Contacts of the helix formed by residues 89 - 119 (chain J) in PDB entry 2QJK
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 GLY 89 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J VAL 2.9 2.6 + - - -
88J ASN* 1.3 73.2 - - - +
90J GLY* 1.3 64.9 + - - +
91J PHE* 3.3 22.6 - - - -
92J MET* 3.1 11.2 + - - +
93J LEU* 3.0 27.2 + - - +
33L PRO* 6.2 4.0 - - - -
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Residues in contact with GLY 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ILE* 3.1 34.4 - - - +
87J VAL* 2.8 18.5 + - - -
88J ASN 3.1 1.6 - - - -
89J GLY* 1.3 77.2 - - - +
91J PHE* 1.3 64.5 + - - +
93J LEU* 2.8 18.1 + - - +
94J ARG* 2.9 14.7 + - - +
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Residues in contact with PHE 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ILE 3.5 5.9 + - - -
84J MET* 3.5 35.5 + - + +
87J VAL 5.5 0.7 - - - -
89J GLY* 4.2 18.8 - - - -
90J GLY* 1.3 76.0 - - - +
92J MET* 1.3 109.4 + - + +
94J ARG* 3.8 1.0 - - - +
95J TYR* 3.3 30.7 + - + -
220K GLU* 5.6 2.5 - - - +
222K LYS* 3.2 39.7 - - + -
225K ALA* 3.9 10.5 - - + -
226K ARG* 3.5 37.7 - - + -
229K ALA* 5.1 3.1 - - + -
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Residues in contact with MET 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J GLY* 3.1 11.4 + - - +
90J GLY 3.1 0.6 - - - -
91J PHE* 1.3 117.2 - - + +
93J LEU* 1.3 60.0 + - + +
95J TYR* 4.2 2.5 - - + +
96J LEU* 3.2 40.6 + - + +
264J PHE* 5.7 7.9 - - - -
267J VAL* 4.5 21.8 - - - +
268J GLY* 5.5 1.3 - - - -
226K ARG* 3.5 23.6 - - + +
229K ALA* 4.3 17.3 - - + -
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Residues in contact with LEU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J THR* 4.1 24.7 - - + -
64J VAL* 3.4 30.3 - - + -
65J LEU* 4.1 15.2 - - + +
83J ILE* 6.2 0.2 - - + -
87J VAL* 5.2 2.0 - - + -
88J ASN 4.8 0.4 - - - +
89J GLY 3.0 20.0 + - - +
90J GLY* 2.8 12.7 + - - +
92J MET* 1.3 78.7 - - + +
94J ARG* 1.3 68.6 + - - +
96J LEU* 3.0 13.1 + - + +
97J HIS* 2.9 21.1 + - - +
33L PRO* 4.9 11.2 - - + +
34L LEU* 4.6 14.1 - - + -
37L GLN* 4.1 18.4 - - + -
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Residues in contact with ARG 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J LEU* 4.2 15.7 - - + +
77J PHE* 6.0 2.8 - - - -
80J VAL* 3.3 31.2 - - + +
81J GLU* 5.0 1.2 + - - -
83J ILE* 4.8 3.4 - - + -
84J MET* 3.5 44.3 - - + +
90J GLY 2.9 10.3 + - - +
93J LEU* 1.3 78.6 - - - +
95J TYR* 1.3 72.9 + - - +
97J HIS* 2.9 11.1 + - - +
98J ALA* 3.0 14.6 + - - -
150J PRO* 4.0 12.1 - - - +
279J ASN 5.8 1.8 + - - -
280J TYR* 4.2 21.9 + - - -
502J HEM 2.9 53.9 + - - +
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Residues in contact with TYR 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J MET* 3.5 20.4 - - + -
91J PHE* 3.3 22.0 + - + +
92J MET* 4.2 2.5 - - + +
94J ARG* 1.3 86.8 - - - +
96J LEU* 1.3 63.7 + - - +
98J ALA* 4.6 4.0 - - + -
99J ASN* 2.9 36.0 + - - +
267J VAL* 3.9 16.8 - - + -
271J PRO* 3.6 21.3 - - + -
272J ASN* 3.1 33.8 + - - -
280J TYR* 3.6 7.2 - - - -
105K LYS* 3.1 13.2 + - - -
220K GLU* 2.7 24.1 + - - -
226K ARG* 3.4 32.5 - - + -
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Residues in contact with LEU 96 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J LEU* 4.5 14.3 - - + +
58J GLN* 4.0 0.5 - - - +
61J THR* 4.4 13.9 - - + -
92J MET* 3.2 38.9 + - + +
93J LEU* 3.0 18.6 + - + +
95J TYR* 1.3 75.8 - - - +
97J HIS* 1.3 53.6 + - - +
99J ASN 3.8 0.2 - - - -
100J GLY* 2.7 33.6 + - - -
263J PHE* 3.4 38.1 - - + -
264J PHE* 4.1 23.8 - - + -
267J VAL* 4.0 15.5 - - + -
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Residues in contact with HIS 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN* 2.9 65.1 + - - +
61J THR* 3.2 20.4 + - - +
62J GLY* 3.8 7.2 + - - -
65J LEU* 3.6 21.8 - - + -
93J LEU 2.9 6.8 + - - +
94J ARG* 3.4 7.9 - - - +
96J LEU* 1.3 75.8 - - - +
98J ALA* 1.3 64.4 + - - +
101J ALA* 3.3 3.5 + - - +
502J HEM 2.0 85.9 + + + +
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Residues in contact with ALA 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J ARG* 3.0 17.8 + - - +
95J TYR* 3.9 7.9 - - + +
97J HIS* 1.3 73.5 - - - +
99J ASN* 1.3 61.4 + - - +
100J GLY 2.9 3.8 - - - -
101J ALA* 2.8 31.4 + - - +
102J SER* 3.5 3.9 + - - -
502J HEM 4.0 34.5 - - + +
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Residues in contact with ASN 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J TYR* 2.9 34.9 + - - +
98J ALA* 1.3 76.6 - - - +
100J GLY* 1.3 62.5 + - - +
101J ALA 3.2 0.2 - - - -
102J SER* 3.3 11.3 + - - -
103J LEU 3.0 19.4 + - - -
263J PHE* 3.6 24.7 - - + -
266J ILE* 4.1 15.6 - - + +
267J VAL* 4.3 10.7 - - + +
270J MET 4.7 0.2 - - - +
271J PRO* 3.2 43.1 + - - +
274J LEU* 4.2 16.6 - - + +
504J LOP 5.0 2.2 - - + +
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Residues in contact with GLY 100 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J CYS* 4.1 4.0 - - - -
57J LEU* 4.5 7.0 - - - -
58J GLN* 3.0 23.2 - - - +
96J LEU 2.7 16.3 + - - -
98J ALA 2.9 0.8 - - - -
99J ASN* 1.3 79.3 - - - +
101J ALA* 1.3 51.9 + - - +
103J LEU* 3.4 4.7 + - - +
104J PHE* 2.8 34.3 + - - +
263J PHE* 4.1 10.8 - - - -
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Residues in contact with ALA 101 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN* 3.4 4.6 + - - -
97J HIS 3.3 7.3 + - - +
98J ALA 2.8 12.3 + - - +
100J GLY* 1.3 73.2 - - - +
102J SER* 1.3 66.6 + - - +
104J PHE* 2.9 11.1 + - - +
105J PHE* 2.9 29.9 + - + -
143J ALA* 5.5 0.4 - - + -
297J TYR* 4.3 13.2 - - + +
502J HEM 3.9 39.9 - - + -
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Residues in contact with SER 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J ALA 3.5 5.3 + - - -
99J ASN* 3.3 11.1 + - - -
101J ALA* 1.3 77.5 - - - +
103J LEU* 1.3 64.3 + - - +
105J PHE* 3.0 3.5 + - - -
106J ILE* 2.9 29.2 + - - +
274J LEU* 3.3 39.2 + - - +
296J TRP* 3.4 27.0 + - - +
297J TYR* 4.3 8.5 - - - -
504J LOP 5.6 0.2 - - - -
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Residues in contact with LEU 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J TRP* 5.9 2.9 - - + -
50J VAL* 4.5 11.9 - - + -
53J PHE* 4.9 11.4 - - + -
54J CYS* 3.4 22.0 - - - -
57J LEU* 5.3 2.2 - - + -
99J ASN 3.0 12.9 + - - +
100J GLY 3.5 7.0 - - - +
102J SER* 1.3 75.2 - - - +
104J PHE* 1.3 63.7 + - - +
106J ILE* 3.3 11.0 + - + +
107J ALA* 3.0 24.2 + - + +
259J VAL* 4.1 24.0 - - + -
260J LEU* 4.9 2.0 - - + -
263J PHE* 4.2 29.8 - - + -
504J LOP 4.1 33.5 - - + +
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Residues in contact with PHE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J LEU* 3.4 36.9 - - + +
54J CYS* 3.5 16.8 - - + -
55J LEU* 4.2 27.8 - - + -
58J GLN* 4.3 9.0 - - + -
100J GLY 2.8 13.9 + - - +
101J ALA* 2.9 14.8 + - - +
103J LEU* 1.3 77.3 - - - +
105J PHE* 1.3 49.5 + - + +
107J ALA* 4.6 0.2 - - - -
108J VAL* 2.7 30.5 + - - +
139J MET* 3.5 34.1 - - + -
205J ILE* 5.2 1.1 - - + -
501J HEM 4.2 11.4 - - + -
502J HEM 4.0 42.4 - - + -
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Residues in contact with PHE 105 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J ALA* 2.9 22.4 + - + -
102J SER 3.7 4.3 - - - +
104J PHE* 1.3 73.6 - - + +
106J ILE* 1.3 70.2 + - - +
107J ALA 2.8 1.8 - - - -
108J VAL* 2.7 33.9 + - + +
109J TYR* 2.9 30.4 + + + -
136J TYR* 4.3 8.3 - + - -
139J MET* 4.0 20.9 - - + -
140J MET* 3.9 34.5 - - + -
143J ALA* 3.7 23.3 - - + -
296J TRP* 4.1 2.5 - - + -
297J TYR* 3.2 61.7 - + + -
502J HEM 5.5 3.1 - - + -
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Residues in contact with ILE 106 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J TRP* 5.4 4.5 - - + -
102J SER* 2.9 27.9 + - - +
103J LEU* 3.6 9.9 - - + +
105J PHE* 1.3 71.2 - - - +
107J ALA* 1.3 64.3 + - - +
109J TYR* 3.7 6.3 + - - +
110J LEU* 3.3 35.2 + - + +
274J LEU* 5.3 6.3 - - + -
296J TRP* 3.5 26.4 - - + -
504J LOP 4.1 45.3 - - + -
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Residues in contact with ALA 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J TRP* 4.2 24.4 - - + +
50J VAL* 4.5 14.4 - - + +
51J LEU* 3.5 19.7 - - + +
103J LEU* 3.0 16.9 + - + +
104J PHE* 3.5 8.1 - - - +
105J PHE 2.7 4.0 + - - -
106J ILE* 1.3 75.4 - - - +
108J VAL* 1.3 51.9 + - - +
110J LEU* 3.0 5.9 + - - +
111J HIS* 2.7 35.8 + - - +
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Residues in contact with VAL 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J LEU* 3.7 10.2 - - + +
104J PHE 2.7 22.2 + - - +
105J PHE* 2.7 32.5 + - + +
107J ALA* 1.3 73.4 - - - +
109J TYR* 1.3 53.4 + - + +
111J HIS* 3.3 5.7 - - - +
112J ILE* 2.5 41.1 + - + +
136J TYR* 4.5 11.4 - - + -
139J MET* 3.9 24.5 - - + -
501J HEM 3.9 30.1 - - + -
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Residues in contact with TYR 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J PHE* 2.9 37.0 + + + +
106J ILE* 4.1 4.9 - - - +
108J VAL* 1.3 76.6 - - - +
110J LEU* 1.3 58.8 + - + +
112J ILE* 3.5 12.1 - - + +
113J PHE* 2.8 44.2 + + + -
136J TYR* 2.7 42.9 + + - -
140J MET* 5.0 0.9 - - - -
296J TRP* 4.2 22.9 - + - -
297J TYR* 2.9 28.2 + - - -
300J PRO* 5.1 1.2 - - + +
301J PHE* 4.0 5.3 - + - -
374J PHE* 3.7 44.2 - + + -
504J LOP 4.9 9.9 - - + -
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Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J MET* 5.0 9.7 - - + +
47J TRP* 3.4 55.3 - - + +
106J ILE* 3.3 24.0 + - + +
107J ALA 3.0 8.1 + - - +
109J TYR* 1.3 76.6 - - + +
111J HIS* 1.3 64.3 + - - +
113J PHE* 4.2 2.6 - - - +
114J ARG* 2.9 26.7 + - - +
504J LOP 4.1 62.4 - - + +
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Residues in contact with HIS 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J MET 5.7 0.2 + - - -
47J TRP* 4.2 10.3 - - + +
48J GLY* 3.8 8.9 + - - -
51J LEU* 3.4 12.3 - - + -
107J ALA 2.7 17.5 + - - +
108J VAL* 3.3 10.5 - - - +
110J LEU* 1.3 73.5 - - - +
112J ILE* 1.3 62.4 + - - +
114J ARG* 3.4 20.7 + - - +
115J GLY* 3.2 16.8 + - - -
129J TRP* 5.8 0.2 - - - -
501J HEM 1.9 121.0 + + + +
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Residues in contact with ILE 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J VAL 2.5 22.6 + - - +
109J TYR* 3.5 17.7 - - + +
111J HIS* 1.3 70.2 - - - +
113J PHE* 1.3 75.2 + - + +
115J GLY* 2.9 13.0 + - - -
116J LEU* 3.0 32.1 + - + +
129J TRP* 4.3 9.0 - - + -
133J MET* 5.3 0.7 - - - -
136J TYR* 4.4 24.9 - - + -
343J MET* 4.3 32.3 - - + -
501J HEM 3.7 33.7 - - + -
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Residues in contact with PHE 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 2.8 29.8 + + + +
110J LEU 4.2 0.9 - - - +
112J ILE* 1.3 75.8 - - + +
114J ARG* 1.3 66.6 + - - +
116J LEU* 3.2 17.3 + - + +
117J TYR* 3.0 25.1 + - - +
367J PHE* 3.8 16.5 - + + -
370J LEU* 4.0 27.4 - - + -
371J ALA* 4.1 11.0 - - - -
374J PHE* 3.6 46.7 - + + -
400J TRP* 4.7 7.4 - + - -
504J LOP 3.5 54.7 - - + -
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Residues in contact with ARG 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J MET* 3.2 57.0 + - + +
45J TRP* 3.5 26.2 - - - -
110J LEU 2.9 22.2 + - - +
111J HIS* 3.4 21.3 + - - +
113J PHE* 1.3 76.4 - - - +
115J GLY* 1.3 77.0 + - - +
117J TYR* 3.4 0.3 + - - +
118J TYR* 3.1 35.7 + - + -
120J SER* 4.0 8.5 + - - -
501J HEM 2.8 67.9 + - - +
504J LOP 3.6 14.5 + - - +
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Residues in contact with GLY 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J HIS 3.2 6.4 + - - -
112J ILE 2.9 9.6 + - - -
114J ARG* 1.3 93.7 - - - +
116J LEU* 1.3 61.0 + - - -
118J TYR 3.2 0.9 + - - -
119J GLY 3.1 20.3 + - - -
120J SER* 3.1 21.4 + - - -
121J TYR* 3.6 7.8 - - - -
129J TRP* 4.6 8.1 - - - -
501J HEM 5.2 1.6 - - - -
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Residues in contact with LEU 116 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ILE* 3.0 26.9 + - + +
113J PHE* 3.2 32.7 + - + +
115J GLY* 1.3 73.9 - - - +
117J TYR* 1.3 60.9 + - - +
119J GLY 3.8 2.3 + - - -
121J TYR* 3.4 34.5 + - + +
129J TRP* 3.8 26.9 - - + -
343J MET* 4.8 5.6 - - + -
346J VAL* 4.1 14.6 - - + -
363J PHE* 3.6 11.5 - - - -
367J PHE* 4.0 11.4 - - + -
370J LEU* 4.3 13.5 - - + -
400J TRP* 6.0 0.7 - - + -
403J TYR* 4.9 5.7 + - + +
404J PHE* 4.4 15.3 - - + -
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Residues in contact with TYR 117 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE 3.0 10.6 + - - +
114J ARG 3.7 2.9 - - - +
116J LEU* 1.3 78.4 - - - +
118J TYR* 1.3 88.8 + + + +
119J GLY 3.5 0.4 - - - -
357J GLY* 3.1 28.6 + - - -
358J ARG* 3.5 28.6 - - - -
363J PHE* 4.3 7.0 - + - -
364J LYS* 3.6 21.6 + - + +
367J PHE* 3.3 47.1 - + + -
368J TRP* 4.2 17.4 + - - -
504J LOP 3.3 45.2 + - - +
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Residues in contact with TYR 118 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J ASN* 3.4 16.7 + - - -
44J MET* 4.8 2.5 - - + -
45J TRP* 3.8 20.9 - + + -
114J ARG* 3.1 41.8 + - + +
117J TYR* 1.3 104.3 - + - +
119J GLY* 1.3 62.8 + - - +
120J SER* 3.1 13.2 + - - +
222J ASN* 3.2 16.6 + - - +
223J ASN 4.4 0.7 - - - +
224J PRO* 3.4 44.4 - - + -
355J ARG* 3.8 15.0 - - - +
356J SER* 3.9 9.4 - - - +
357J GLY 4.1 2.7 - - - +
504J LOP 3.0 42.8 + - - -
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Residues in contact with GLY 119 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J GLY 3.1 5.6 + - - -
116J LEU 3.8 2.4 + - - -
117J TYR 3.5 3.4 + - - -
118J TYR* 1.3 77.0 - - - +
120J SER* 1.3 56.2 + - - +
121J TYR* 3.0 15.0 - - - -
122J LYS* 2.9 42.6 + - - +
355J ARG* 3.6 26.7 + - - +
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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