Contacts of the helix formed by residues 70 - 101 (chain R) in PDB entry 6CMO
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 THR 70 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 5.2 5.1 + - - -
68R LEU 3.6 1.1 + - - +
69R ARG* 1.3 75.7 - - - +
71R PRO* 1.3 77.9 - - - +
72R LEU* 3.6 25.1 - - + +
73R ASN* 3.2 46.2 + - - +
74R TYR* 3.2 20.7 + - - -
148R PHE* 5.4 3.8 - - - -
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Residues in contact with PRO 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R THR* 1.3 90.5 - - - +
72R LEU* 1.3 61.4 + - + +
74R TYR* 3.5 28.8 - - + +
75R ILE* 3.9 5.1 + - - +
134R GLU* 5.5 4.9 - - - +
148R PHE* 4.5 23.6 - - + -
149R GLY* 4.1 28.0 - - - +
150R GLU* 4.9 12.3 - - + +
153R ALA* 4.1 18.3 - - + +
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Residues in contact with LEU 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 5.0 12.6 - - - +
351A CYS* 4.1 27.8 - - + +
70R THR* 3.6 24.7 - - + +
71R PRO* 1.3 74.8 - - + +
73R ASN* 1.3 64.6 + - - +
74R TYR 3.1 2.0 - - - -
75R ILE* 3.0 28.2 + - - +
76R LEU* 3.0 25.2 + - + +
131R LEU* 5.1 7.7 - - + +
134R GLU* 3.8 29.3 + - - +
135R ARG* 5.1 14.1 - - + +
138R VAL* 6.4 1.1 - - + -
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Residues in contact with ASN 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R LEU* 2.5 30.4 + - - +
69R ARG* 5.0 1.8 - - - -
70R THR* 3.2 25.4 + - + +
72R LEU* 1.3 76.1 - - - +
74R TYR* 1.3 60.1 + - - +
75R ILE 3.3 0.2 - - - -
76R LEU* 3.3 27.0 - - + +
77R LEU* 2.9 36.1 + - + +
310R ASN* 5.3 2.7 + - - +
312R GLN* 5.7 1.2 + - - -
313R PHE* 3.4 34.0 - - + -
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Residues in contact with TYR 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ARG* 4.9 16.9 - - + +
70R THR 3.2 33.1 + - - -
71R PRO* 3.5 19.5 - - + +
72R LEU 3.1 0.6 - - - -
73R ASN* 1.3 76.5 - - - +
75R ILE* 1.3 59.4 + - + +
77R LEU* 3.4 24.0 - - + +
78R ASN* 2.9 29.3 + - - +
150R GLU* 5.7 9.0 - - + -
153R ALA* 5.4 7.2 - - + -
157R VAL* 5.1 8.9 - - + +
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R PRO 4.2 11.7 - - - +
72R LEU* 3.0 12.6 + - + +
74R TYR* 1.3 76.8 - - + +
76R LEU* 1.3 59.8 + - + +
78R ASN* 3.2 8.2 + - - +
79R LEU* 3.0 27.2 + - - +
127R SER* 4.0 20.3 + - - +
130R VAL* 4.2 29.4 - - + +
131R LEU* 4.5 15.7 - - + -
134R GLU* 4.3 29.6 - - + +
153R ALA* 5.0 15.7 - - + +
156R GLY* 6.1 1.3 - - - -
157R VAL* 4.9 14.4 - - + +
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Residues in contact with LEU 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R LEU* 3.0 27.5 + - + +
73R ASN* 3.3 27.6 - - + +
75R ILE* 1.3 78.7 - - + +
77R LEU* 1.3 56.6 + - - +
79R LEU* 3.3 14.6 + - + +
80R ALA* 3.0 26.3 + - - +
131R LEU* 4.0 31.0 - - + -
135R ARG* 5.1 7.9 - - - +
306R TYR* 4.5 20.9 - - + +
307R ILE* 4.8 18.3 - - + +
309R MET* 5.9 2.0 - - + -
310R ASN* 6.4 1.6 - - + -
313R PHE* 5.1 7.0 - - + -
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Residues in contact with LEU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R THR* 6.0 2.0 - - + -
62R THR* 4.7 28.5 - - + +
69R ARG* 6.5 0.9 - - + -
73R ASN* 2.9 27.8 + - + +
74R TYR* 3.4 31.2 - - + +
76R LEU* 1.3 72.6 - - - +
78R ASN* 1.3 65.9 + - + +
80R ALA* 4.2 6.3 - - - -
81R VAL* 2.9 47.3 + - + +
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Residues in contact with ASN 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R TYR 2.9 19.6 + - - +
75R ILE* 3.2 9.3 + - + +
77R LEU* 1.3 79.2 - - + +
79R LEU* 1.3 54.3 + - - +
81R VAL* 4.5 5.1 - - - +
82R ALA* 2.8 46.0 + - - +
127R SER* 5.6 3.0 + - - +
157R VAL* 3.4 41.4 + - + +
160R THR* 5.2 6.5 - - - +
161R TRP* 3.6 30.7 + - - +
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Residues in contact with LEU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R ILE 3.0 9.1 + - - +
76R LEU* 3.5 16.8 - - + +
78R ASN* 1.3 74.8 - - - +
80R ALA* 1.3 61.4 + - + +
82R ALA* 4.0 2.5 - - - +
83R ASP* 3.0 35.7 + - + +
123R ILE* 4.9 5.1 - - + +
124R ALA* 4.1 25.4 - - + +
127R SER* 3.5 34.0 + - - +
128R LEU* 5.5 9.9 - - + +
302R ASN* 5.1 9.6 - - + -
303R PRO* 4.9 23.3 - - + -
306R TYR* 5.3 11.4 - - + -
307R ILE* 6.0 4.7 - - + -
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Residues in contact with ALA 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ASN* 4.7 5.1 - - - +
58R THR* 3.9 28.3 - - + -
76R LEU 3.0 16.6 + - - +
77R LEU* 3.3 7.8 + - - +
79R LEU* 1.3 80.2 - - + +
81R VAL* 1.3 61.4 + - + +
83R ASP* 3.0 9.3 + - - +
84R LEU* 2.9 33.7 + - + +
303R PRO* 6.0 5.2 - - + -
307R ILE* 5.4 7.9 - - + -
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Residues in contact with VAL 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R THR* 6.1 1.1 - - + -
59R LEU* 3.8 28.9 - - + -
62R THR* 5.7 5.8 - - + +
77R LEU* 2.9 39.2 + - + +
78R ASN* 4.2 6.7 - - - +
80R ALA* 1.3 73.7 - - + +
82R ALA* 1.3 68.5 + - + +
84R LEU* 3.2 14.9 + - + +
85R PHE* 3.0 21.5 + - - +
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Residues in contact with ALA 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R ASN* 2.8 31.7 + - - +
79R LEU 4.0 1.6 - - - +
81R VAL* 1.3 79.5 - - - +
83R ASP* 1.3 61.0 + - - +
85R PHE* 3.0 16.8 + - - +
86R MET* 3.0 23.5 + - + +
123R ILE* 3.7 26.7 - - + -
161R TRP* 5.4 7.4 - - + +
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Residues in contact with ASP 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ASN* 5.6 4.9 - - - +
79R LEU* 3.0 27.4 + - + +
80R ALA* 3.3 5.8 - - - +
82R ALA* 1.3 75.0 - - - +
84R LEU* 1.3 57.7 + - - +
86R MET* 4.6 7.0 - - - +
87R VAL* 2.9 36.0 + - - +
91R PHE* 6.0 0.9 - - - -
123R ILE* 5.1 2.2 - - - +
299R ALA* 3.2 30.8 - - - +
300R ILE* 5.1 0.2 - - - -
302R ASN* 5.2 1.6 - - - +
303R PRO* 3.2 23.5 - - + +
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Residues in contact with LEU 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R PHE* 4.7 15.3 - - + -
55R ASN* 3.6 50.5 - - + +
58R THR* 5.9 0.7 - - - -
59R LEU* 4.9 16.2 - - + -
80R ALA* 2.9 34.1 + - + +
81R VAL* 3.2 20.0 - - + +
83R ASP* 1.3 75.3 - - - +
85R PHE* 1.3 62.5 + - - +
87R VAL* 3.3 7.2 - - + +
88R LEU* 3.0 47.8 + - + +
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Residues in contact with PHE 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R VAL 3.0 12.5 + - - +
82R ALA* 3.0 11.6 + - - +
84R LEU* 1.3 75.8 - - - +
86R MET* 1.3 79.7 + - - +
88R LEU* 3.9 4.8 - - - +
89R GLY* 3.1 21.5 + - - -
116R PHE* 3.5 33.5 - + - -
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Residues in contact with MET 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R ALA* 3.0 21.2 + - - +
83R ASP* 4.2 7.6 - - - +
85R PHE* 1.3 97.2 - - - +
87R VAL* 1.4 63.0 + - - +
90R GLY* 3.0 25.4 + - - +
91R PHE* 3.7 6.8 + - + -
116R PHE* 3.2 50.3 - - + +
117R ALA* 5.6 3.6 - - - -
119R LEU* 4.0 11.7 - - + -
120R GLY* 3.5 30.5 - - - +
123R ILE* 5.0 10.1 - - + -
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Residues in contact with VAL 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 5.3 14.6 - - + +
55R ASN* 5.0 11.4 - - - +
83R ASP* 2.9 32.6 + - - +
84R LEU* 3.3 13.7 - - - +
86R MET* 1.4 76.0 - - - +
88R LEU* 1.3 73.4 + - + +
91R PHE* 2.8 62.3 + - + +
92R THR* 3.4 2.9 + - - +
300R ILE* 6.0 9.0 - - + -
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Residues in contact with LEU 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 5.7 6.1 - - + -
52R PHE* 5.1 14.6 - - + -
84R LEU* 3.0 44.1 + - + +
85R PHE* 3.9 4.5 - - - +
87R VAL* 1.3 88.4 - - + +
89R GLY* 1.3 57.4 + - - +
92R THR* 2.2 48.0 + - + -
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Residues in contact with GLY 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R PHE 3.1 12.3 + - - -
88R LEU* 1.3 81.2 - - - +
90R GLY* 1.3 58.0 + - - +
92R THR* 3.5 2.0 + - - -
93R SER* 2.7 31.1 + - - -
113R GLN* 6.1 0.4 - - - -
116R PHE* 5.7 7.6 - - - -
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Residues in contact with GLY 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R MET* 3.0 12.8 + - - +
89R GLY* 1.3 75.1 - - - +
91R PHE* 1.3 67.2 + - - +
93R SER* 3.2 4.7 + - - -
94R THR* 3.0 29.9 + - - +
113R GLN* 4.0 25.6 + - - -
116R PHE* 5.0 9.4 - - - +
117R ALA* 5.4 4.9 - - - -
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Residues in contact with PHE 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R MET* 6.5 0.9 - - - -
48R ILE* 5.5 4.9 - - + -
83R ASP* 6.0 1.1 - - - -
86R MET* 3.7 7.4 + - + -
87R VAL* 2.8 46.3 + - + +
90R GLY* 1.3 80.6 - - - +
92R THR* 1.3 61.2 + - - +
94R THR* 2.3 29.4 + - + +
95R LEU* 2.9 13.2 + - - +
117R ALA* 4.9 19.7 - - + -
296R LYS* 3.5 57.0 - - + -
299R ALA* 4.4 14.8 - - + -
300R ILE* 5.5 3.4 - - + -
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Residues in contact with THR 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 3.8 26.9 - - + -
88R LEU* 2.2 43.3 + - + +
89R GLY* 3.5 3.3 + - - -
91R PHE* 1.3 74.1 - - - +
93R SER* 1.3 61.6 + - - +
95R LEU* 3.8 7.8 - - + +
96R TYR* 3.0 48.3 + - + -
----------------------------------------------------------
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Residues in contact with SER 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R GLY 2.7 25.8 + - - -
90R GLY 3.3 6.3 - - - -
91R PHE 3.2 0.2 - - - -
92R THR* 1.3 78.0 + - - +
94R THR* 1.3 56.2 + - - +
96R TYR* 3.4 1.9 + - - -
97R THR* 3.0 33.3 + - - +
105R PHE* 3.7 23.3 - - - -
109R GLY 5.9 0.2 - - - -
113R GLN* 3.7 26.0 - - - +
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Residues in contact with THR 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R MET* 5.1 13.3 - - - +
90R GLY 3.0 19.6 + - - +
91R PHE* 2.3 40.9 + - + +
93R SER* 1.3 74.8 - - - +
95R LEU* 1.3 57.7 + - - +
97R THR* 3.4 10.2 - - - +
98R SER* 2.9 31.6 + - - -
113R GLN* 3.3 17.9 - - - +
185R CYS* 4.7 6.0 - - - +
186R SER* 4.8 10.3 - - - +
296R LYS* 5.1 14.3 - - + +
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Residues in contact with LEU 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R ALA* 3.9 22.2 - - + +
44R MET* 4.1 16.8 - - + -
45R PHE* 4.2 25.4 - - + +
48R ILE* 5.2 10.1 - - + -
91R PHE 2.9 11.7 + - - +
92R THR* 3.8 9.4 - - + +
93R SER 3.3 0.2 - - - -
94R THR* 1.3 82.4 + - - +
96R TYR* 1.3 76.4 + - + +
98R SER* 2.8 23.4 + - - +
99R LEU* 2.9 27.6 + - + +
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Residues in contact with TYR 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92R THR* 3.0 31.9 + - + +
93R SER* 4.0 3.6 - - - +
95R LEU* 1.3 94.7 - - + +
97R THR* 1.3 58.7 + - - +
99R LEU* 3.0 18.2 + - + +
100R HIS* 3.0 26.9 + - - +
104R VAL* 5.3 0.6 - - - +
105R PHE* 4.1 20.2 - + + -
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Residues in contact with THR 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R SER 3.0 21.5 + - - +
94R THR* 3.4 8.1 - - - +
96R TYR* 1.3 77.5 - - - +
98R SER* 1.3 62.4 + - - +
100R HIS 3.7 0.9 + - - +
101R GLY 3.5 8.8 + - - -
102R TYR* 3.1 33.4 + - - +
103R PHE* 3.9 9.9 - - + -
104R VAL* 3.8 22.5 + - - +
105R PHE* 4.6 11.8 + - + +
113R GLN* 5.2 3.6 - - - +
185R CYS* 3.3 35.3 + - + +
----------------------------------------------------------
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Residues in contact with SER 98 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 5.2 8.9 - - - -
40R LEU* 6.2 2.9 - - - -
41R ALA* 4.0 24.4 - - - +
44R MET* 5.6 3.0 - - - +
94R THR 2.9 17.5 + - - -
95R LEU* 2.8 31.5 + - - +
97R THR* 1.3 76.9 - - - +
99R LEU* 1.3 64.0 + - - +
101R GLY* 3.3 12.9 + - - +
185R CYS* 4.8 14.4 - - - -
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Residues in contact with LEU 99 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R ALA* 6.0 1.3 - - - -
95R LEU* 2.9 26.9 + - + +
96R TYR* 3.0 22.6 + - + +
98R SER* 1.3 79.3 + - - +
100R HIS* 1.3 62.7 + - - +
101R GLY* 3.4 0.7 + - - -
----------------------------------------------------------
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Residues in contact with HIS 100 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R TYR* 4.8 2.3 + - - -
96R TYR 3.0 13.7 + - - +
97R THR 3.7 4.9 + - - +
98R SER 3.4 0.2 - - - -
99R LEU* 1.3 77.2 - - - +
101R GLY* 1.3 58.1 + - - +
102R TYR* 3.5 33.9 + + - +
104R VAL* 3.3 44.4 - - + +
----------------------------------------------------------
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Residues in contact with GLY 101 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R TYR* 4.1 26.8 - - - -
37R PHE* 4.3 15.4 - - - -
97R THR 3.5 4.9 + - - -
98R SER* 3.3 12.6 + - - -
99R LEU 3.2 4.4 - - - -
100R HIS* 1.3 77.5 - - - +
102R TYR* 1.3 64.2 + - - +
184R GLN* 5.4 0.5 + - - -
185R CYS* 4.8 6.8 - - - -
----------------------------------------------------------
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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).
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