Contacts of the helix formed by residues 90 - 114 (chain J) in PDB entry 2FRV
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 GLU 90 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ILE 3.8 1.4 + - - -
89J PRO* 1.3 72.0 - - - +
91J ASN* 1.3 58.1 + - - +
93J THR* 3.0 11.9 + - + -
94J LEU* 2.9 40.7 + - + +
431J LYS* 5.2 13.8 - - - +
435J ASN* 2.9 30.1 + - - +
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Residues in contact with ASN 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J PRO* 3.2 0.4 - - - +
90J GLU* 1.3 77.6 - - - +
92J ALA* 1.3 62.4 + - - +
94J LEU* 4.0 2.1 - - - +
95J MET* 3.1 26.2 + - - +
234J LEU* 4.7 3.6 - - - +
432J LEU* 3.7 21.8 - - + +
435J ASN* 2.8 34.5 + - - +
436J VAL* 4.1 10.1 - - - +
440J LYS* 2.8 26.9 + - - -
441J ASP* 3.5 16.6 - - - +
442J ASP 3.1 19.5 + - - +
443J LEU* 3.8 10.8 - - + +
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Residues in contact with ALA 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ILE* 4.2 7.9 - - + -
89J PRO* 2.6 17.1 + - + +
91J ASN* 1.3 73.9 - - - +
93J THR* 1.3 66.0 + - - +
96J ARG* 3.0 33.1 + - - -
227J GLY* 3.7 18.2 - - - -
228J CYS* 3.8 14.7 - - - -
443J LEU* 3.2 31.1 - - - +
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Residues in contact with THR 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ILE* 3.3 18.0 + - - +
89J PRO 3.0 7.0 + - - -
90J GLU* 3.0 13.6 + - + -
92J ALA* 1.3 79.9 - - - +
94J LEU* 1.3 65.5 + - + +
96J ARG* 3.4 2.6 + - - +
97J ASN* 3.2 27.6 + - - +
287J PRO 3.2 28.0 - - - +
288J THR* 4.4 11.6 + - - +
290J GLU* 2.8 33.9 + - - +
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Residues in contact with LEU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J GLU* 2.9 28.8 + - + +
91J ASN* 4.0 7.4 - - - +
92J ALA 3.4 0.2 - - - -
93J THR* 1.3 77.4 - - + +
95J MET* 1.3 51.9 + - - +
97J ASN* 3.2 9.7 + - - +
98J LEU* 2.9 39.1 + - - +
428J TRP* 4.0 40.3 - - + +
431J LYS* 3.9 22.7 - - + -
432J LEU* 3.8 31.2 - - + +
435J ASN* 3.9 21.3 - - - +
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Residues in contact with MET 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ASN 3.1 16.2 + - - +
92J ALA 4.3 2.0 - - - +
94J LEU* 1.3 73.9 - - - +
96J ARG* 1.3 61.1 + - - +
98J LEU* 3.5 10.6 + - + +
99J THR* 2.9 29.8 + - - -
213J PHE* 4.1 21.9 - - + +
222J PHE* 3.7 21.1 - - + -
228J CYS* 4.1 15.3 - - - -
230J ASN* 3.9 27.6 - - - +
233J SER* 3.7 15.7 - - - +
234J LEU* 3.5 32.5 - - + -
432J LEU* 4.4 6.5 - - + +
443J LEU* 4.2 7.6 - - + -
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Residues in contact with ARG 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J TYR* 2.6 31.6 + - - +
74J LEU* 4.1 13.6 - - + +
77J VAL* 3.5 24.5 - - - +
78J ARG* 4.1 18.4 - - - +
81J ASP* 2.8 26.2 + - - -
88J ILE* 3.7 19.2 - - - +
92J ALA* 3.0 26.9 + - - +
93J THR* 3.7 4.9 - - - +
95J MET* 1.3 74.6 - - - +
97J ASN* 1.3 59.3 + - - +
100J MET* 3.3 18.7 + - - +
222J PHE* 4.6 2.2 - - + -
223J THR* 4.1 12.4 - - + +
224J VAL 3.3 13.3 + - - -
227J GLY* 2.9 31.9 + - - -
228J CYS* 3.6 18.4 - - - -
290J GLU* 4.3 7.0 + - - +
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Residues in contact with ASN 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J ARG* 4.2 8.0 + - - -
93J THR* 3.2 18.7 + - - +
94J LEU* 3.4 12.2 - - - +
96J ARG* 1.3 76.2 - - - +
98J LEU* 1.3 65.4 + - - +
99J THR 3.2 0.4 - - - -
100J MET* 3.3 2.2 + - - +
101J GLY 2.9 18.2 + - - -
285J GLU* 4.8 0.2 - - - +
286J PHE* 3.6 27.7 + - + +
287J PRO* 3.4 40.6 + - - +
290J GLU* 4.9 0.3 - - - +
428J TRP* 3.3 40.7 - - + +
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Residues in contact with LEU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J LEU 2.9 20.6 + - - +
95J MET* 3.8 12.1 - - - +
96J ARG 3.5 0.2 - - - -
97J ASN* 1.3 79.7 - - - +
99J THR* 1.3 56.4 + - - +
101J GLY* 3.3 0.7 + - - -
102J ALA* 3.0 28.2 + - - +
213J PHE* 3.8 32.1 - - + -
242J PHE* 4.2 12.3 - - + -
425J VAL* 3.6 41.6 - - + +
428J TRP* 3.8 26.9 - - + +
429J LEU* 4.0 16.8 - - + +
432J LEU* 4.5 9.6 - - + -
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Residues in contact with THR 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J TYR* 3.8 35.8 - - + -
95J MET 2.9 19.9 + - - -
96J ARG 4.0 0.4 - - - -
97J ASN 3.2 0.4 - - - -
98J LEU* 1.3 77.7 - - - +
100J MET* 1.3 57.9 + - - +
102J ALA* 3.7 7.0 + - - +
103J GLN* 3.2 24.1 + - - +
210J MET* 4.0 29.9 - - + +
213J PHE* 3.3 23.7 - - - +
214J GLY* 4.7 0.4 - - - -
220J THR* 4.3 3.1 - - + -
222J PHE* 3.5 14.3 - - + -
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Residues in contact with MET 100 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J TYR* 3.8 9.8 - - + -
71J VAL* 3.6 30.3 - - + -
74J LEU* 3.6 18.2 - - + -
96J ARG 3.3 16.7 + - - +
97J ASN* 3.9 4.7 - - - +
98J LEU 3.2 0.4 - - - -
99J THR* 1.3 74.2 - - - +
101J GLY* 1.3 66.4 + - - +
103J GLN* 3.1 7.3 + - - +
104J TYR* 3.0 56.0 + - + -
285J GLU* 4.1 10.1 - - + +
286J PHE* 3.7 18.6 - - + -
459J VAL* 3.3 33.9 - - + -
460J ASN 4.5 3.4 - - - +
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Residues in contact with GLY 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J ASN 2.9 16.2 + - - -
98J LEU 3.8 1.3 - - - -
99J THR 3.3 0.2 - - - -
100J MET* 1.3 77.5 - - - +
102J ALA* 1.3 56.8 + - - +
104J TYR* 3.1 7.6 + - - +
105J MET* 3.0 30.5 + - - +
286J PHE* 3.9 13.7 - - - -
421J ALA* 4.7 4.5 - - - +
425J VAL* 3.8 21.3 - - - +
428J TRP* 4.4 0.9 - - - -
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Residues in contact with ALA 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J LEU 3.0 17.1 + - - +
99J THR* 3.9 5.6 - - - +
101J GLY* 1.3 77.6 - - - +
103J GLN* 1.3 58.9 + - - +
105J MET* 3.5 13.3 + - - +
106J HIS* 3.3 23.7 + - - +
206J ALA* 4.3 7.6 - - - +
209J ALA* 5.0 2.7 - - + -
210J MET* 4.0 30.2 - - + +
242J PHE* 4.8 12.8 - - + -
425J VAL* 4.4 2.4 - - - +
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Residues in contact with GLN 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J VAL 3.2 18.4 + - - +
68J CYS* 3.7 4.4 - - - +
69J THR* 3.7 23.6 - - - +
70J TYR* 4.8 2.0 - - + -
71J VAL* 4.1 11.9 - - + -
99J THR 3.2 14.1 + - - +
100J MET* 3.1 14.6 + - - +
102J ALA* 1.3 72.3 - - - +
104J TYR* 1.3 61.2 + - - +
106J HIS* 4.7 8.0 + - - +
107J ASP* 2.8 68.3 + - - +
210J MET* 3.5 27.6 - - + +
217J ASN* 4.3 2.1 - - - +
462J PRO* 4.0 12.1 - - + -
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Residues in contact with TYR 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J MET* 3.0 45.8 + - + -
101J GLY 3.1 7.2 + - - +
103J GLN* 1.3 73.0 - - - +
105J MET* 1.3 70.6 + - - +
106J HIS 3.2 0.3 + - - -
108J HIS* 3.2 35.4 + + - +
285J GLU* 3.9 11.3 - - - +
286J PHE* 4.2 16.6 - + - -
298J THR* 5.4 1.2 + - + -
417J GLN* 3.7 40.0 + - + +
418J CYS* 4.7 1.6 - - - -
421J ALA* 3.7 26.5 - - + -
460J ASN* 2.6 40.0 + - - -
461J ALA 4.1 1.9 + - - -
462J PRO* 4.0 20.2 - - + -
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Residues in contact with MET 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J GLY 3.0 13.2 + - - +
102J ALA* 3.5 15.5 - - - +
104J TYR* 1.3 83.4 - - + +
106J HIS* 1.3 57.4 + - - +
109J LEU* 3.4 25.2 + - - +
206J ALA* 5.0 3.6 - - + -
246J TYR* 4.0 29.8 - - + -
249J VAL* 3.4 31.6 - - + -
250J ARG* 3.7 18.2 - - - +
253J ILE* 3.4 18.7 - - + +
418J CYS* 4.0 14.9 - - - +
422J ALA* 4.1 27.1 - - + +
425J VAL* 4.5 6.7 - - - -
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Residues in contact with HIS 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLU* 4.0 6.3 - - - -
26I ARG* 3.4 36.9 + - - -
67J VAL 5.6 2.2 + - - -
102J ALA 3.3 14.2 + - - +
103J GLN* 3.9 13.7 + - - +
104J TYR 3.3 0.6 - - - -
105J MET* 1.3 74.6 - - - +
107J ASP* 1.3 71.1 + - - +
109J LEU* 3.4 5.8 + - - +
110J VAL* 2.9 36.1 + - + +
203J GLN* 3.1 48.8 + - + +
206J ALA* 3.6 20.8 - - + +
207J ALA* 3.8 9.8 - - + +
210J MET* 5.8 1.6 - - - -
217J ASN* 5.1 3.7 + - - +
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Residues in contact with ASP 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J VAL* 3.9 9.7 - - - +
68J CYS* 3.8 5.0 - - - -
103J GLN* 2.8 40.6 + - - +
104J TYR 4.2 0.7 - - - +
106J HIS* 1.3 85.0 + - - +
108J HIS* 1.3 51.8 + - - +
110J VAL* 3.2 4.1 + - - +
111J HIS* 2.8 33.0 + - - +
462J PRO* 3.4 21.4 - - + +
463J ARG* 2.8 45.7 + - - -
528J ASP* 4.5 1.7 - - - +
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Residues in contact with HIS 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J TYR* 3.2 25.3 + + + +
107J ASP* 1.3 74.1 - - - +
109J LEU* 1.3 59.3 + - - +
111J HIS* 3.7 4.9 - - - +
112J PHE* 3.0 30.7 + - - +
257J TYR* 3.7 10.0 + - + +
371J PRO* 4.1 1.6 - - + +
414J ARG* 3.5 32.0 + - + +
417J GLN* 2.8 47.1 + - + -
418J CYS* 3.1 37.6 - - + +
462J PRO* 3.6 20.4 + - + +
528J ASP* 4.8 4.9 - - - -
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Residues in contact with LEU 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J MET 3.4 19.5 + - - +
106J HIS* 3.5 5.4 - - - +
108J HIS* 1.3 74.8 - - - +
110J VAL* 1.3 68.2 + - + +
112J PHE* 3.4 1.6 + - - -
113J TYR* 3.3 47.2 + - + +
114J HIS* 4.8 1.4 + - - -
199J ALA* 4.6 5.2 - - + +
202J VAL* 3.8 32.8 - - + -
203J GLN* 4.4 15.5 - - + +
206J ALA* 5.2 1.1 - - + -
249J VAL* 4.8 8.1 - - + -
252J PHE* 3.4 30.3 - - + -
253J ILE* 4.3 11.2 - - + -
257J TYR* 4.2 16.1 - - + -
418J CYS* 4.8 0.2 - - - -
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Residues in contact with VAL 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLU* 4.6 16.8 - - - +
25I LEU* 5.4 9.0 - - + -
67J VAL* 6.4 0.7 - - + -
106J HIS* 2.9 33.8 + - + +
107J ASP* 3.8 3.8 - - - +
109J LEU* 1.3 77.4 - - - +
111J HIS* 1.3 64.8 + - - +
114J HIS* 3.1 43.9 + - + +
115J LEU* 3.5 16.0 + - + -
203J GLN* 3.5 37.7 - - + +
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Residues in contact with HIS 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG 5.4 0.9 - - - -
107J ASP* 2.8 19.9 + - - +
108J HIS* 3.7 5.4 - - - +
109J LEU 3.3 0.2 - - - -
110J VAL* 1.3 75.5 - - - +
112J PHE* 1.3 67.2 + - - +
115J LEU* 3.2 25.7 + - + +
116J HIS* 2.9 49.2 + + - +
414J ARG* 3.5 35.2 + - - -
463J ARG* 5.5 0.4 - - - +
525J HIS* 2.9 35.8 + - - +
528J ASP* 3.3 38.0 - - - +
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Residues in contact with PHE 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J HIS 3.0 13.4 + - - +
109J LEU 4.1 2.2 - - - +
111J HIS* 1.3 80.0 + - - +
113J TYR* 1.3 88.8 + + - +
116J HIS* 3.4 12.5 - - + +
117J ALA* 2.8 45.1 + - + +
120J TRP* 6.1 4.0 - + - -
257J TYR* 3.1 44.6 - + + +
260J ASP* 4.2 12.3 - - + -
261J LEU* 3.9 36.3 - - + -
264J VAL* 5.3 12.1 - - + -
411J THR* 5.0 9.9 - - + -
414J ARG* 6.0 0.2 - - - -
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Residues in contact with TYR 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J LEU* 3.3 33.9 + - + +
112J PHE* 1.3 104.2 - + - +
114J HIS* 1.3 78.3 + - + +
117J ALA* 3.5 18.7 + - + +
118J LEU 4.8 1.0 + - - -
192J ALA* 4.7 6.3 - - + -
195J HIS* 3.6 21.1 - - + -
196J TYR* 2.9 39.9 - - + -
199J ALA* 3.5 16.8 - - + -
252J PHE* 3.9 9.4 - + - -
256J VAL* 3.4 10.8 + - + +
257J TYR* 3.4 22.1 - - + -
260J ASP* 2.9 22.2 + - + +
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Residues in contact with HIS 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 6.3 1.2 - - + +
47I THR 4.6 1.2 - - - +
48I LEU* 4.5 22.5 - - + +
16J ARG* 3.6 18.8 - - - +
110J VAL* 3.1 41.5 + - + +
113J TYR* 1.3 82.4 - - + +
115J LEU* 1.3 67.0 + - + +
117J ALA 5.3 0.2 - - - -
118J LEU* 4.9 2.6 - - - +
196J TYR* 3.2 55.1 + + + +
199J ALA* 3.7 33.2 - - + +
200J LEU* 3.5 26.1 - - + +
203J GLN* 4.5 1.5 - - + +
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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