Contacts of the helix formed by residues 83 - 106 (chain h) 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 MET 83 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31h ALA* 3.8 17.9 - - - +
34h GLN* 5.7 3.1 - - + -
35h GLY* 5.9 2.0 - - - +
82h GLY* 1.3 69.6 - - - -
84h THR* 1.3 62.2 + - - +
85h ALA* 4.8 3.1 - - + +
86h ASP* 3.8 25.5 - - - +
87h SER* 2.7 31.9 + - - -
132h ARG* 4.1 9.2 - - - +
135h GLY* 2.6 38.9 + - - +
136h CYS* 4.2 0.2 - - - +
14n PHE* 4.1 17.5 - - - -
18n GLY 5.2 2.5 - - - +
19n ARG* 6.2 0.9 - - - -
20n VAL* 4.6 14.4 - - + +
23n VAL* 6.6 0.2 - - + -
154n SER* 6.4 2.2 - - - -
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Residues in contact with THR 84 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68h HIS* 5.3 10.4 - - + -
82h GLY 3.3 5.7 + - - -
83h MET* 1.3 71.8 - - - +
85h ALA* 1.3 66.3 + - - +
87h SER* 3.0 9.4 + - - -
88h ARG* 3.0 59.6 + - - +
156n VAL* 3.4 32.2 - - + +
158n TYR* 4.2 13.2 + - - +
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Residues in contact with ALA 85 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83h MET* 3.5 3.3 - - + +
84h THR* 1.3 79.8 - - - +
86h ASP* 1.3 65.8 + - - +
88h ARG* 3.1 8.0 + - - +
89h SER* 3.0 22.9 + - - -
117n MET* 5.0 1.0 - - - +
120n HIS* 3.6 17.0 - - + +
154n SER* 3.2 31.9 - - - +
155n GLY 3.9 21.1 - - - -
156n VAL* 4.1 4.6 - - + +
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Residues in contact with ASP 86 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83h MET* 3.5 23.1 + - + +
85h ALA* 1.3 77.9 - - - +
87h SER* 1.3 64.1 + - - +
89h SER* 3.2 3.2 + - - -
90h GLN* 2.9 25.1 + - - +
132h ARG* 2.6 31.2 + - - -
134h LEU* 3.4 13.5 - - + +
135h GLY 3.0 21.0 + - - +
136h CYS* 3.9 16.6 - - - -
120n HIS* 3.0 26.4 + - - -
123n THR* 4.9 0.3 + - - -
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Residues in contact with SER 87 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68h HIS* 6.1 1.6 - - - -
70h PHE* 5.5 1.8 - - - -
80h MET* 3.6 36.9 - - - +
81h THR 4.4 1.4 + - - -
82h GLY 4.1 5.5 + - - -
83h MET 2.7 20.5 + - - -
84h THR* 3.0 10.7 + - - -
86h ASP* 1.3 77.3 - - - +
88h ARG* 1.3 60.1 + - - +
90h GLN* 3.3 3.5 + - - +
91h VAL* 2.8 33.4 + - - +
136h CYS* 3.3 15.6 - - - +
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Residues in contact with ARG 88 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65h THR 4.6 6.7 + - - -
67h THR 4.5 11.9 + - - -
68h HIS* 6.1 2.0 - - - -
70h PHE* 3.7 30.8 - - + -
84h THR* 3.0 40.8 + - - +
85h ALA* 3.1 7.5 + - - +
87h SER* 1.3 75.5 - - - +
89h SER* 1.3 66.0 + - - +
91h VAL* 3.2 7.7 + - - +
92h GLN* 3.0 27.5 + - - +
113n ASP* 4.8 13.5 - - - -
117n MET* 3.9 8.7 - - + -
155n GLY 5.0 2.6 + - - -
156n VAL* 4.7 1.6 - - - +
157n SER* 3.6 29.6 + - - +
158n TYR* 3.7 27.3 + - - -
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Residues in contact with SER 89 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85h ALA 3.0 7.0 + - - -
86h ASP 3.3 7.6 - - - -
88h ARG* 1.3 77.7 - - - +
90h GLN* 1.3 64.1 + - - +
92h GLN* 3.2 6.2 + - - +
93h ARG* 3.1 21.2 + - - +
134h LEU* 4.5 7.4 - - - +
117n MET* 3.2 23.6 - - - +
120n HIS* 3.1 39.7 + - - -
124n LEU* 5.4 0.5 - - - +
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Residues in contact with GLN 90 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80h MET* 3.4 20.8 - - + +
86h ASP 2.9 16.3 + - - +
87h SER 3.7 3.8 - - - +
89h SER* 1.3 76.7 + - - +
91h VAL* 1.3 57.0 + - - +
93h ARG* 3.3 7.8 + - + +
94h ALA* 2.9 28.4 + - - +
118h ILE* 3.7 25.3 - - + +
122h SER* 3.4 25.4 + - - +
134h LEU* 4.1 16.6 - - + +
136h CYS* 3.5 21.6 + - - -
138h MET* 3.6 19.5 + - + +
154h CYS* 4.5 3.6 - - - -
155h ASP 5.3 4.0 + - - -
156h PRO* 6.2 1.2 - - - +
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Residues in contact with VAL 91 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70h PHE* 3.6 42.0 - - + -
72h ILE* 3.9 13.9 - - + -
78h CYS* 3.9 8.3 - - - -
80h MET* 3.7 17.7 - - + -
87h SER 2.8 19.5 + - - +
88h ARG* 3.5 11.0 - - - +
89h SER 3.2 0.2 - - - -
90h GLN* 1.3 73.6 - - - +
92h GLN* 1.3 67.7 + - - +
94h ALA* 3.1 3.5 + - - +
95h ARG* 2.9 43.8 + - - +
138h MET* 4.3 4.9 - - + -
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Residues in contact with GLN 92 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88h ARG 3.0 16.0 + - - +
89h SER 3.5 7.9 - - - +
91h VAL* 1.3 76.6 - - - +
93h ARG* 1.3 64.3 + - - +
95h ARG* 3.2 36.5 + - - +
96h TYR* 3.0 23.3 + - - +
113n ASP* 5.3 11.2 + - + +
114n ARG* 5.1 5.6 + - - -
117n MET* 4.2 26.9 - - + -
65o PHE* 3.9 14.9 - - - -
69o GLU* 3.4 27.6 + - - +
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Residues in contact with ARG 93 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89h SER 3.1 10.2 + - - +
90h GLN* 3.6 12.8 - - + +
92h GLN* 1.3 80.2 - - - +
94h ALA* 1.3 62.7 + - - +
96h TYR* 3.3 16.6 + - - +
97h GLU* 3.0 54.0 + - - +
117h ARG* 4.1 9.1 - - - +
118h ILE* 4.3 3.6 - - + -
121h ILE* 3.4 47.7 - - + +
125h TYR* 5.0 4.9 + - - -
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Residues in contact with ALA 94 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72h ILE* 4.0 14.4 - - + -
90h GLN 2.9 14.7 + - - +
91h VAL 3.1 7.6 + - - +
93h ARG* 1.3 76.6 - - - +
95h ARG* 1.3 63.9 + - - +
97h GLU* 3.3 2.8 + - - +
98h ALA* 2.9 24.6 + - - +
114h LEU* 3.7 15.0 - - + +
118h ILE* 3.6 21.7 - - + +
138h MET* 3.9 17.7 - - + -
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Residues in contact with ARG 95 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70h PHE* 5.0 7.3 - - - -
71h LYS* 2.8 32.1 + - - +
72h ILE* 3.7 29.9 - - + +
91h VAL* 2.9 31.7 + - - +
92h GLN* 3.3 34.9 - - - +
94h ALA* 1.3 78.8 - - - +
96h TYR* 1.3 61.9 - - - +
98h ALA* 3.2 3.5 + - - +
99h ALA* 3.0 25.1 + - - +
113n ASP* 5.5 2.6 + - - -
65o PHE* 3.8 17.7 - - + -
68o ILE* 3.4 30.1 + - + +
69o GLU* 3.5 21.6 + - - +
71o ASN* 5.6 2.2 - - - +
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Residues in contact with TYR 96 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92h GLN 3.0 17.1 + - - +
93h ARG* 3.6 17.3 - - - +
95h ARG* 1.3 78.6 - - - +
97h GLU* 1.3 72.1 + - - +
99h ALA* 3.8 0.5 - - - +
100h ASN* 3.0 48.3 + - + +
61o TYR* 3.2 29.3 + + - -
65o PHE* 3.6 25.8 - + + -
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Residues in contact with GLU 97 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93h ARG* 3.0 47.0 + - - +
94h ALA 3.3 4.7 + - - +
96h TYR* 1.3 86.8 - - - +
98h ALA* 1.3 56.6 + - - +
100h ASN* 3.7 13.5 - - - +
101h TRP* 3.0 27.2 + - - +
109h ILE* 4.2 5.2 - - + +
114h LEU* 4.5 8.5 - - + -
117h ARG* 3.0 57.3 + - + +
118h ILE* 4.6 2.7 - - + -
121h ILE* 4.0 5.1 - - + +
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Residues in contact with ALA 98 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72h ILE* 4.4 7.9 - - + +
73h THR* 4.0 22.9 - - + +
94h ALA 2.9 13.6 + - - +
95h ARG* 3.2 9.2 + - - +
97h GLU* 1.3 75.6 - - - +
99h ALA* 1.3 65.2 + - - +
101h TRP* 3.0 13.3 + - - +
102h LYS* 3.0 13.7 + - - +
109h ILE* 3.8 32.7 + - + +
114h LEU* 4.6 2.9 - - + +
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Residues in contact with ALA 99 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73h THR* 6.3 0.9 - - - -
95h ARG 3.0 16.3 + - - +
96h TYR 3.8 2.7 - - - +
98h ALA* 1.3 76.1 - - - +
100h ASN* 1.3 63.9 + - - +
102h LYS* 3.2 8.1 + - - +
103h TYR* 3.0 23.6 + - - +
61o TYR* 4.1 21.1 - - + +
65o PHE* 4.0 26.5 - - + +
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Residues in contact with ASN 100 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96h TYR* 3.0 42.2 + - + +
97h GLU* 3.7 17.6 - - - +
99h ALA* 1.3 77.3 - - - +
101h TRP* 1.3 62.0 + - - +
103h TYR* 3.2 7.6 + - - +
104h LYS* 3.0 58.7 + - - +
61o TYR* 4.1 13.9 + - + -
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Residues in contact with TRP 101 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97h GLU 3.0 16.4 + - - +
98h ALA 3.0 9.4 + - - +
100h ASN* 1.3 75.8 + - - +
102h LYS* 1.3 59.3 + - - +
104h LYS* 4.7 2.5 - - - -
105h TYR* 2.9 54.7 + + - +
107h TYR* 3.2 47.2 + - - -
108h GLU 4.0 0.8 + - - -
109h ILE* 3.5 37.0 - - + +
110h PRO* 3.9 14.6 - - + -
113h MET* 3.9 24.9 - - + -
66p HIS* 3.2 26.9 - + - -
70p THR* 3.8 18.4 - - + -
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Residues in contact with LYS 102 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98h ALA 3.0 8.6 + - - +
99h ALA* 3.2 9.6 + - - +
101h TRP* 1.3 80.0 - - - +
103h TYR* 1.3 58.8 + - - +
106h GLY* 2.9 35.9 + - - -
107h TYR* 3.6 17.0 - - - +
108h GLU* 3.7 40.6 - - - +
109h ILE 5.5 0.2 - - - +
81p ARG* 3.0 18.8 + - - +
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Residues in contact with TYR 103 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99h ALA 3.0 15.2 + - - +
100h ASN* 3.6 9.4 - - - +
102h LYS* 1.3 80.7 - - - +
104h LYS* 1.3 65.6 + - + +
54o ALA 5.3 1.0 + - - -
57o ASP* 3.8 44.8 - - + +
58o ALA* 4.0 14.5 - - - +
61o TYR* 4.0 37.0 - + + -
81p ARG* 3.4 17.8 + - - +
85p GLN* 3.3 37.2 + - - +
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Residues in contact with LYS 104 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100h ASN* 3.0 46.5 + - - +
101h TRP* 3.8 2.7 - - - +
103h TYR* 1.3 83.9 - - + +
105h TYR* 1.3 98.6 + - + +
81p ARG* 3.5 17.7 - - - +
82p MET* 4.4 9.0 + - - +
85p GLN* 4.7 10.3 + - - +
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Residues in contact with TYR 105 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101h TRP* 2.9 51.1 + + - +
104h LYS* 1.3 112.6 + - + +
106h GLY* 1.3 63.7 + - - +
107h TYR* 3.4 13.6 + - + -
66p HIS* 3.0 34.4 + + - -
77p VAL* 4.0 2.2 - - - +
78p THR* 2.9 49.6 + - + +
81p ARG* 4.6 1.1 - - - -
82p MET* 3.3 34.5 - - + -
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Residues in contact with GLY 106 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102h LYS* 2.9 32.1 + - - -
104h LYS 3.7 0.8 - - - -
105h TYR* 1.3 78.1 - - - +
107h TYR* 1.3 59.7 + - - +
77p VAL* 4.0 21.4 - - - +
81p ARG* 3.2 22.4 + - - +
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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