS* 1.3 65.4 + - - +
104D ASN* 3.2 11.6 + - + +
105D ILE* 3.2 43.6 + - + +
134D ASP* 5.7 0.7 - - - -
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Residues in contact with CYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 3.8 22.4 - - + -
58D VAL* 4.3 19.7 - - + -
84D PHE* 3.8 9.0 - - + -
86D ILE* 4.5 14.1 - - - -
89D ILE* 5.7 1.3 - - - -
94D MET* 5.9 1.1 - - - -
97D CYS* 3.0 39.9 + - - +
98D LEU* 3.9 10.1 - - - +
101D TYR* 1.3 74.9 - - - +
103D PRO* 1.4 64.3 - - + +
105D ILE* 3.5 21.9 + - - +
106D LEU* 3.6 13.5 - - - +
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Residues in contact with PRO 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D VAL* 4.9 4.6 - - + -
60D LEU* 3.8 30.9 - - + +
98D LEU 3.1 23.1 - - - +
99D GLY 3.6 16.6 - - - +
100D ALA 3.4 14.4 - - - +
102D CYS* 1.4 85.7 - - + +
104D ASN* 1.4 57.7 + - - +
105D ILE 3.2 0.9 - - - -
106D LEU* 3.3 13.9 + - + +
107D PHE* 3.0 30.3 + - - +
133D PHE* 4.7 12.2 - - + -
281G PHE* 4.2 9.0 - - + -
286G MET* 5.5 2.7 - - + -
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Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ALA 3.2 22.3 + - - +
101D TYR* 3.2 14.9 + - + +
103D PRO* 1.4 75.3 - - - +
105D ILE* 1.3 62.0 + - - +
107D PHE* 3.9 2.3 - - - +
108D PRO* 3.1 23.7 - - - +
131D VAL 4.5 5.5 + - - -
132D ASN* 5.7 1.4 - - - +
133D PHE* 3.7 29.1 - - + +
134D ASP* 5.8 2.7 + - - +
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN* 6.2 2.5 - - - +
130B PRO* 5.6 0.9 - - + -
132B ASN* 4.9 10.3 - - + +
11D PHE* 4.8 9.4 - - + -
13D ILE* 3.4 32.3 - - + -
16D ILE* 5.2 2.0 - - + -
84D PHE* 4.2 8.7 - - + -
101D TYR* 3.3 48.0 - - + +
102D CYS* 3.5 11.2 - - - +
103D PRO 3.2 0.4 - - - -
104D ASN* 1.3 81.9 - - - +
106D LEU* 1.3 63.9 + - + +
108D PRO* 3.3 12.5 - - - +
109D TYR* 3.5 21.7 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 4.6 13.2 - - + -
58D VAL* 3.2 35.4 - - + +
60D LEU* 3.8 22.7 - - + -
80D GLN* 3.5 30.4 - - + +
81D GLY 4.2 1.6 - - - +
82D GLY* 3.7 27.4 - - - +
84D PHE* 3.7 13.5 - - + -
102D CYS 3.6 15.5 - - - +
103D PRO* 3.3 8.2 + - + +
105D ILE* 1.3 77.2 - - - +
107D PHE* 1.3 59.7 + - - +
108D PRO 3.5 0.2 - - - -
109D TYR* 3.2 6.7 + - - +
110D ALA* 3.0 25.7 + - - +
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Residues in contact with PHE 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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42D LEU* 5.3 6.7 - - + -
44D LEU* 5.3 6.7 - - + -
60D LEU* 4.9 7.0 - - + -
62D VAL* 3.9 33.2 - - + -
103D PRO 3.0 17.2 + - - +
104D ASN* 3.9 5.8 - - - +
106D LEU* 1.3 77.6 - - - +
108D PRO* 1.4 63.5 - - + +
110D ALA* 3.7 5.2 - - - +
111D ARG* 2.9 49.2 + - + +
128D LEU* 3.7 33.2 - - + -
129D ALA 3.9 20.0 - - - -
130D PRO* 4.9 4.5 - - + -
131D VAL* 5.2 2.9 - - + -
133D PHE* 4.0 30.7 - + + -
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Residues in contact with PRO 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN* 4.3 18.6 - - - +
108B PRO* 3.7 23.0 - - + +
109B TYR* 4.9 0.2 - - - -
104D ASN 3.1 20.6 - - - +
105D ILE* 3.3 13.2 - - - +
107D PHE* 1.4 91.1 - - + +
109D TYR* 1.3 58.6 + - + +
111D ARG* 3.6 31.8 + - - +
112D GLU* 3.1 28.2 + - - +
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Residues in contact with TYR 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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104B ASN* 5.7 0.9 + - - -
107B PHE* 3.9 15.1 - + - -
108B PRO* 4.1 21.5 - - + -
111B ARG* 3.4 38.7 + - - -
129B ALA 5.0 0.2 - - - -
130B PRO* 3.4 31.0 - - + +
16D ILE* 4.1 28.8 - - + +
80D GLN* 3.4 31.1 + - - +
105D ILE* 3.5 28.7 - - + -
106D LEU* 3.2 6.3 + - - +
108D PRO* 1.3 77.9 - - + +
110D ALA* 1.3 65.9 + - - +
112D GLU* 3.6 10.5 + - - +
113D CYS* 3.2 19.9 + - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 4.6 4.5 - - + +
62D VAL* 3.8 26.9 - - + -
78D VAL* 4.2 8.6 - - + +
80D GLN* 3.7 23.9 - - + +
106D LEU 3.0 17.0 + - - +
107D PHE* 3.4 7.2 + - - +
109D TYR* 1.3 73.3 - - - +
111D ARG* 1.4 64.4 + - - +
113D CYS* 3.4 4.2 + - - +
114D ILE* 3.1 29.2 + - - +
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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
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16B ILE* 5.1 2.7 - - - -
105B ILE* 3.6 38.0 + - - +
109B TYR* 3.2 27.4 + - - +
62D VAL* 5.3 1.0 - - - +
107D PHE* 2.9 36.8 + - + +
108D PRO* 3.6 36.2 + - - +
110D ALA* 1.4 75.1 - - - +
112D GLU* 1.3 53.4 + - - +
114D ILE* 3.1 9.4 + - - +
115D THR* 2.7 35.2 + - - +
126D LEU 4.5 0.2 - - - +
127D ASN* 4.3 0.9 - - - +
128D LEU* 2.9 65.6 + - + +
130D PRO* 4.3 17.8 - - - +
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Residues in contact with GLU 112 (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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108B PRO* 3.6 31.9 - - + +
109B TYR* 3.8 24.6 - - + +
112B GLU* 3.5 24.9 - - - +
120C ARG* 2.9 41.1 + - - -
108D PRO 3.1 15.0 + - - +
109D TYR* 3.8 9.1 - - - +
111D ARG* 1.3 79.0 - - - +
113D CYS* 1.3 57.8 + - - +
115D THR* 3.1 9.4 + - - -
116D SER* 3.0 29.6 + - - -
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Residues in contact with CYS 113 (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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117C MET* 4.4 0.7 - - - -
120C ARG* 3.3 26.8 - - - +
18D THR* 3.6 10.3 - - + -
21D ILE* 3.5 34.8 - - - -
78D VAL* 3.6 27.1 - - + -
109D TYR 3.2 16.4 + - - +
110D ALA 3.6 4.9 - - - +
111D ARG 3.3 0.2 - - - -
112D GLU* 1.3 79.1 - - - +
114D ILE* 1.3 60.2 + - - +
116D SER* 4.3 1.7 - - - -
117D MET* 3.3 26.5 + - - +
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Residues in contact with ILE 114 (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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62D VAL* 3.5 44.2 - - + +
64D VAL* 3.7 21.8 - - + -
76D CYS* 3.6 28.0 - - + -
78D VAL* 3.5 16.2 - - + +
110D ALA 3.1 17.9 + - - +
111D ARG* 3.1 10.5 + - - +
113D CYS* 1.3 74.7 - - - +
115D THR* 1.3 64.7 + - - +
117D MET* 3.0 20.2 + - + +
118D VAL* 3.1 23.9 + - + +
126D LEU* 5.3 2.9 - - + -
128D LEU* 4.7 8.3 - - + -
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Residues in contact with THR 115 (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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109B TYR* 3.6 30.4 + - + -
111D ARG 2.7 23.1 + - - -
112D GLU 3.5 7.2 - - - -
114D ILE* 1.3 75.2 - - - +
116D SER* 1.3 60.7 + - - +
118D VAL* 3.6 2.1 + - - +
119D SER* 3.3 20.1 + - - -
125D GLN* 3.6 39.9 - - + +
126D LEU 2.8 29.7 + - - +
127D ASN* 3.9 4.9 - - - +
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Residues in contact with SER 116 (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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120A ARG* 5.0 1.6 + - - -
112B GLU* 3.3 9.4 + - - -
120C ARG* 3.0 33.9 + - - -
112D GLU* 3.0 16.9 + - - -
113D CYS 4.3 0.4 - - - -
115D THR* 1.3 73.8 - - - +
117D MET* 1.4 62.1 + - - +
119D SER* 2.7 21.5 + - - -
120D ARG* 3.1 38.2 + - - +
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Residues in contact with MET 117 (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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18C THR* 4.0 3.5 + - - -
21C ILE* 3.9 16.7 - - + +
117C MET* 3.8 17.7 - - + -
21D ILE* 3.1 24.7 - - + -
22D SER 4.0 7.2 - - - +
23D PHE* 3.4 34.8 - - + -
76D CYS* 3.4 24.7 - - + -
77D GLU 4.1 0.2 - - - +
78D VAL* 3.4 31.4 - - + -
113D CYS 3.3 14.5 + - - +
114D ILE* 3.0 7.9 + - - +
116D SER* 1.4 77.8 - - - +
118D VAL* 1.3 56.5 + - - +
120D ARG* 3.2 5.9 + - - +
121D GLY* 3.0 24.3 + - - -
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Residues in contact with VAL 118 (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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23D PHE* 4.1 7.9 - - - -
74D PHE* 3.8 26.0 - - + -
76D CYS* 3.5 20.2 - - - -
114D ILE* 3.1 24.4 + - + +
115D THR* 3.9 6.7 - - - +
117D MET* 1.3 74.3 - - - +
119D SER* 1.3 60.0 + - - +
121D GLY* 3.2 6.9 + - - -
123D PHE* 3.0 43.9 + - + +
124D PRO 3.1 28.3 - - - +
125D GLN* 4.1 3.4 - - - -
126D LEU* 4.6 6.5 - - + +
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 3.3 38.2 + - - -
125A GLN* 5.6 3.1 + - - +
115D THR 3.3 12.1 + - - -
116D SER* 2.7 25.6 + - - -
118D VAL* 1.3 78.4 - - - +
120D ARG* 1.4 57.5 + - - +
122D THR* 3.2 19.2 + - - +
123D PHE 3.6 11.2 + - - -
125D GLN* 4.3 14.2 + - - +
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Residues in contact with ARG 120 (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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116A SER* 5.5 0.7 - - - -
120A ARG* 3.4 19.0 - - - +
125A GLN* 5.2 2.0 + - - +
112B GLU* 3.9 0.4 + - - -
17C TYR* 3.5 7.4 - - - +
18C THR* 3.1 35.8 + - + +
21C ILE* 4.1 6.3 - - + -
109C TYR 5.2 0.6 + - - -
112C GLU* 3.0 41.2 + - - +
113C CYS* 3.4 40.3 - - - +
116C SER* 3.1 24.3 + - - -
117C MET* 5.7 3.4 - - - +
120C ARG* 4.9 0.6 - - - +
116D SER* 3.1 36.2 + - - +
117D MET* 3.2 8.5 + - - +
119D SER* 1.4 73.4 - - - +
121D GLY* 1.4 57.7 + - - +
122D THR* 3.1 9.8 + - - +
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Residues in contact with GLY 121 (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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17C TYR* 3.9 4.0 - - - +
18C THR* 3.2 23.5 + - - -
23D PHE* 3.7 12.6 - - - -
25D ALA* 6.0 0.2 - - - -
32D PHE* 3.5 8.7 - - - -
117D MET 3.0 10.1 + - - -
118D VAL 3.2 4.8 + - - -
120D ARG* 1.4 73.8 - - - +
122D THR* 1.4 70.1 + - - +
123D PHE* 3.2 21.7 + - - -
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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
------------------------------------------------------------
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