Contacts of the helix formed by residues 79 - 102 (chain A) in PDB entry 1GQA
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 ASP 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ALA* 2.9 13.1 + - + +
76A ILE 3.6 4.3 - - - +
78A GLN* 1.3 81.0 - - + +
80A ALA* 1.3 65.8 + - - +
81A ASP* 3.7 4.7 + - - +
82A GLY* 2.8 32.8 + - - -
83A PHE* 3.0 22.0 + - - +
126A PHE* 4.0 14.2 - - + -
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ILE 3.7 10.4 + - - +
77A TRP* 4.3 6.8 + - - +
78A GLN 3.8 2.2 + - - -
79A ASP* 1.3 75.2 - - - +
81A ASP* 1.3 61.7 + - - +
83A PHE* 3.4 3.8 + - - +
84A GLN* 3.1 29.6 + - - +
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Residues in contact with ASP 81 (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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79A ASP* 3.1 4.5 + - - +
80A ALA* 1.3 79.8 - - - +
82A GLY* 1.3 63.9 + - - +
84A GLN* 3.6 5.6 + - - +
85A ALA* 3.2 21.8 + - - +
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Residues in contact with GLY 82 (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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79A ASP* 2.8 32.5 + - - -
81A ASP* 1.3 72.3 - - - +
83A PHE* 1.3 62.8 + - - +
85A ALA* 3.4 7.8 + - - +
86A LYS* 3.1 28.5 + - - +
126A PHE* 3.9 7.6 - - - -
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Residues in contact with PHE 83 (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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58A TYR* 3.4 50.7 - + - -
76A ILE* 3.7 36.8 - - + +
79A ASP 3.0 16.4 + - - +
80A ALA* 3.7 5.2 - - - +
81A ASP 3.2 0.2 - - - -
82A GLY* 1.3 77.4 - - - +
84A GLN* 1.3 67.3 + - + +
86A LYS* 3.2 3.1 + - - -
87A GLY* 3.0 18.9 + - - -
122A CYS* 3.9 4.9 - - - -
126A PHE* 3.7 30.1 - + + -
131A HEC 3.8 35.6 - - + +
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Residues in contact with GLN 84 (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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80A ALA 3.1 16.1 + - - +
81A ASP* 4.3 6.3 - - - +
82A GLY 3.5 0.2 - - - -
83A PHE* 1.3 79.5 - - + +
85A ALA* 1.3 56.9 + - - +
87A GLY* 3.3 7.7 + - - +
88A MET* 2.7 39.0 + - - +
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Residues in contact with ALA 85 (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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81A ASP 3.2 14.3 + - - +
82A GLY* 3.5 11.4 - - - +
83A PHE 3.2 0.4 - - - -
84A GLN* 1.3 77.5 - - - +
86A LYS* 1.3 63.2 + - + +
88A MET* 3.3 6.7 + - - +
89A ALA* 3.0 24.4 + - - +
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Residues in contact with LYS 86 (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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82A GLY* 3.1 16.4 + - - +
83A PHE 3.2 4.7 + - - +
85A ALA* 1.3 76.4 - - + +
87A GLY* 1.3 61.5 + - - +
89A ALA* 3.4 7.1 + - - +
90A PHE* 3.2 21.5 + - - +
118A THR* 5.1 2.9 - - - +
121A SER* 2.7 44.0 + - - +
122A CYS* 4.2 23.3 - - + +
124A ASP* 5.5 0.8 - - - +
125A ASP* 2.7 32.4 + - - -
126A PHE* 4.0 12.6 - - + -
131A HEC 4.2 5.9 - - - +
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Residues in contact with GLY 87 (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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83A PHE* 3.0 14.1 + - - -
84A GLN* 3.6 10.3 - - - -
86A LYS* 1.3 75.4 - - - +
88A MET* 1.3 57.8 + - - +
90A PHE* 3.2 10.7 + - - +
91A PHE* 2.9 27.4 + - - +
131A HEC 3.9 16.4 - - - +
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Residues in contact with MET 88 (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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84A GLN* 2.7 28.0 + - - +
85A ALA* 3.3 7.4 + - - +
87A GLY* 1.3 72.1 - - - +
89A ALA* 1.3 64.5 + - - +
91A PHE* 3.2 11.1 + - + +
92A GLU* 3.0 51.0 + - + +
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Residues in contact with ALA 89 (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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85A ALA 3.0 16.9 + - - +
86A LYS* 3.8 8.3 - - + +
87A GLY 3.3 0.2 - - - -
88A MET* 1.3 75.9 - - - +
90A PHE* 1.3 62.7 + - - +
92A GLU* 3.4 7.8 + - - +
93A ALA* 3.0 24.4 + - - +
118A THR* 3.8 15.7 - - + +
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Residues in contact with PHE 90 (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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13A TYR* 4.6 14.1 - + - -
14A PHE* 6.1 2.0 - + - -
17A VAL* 4.2 23.8 - - + -
46A LEU* 4.8 5.4 - - + -
50A THR* 3.6 27.6 - - + -
86A LYS 3.2 3.5 + - - +
87A GLY* 3.2 12.1 + - - +
88A MET 3.1 0.4 - - - -
89A ALA* 1.3 78.2 - - - +
91A PHE* 1.3 67.2 + - + +
93A ALA* 3.0 11.8 + - - +
94A VAL* 3.0 33.2 + - + +
115A VAL* 4.3 1.3 - - + -
118A THR* 3.4 24.4 - - - +
131A HEC 3.5 62.1 - + + -
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Residues in contact with PHE 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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50A THR* 3.7 47.7 + - - -
51A LYS* 5.0 18.8 - - + -
87A GLY 2.9 12.8 + - - +
88A MET* 3.2 14.3 + - + +
90A PHE* 1.3 76.9 - - + +
92A GLU* 1.3 79.3 + - + +
94A VAL* 3.3 2.8 + - - +
95A ALA* 3.0 27.1 + - + +
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Residues in contact with GLU 92 (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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88A MET* 3.0 50.5 + - + +
89A ALA* 3.8 6.1 + - - +
91A PHE* 1.3 89.6 - - + +
93A ALA* 1.3 62.6 + - - +
95A ALA* 3.3 7.4 + - - +
96A ALA* 3.2 21.3 + - - +
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Residues in contact with ALA 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 ALA 3.0 17.5 + - - +
90A PHE 3.7 3.8 - - - +
92A GLU* 1.3 76.1 - - - +
94A VAL* 1.3 62.5 + - - +
96A ALA* 3.3 8.8 + - - +
97A LEU 3.1 15.9 + - - -
111A ALA* 4.8 1.9 - - - +
114A LYS* 4.2 9.6 - - + +
115A VAL* 3.6 40.6 - - + +
118A THR* 4.0 10.8 - - + +
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Residues in contact with VAL 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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43A ALA 4.9 0.8 - - - +
46A LEU* 3.9 18.6 - - + -
47A VAL* 3.8 36.7 - - + +
50A THR* 3.9 17.5 - - + +
90A PHE* 3.0 46.2 + - + +
91A PHE 3.7 4.3 - - - +
93A ALA* 1.3 76.4 - - - +
95A ALA* 1.3 64.4 - - - +
97A LEU* 2.9 25.2 + - + +
98A GLU 3.5 3.1 + - - -
115A VAL* 4.3 12.3 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.6 9.6 - - - +
91A PHE* 3.0 20.3 + - + +
92A GLU* 3.5 13.5 - - - +
94A VAL* 1.3 78.2 - - - +
96A ALA* 1.3 60.4 + - - +
97A LEU 3.3 0.3 + - - -
98A GLU* 3.4 6.5 + - - +
99A PRO* 3.3 16.5 - - - +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLU 3.2 8.5 + - - +
93A ALA* 3.6 11.2 - - - +
94A VAL 3.2 0.8 - - - -
95A ALA* 1.3 76.9 - - - +
97A LEU* 1.3 65.6 + - - +
98A GLU 3.2 0.9 + - - -
99A PRO* 3.3 19.2 - - - +
100A ALA* 3.6 11.8 + - - +
111A ALA* 4.6 5.5 - - + +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 5.3 1.8 - - + -
24A LEU* 3.6 26.2 - - + -
43A ALA* 4.3 11.4 - - + +
46A LEU* 3.9 19.1 - - + -
93A ALA 3.1 11.0 + - - +
94A VAL* 2.9 19.5 - - + +
96A ALA* 1.3 79.2 - - - +
98A GLU* 1.3 60.8 + - - +
100A ALA* 3.4 1.0 + - - +
101A ALA* 3.0 21.3 + - - +
108A LEU* 4.0 20.2 - - + -
111A ALA* 3.7 28.7 - - + +
112A VAL* 4.1 11.9 - - + +
115A VAL* 4.1 15.0 - - + -
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Residues in contact with GLU 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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40A LYS* 4.9 5.2 - - - +
43A ALA* 4.2 19.3 - - + +
44A SER* 3.3 24.7 - - - -
47A VAL* 3.9 32.1 - - + +
94A VAL 3.5 1.0 + - - -
95A ALA* 3.4 7.6 + - - +
96A ALA 3.2 0.2 - - - -
97A LEU* 1.3 78.6 - - - +
99A PRO* 1.3 74.0 - - + +
101A ALA* 3.1 18.5 + - - +
102A GLY 4.2 1.4 + - - -
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Residues in contact with PRO 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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40A LYS* 5.9 0.2 - - - -
95A ALA 3.3 12.1 - - - +
96A ALA* 3.3 17.3 - - - +
98A GLU* 1.3 98.0 - - + +
100A ALA* 1.3 60.1 + - - +
101A ALA 3.4 0.3 + - - -
102A GLY* 3.7 7.4 + - - -
103A ALA* 4.0 10.0 + - - +
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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 ALA 3.6 14.8 - - - +
97A LEU 3.4 3.8 + - - +
98A GLU 3.1 0.2 - - - -
99A PRO* 1.3 82.8 - - - +
101A ALA* 1.3 65.1 + - - +
103A ALA* 2.9 21.5 + - - +
104A GLY 4.2 2.4 + - - -
107A GLU* 4.1 16.6 - - + +
108A LEU* 4.2 10.3 + - - -
111A ALA* 3.7 23.6 - - + -
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Residues in contact with ALA 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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24A LEU* 5.5 0.2 - - + -
34A TYR* 2.5 34.0 + - - -
36A ALA* 4.2 0.3 - - - -
39A ALA* 3.8 19.3 - - + +
40A LYS* 3.9 26.9 - - + -
43A ALA* 4.2 5.8 - - + -
97A LEU 3.0 13.7 + - - +
98A GLU 3.1 13.6 + - - +
100A ALA* 1.3 76.4 - - - +
102A GLY* 1.3 52.2 + - - +
108A LEU* 4.2 15.9 - - + +
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Residues in contact with GLY 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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34A TYR* 3.3 10.9 + - - -
36A ALA* 4.0 9.5 - - - +
40A LYS* 3.2 33.4 + - - +
98A GLU 4.2 0.4 + - - -
99A PRO 3.7 6.0 + - - -
100A ALA 2.9 2.4 + - - -
101A ALA* 1.3 75.0 - - - +
103A ALA* 1.3 58.5 + - - +
104A GLY 3.7 0.2 + - - -
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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