Contacts of the helix formed by residues 81 - 106 (chain D) in PDB entry 4O9U
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 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR* 6.0 0.9 - - - -
36C SER* 6.0 1.1 - - - +
82C VAL* 3.8 37.9 - - + +
85C ARG* 5.0 2.7 - - + +
86C MET* 3.3 32.3 - - + -
73D ALA 4.9 7.2 - - - +
76D VAL* 4.3 10.3 - - + +
77D ALA 4.0 6.7 - - - +
78D MET* 3.3 49.8 - - - +
79D THR 3.2 0.8 - - - -
80D ASP* 1.3 74.6 - - - +
82D PRO* 1.4 73.6 - - + +
83D GLN 3.3 2.5 - - - -
84D MET* 3.3 23.9 + - + +
85D VAL* 3.6 12.3 + - + +
337D MET* 4.3 4.0 - - + -
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Residues in contact with PRO 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR* 5.9 1.1 - - + -
35C MET* 5.2 3.4 - - - +
79D THR 3.4 10.8 - - - +
80D ASP 3.4 3.8 - - - -
81D MET* 1.4 92.4 - - - +
83D GLN* 1.3 75.9 + - - +
85D VAL* 3.5 15.0 + - + +
86D ALA 3.5 2.8 + - - -
139D LEU* 3.8 14.4 - - + -
204D PRO* 6.0 0.2 - - + -
207D ILE* 3.3 22.8 - - + +
336D ARG 4.9 0.4 - - - +
337D MET* 3.4 50.9 - - + -
338D PRO* 4.6 5.2 - - + -
340D HIS* 5.7 2.0 - - + -
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Residues in contact with GLN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ASP* 3.8 34.6 + - + +
82D PRO* 1.3 90.3 - - - +
84D MET* 1.3 59.9 + - + +
85D VAL 3.2 0.4 - - - -
86D ALA* 3.0 9.7 + - - +
87D ILE* 2.8 36.5 + - - +
136D PHE* 4.2 28.2 - - + +
139D LEU* 3.2 49.5 + - + +
140D GLN* 4.1 13.6 - - + +
207D ILE* 4.7 2.7 - - - -
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C VAL* 4.2 4.5 - - + -
72D ALA* 3.3 33.0 - - + +
73D ALA* 3.7 7.2 - - - +
76D VAL* 4.4 16.8 - - + -
80D ASP 3.6 19.1 - - - +
81D MET* 3.3 25.5 + - - +
83D GLN* 1.3 76.8 - - + +
85D VAL* 1.3 64.9 + - + +
87D ILE* 3.4 13.1 - - + +
88D TYR* 2.8 67.9 + - + +
136D PHE* 5.8 4.7 - - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR* 5.3 3.6 - - + +
35C MET* 3.6 37.7 - - + -
36C SER* 4.3 22.2 - - - +
39C ASN* 2.9 31.7 - - + +
82C VAL* 5.9 2.2 - - + -
86C MET* 6.2 1.3 - - + -
81D MET* 3.6 15.0 + - + +
82D PRO* 3.6 9.2 - - + +
83D GLN 3.2 0.2 - - - -
84D MET* 1.3 77.3 - - + +
86D ALA* 1.3 51.4 + - - +
89D ASN* 2.7 39.7 + - + +
207D ILE* 3.8 11.4 - - + -
211D ASN* 4.9 5.4 - - - +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PRO 3.5 0.8 + - - -
83D GLN* 3.0 14.5 + - + +
85D VAL* 1.3 79.1 - - - +
87D ILE* 1.3 52.1 + - - +
89D ASN* 3.2 6.9 - - - +
90D GLY 2.6 27.7 + - - -
132D SER* 2.9 34.3 + - - +
135D ALA* 4.8 5.4 - - + -
136D PHE* 5.0 1.6 - - - +
207D ILE* 3.7 35.2 - - + +
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D GLN 2.8 17.3 + - - +
84D MET* 3.4 26.2 - - - +
86D ALA* 1.3 71.4 - - - +
88D TYR* 1.3 70.1 + - + +
90D GLY* 3.1 2.5 + - - +
91D MET* 2.7 49.3 + - + +
132D SER 4.4 2.0 + - - -
133D LEU* 3.6 32.3 - - + -
136D PHE* 4.0 37.0 - - + -
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 3.3 23.3 - - - +
74C ALA* 3.2 24.9 - - + -
75C ASN* 3.0 23.3 + - - +
78C GLY* 3.1 29.6 - - - -
79C GLY* 3.9 0.9 - - - -
82C VAL* 3.7 15.7 - - + -
69D ALA* 3.4 16.6 + - + -
72D ALA* 4.2 3.4 - - + +
73D ALA* 3.3 16.6 + - - +
84D MET* 2.8 48.3 + - + +
87D ILE* 1.3 82.1 - - + +
89D ASN* 1.3 57.2 - - - +
90D GLY 3.0 1.6 - - - -
91D MET* 3.1 9.1 + - + +
92D GLY 2.9 30.3 + - - -
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 3.0 10.4 + - - +
42C HIS* 4.0 5.3 - - - -
85D VAL* 2.7 23.1 + - + +
86D ALA* 3.2 7.2 - - - +
88D TYR* 1.3 73.7 - - - +
90D GLY* 1.3 58.3 + - - +
93D GLY 3.3 9.0 + - - -
128D ALA 3.8 4.0 - - - +
132D SER* 3.3 7.5 + - - -
207D ILE* 2.9 33.7 + - - +
210D TYR* 3.1 16.7 - - - +
211D ASN* 3.1 22.4 - - - +
214D THR* 2.6 41.9 + - - +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ALA 2.6 16.2 + - - -
87D ILE 3.1 5.1 + - - -
88D TYR 3.0 0.2 - - - -
89D ASN* 1.3 73.4 - - - +
91D MET* 1.3 55.0 + - - +
93D GLY* 2.9 3.1 + - - -
94D GLY 2.7 32.2 + - - -
129D PHE* 2.9 35.3 - - - -
132D SER* 3.9 2.9 - - - -
133D LEU* 4.4 4.0 - - - -
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Residues in contact with MET 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 4.0 8.1 - - + +
71C LEU* 2.9 64.4 - - + +
74C ALA* 3.4 29.6 - - + -
75C ASN* 4.0 2.7 - - + -
68D VAL* 6.4 1.6 - - + -
87D ILE* 2.7 43.8 + - + +
88D TYR* 3.1 17.7 + - + +
90D GLY* 1.3 70.9 - - - +
92D GLY* 1.3 51.3 + - - +
94D GLY* 3.2 0.7 + - - -
95D ALA* 2.8 30.8 + - - +
129D PHE* 4.6 2.9 - - - -
133D LEU* 5.9 0.2 - - - -
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Residues in contact with GLY 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.8 18.6 - - - +
75C ASN* 3.3 23.2 - - - +
88D TYR 2.9 15.0 + - - -
91D MET* 1.3 71.9 - - - +
93D GLY* 1.3 56.6 + - - +
95D ALA* 3.3 2.3 + - - +
96D ALA* 2.8 30.0 + - - +
214D THR* 3.7 11.6 - - - +
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASN 3.3 11.4 + - - -
90D GLY 2.9 8.2 + - - -
92D GLY* 1.3 72.1 - - - +
94D GLY* 1.3 64.3 + - - +
96D ALA* 3.3 3.8 + - - +
97D ALA 3.0 16.8 + - - -
125D GLY* 2.9 32.6 - - - +
128D ALA* 4.7 0.9 - - - -
129D PHE* 3.6 4.5 - - - -
214D THR* 3.5 15.7 - - - +
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Residues in contact with GLY 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.6 13.0 - - - -
90D GLY 2.7 14.3 + - - -
91D MET 3.5 3.4 - - - -
93D GLY* 1.3 73.0 - - - +
95D ALA* 1.3 54.6 + - - +
97D ALA* 3.1 8.6 + - - +
98D THR* 3.0 31.0 + - - +
129D PHE* 3.2 27.0 - - - +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.7 25.8 - - + +
49C ALA* 4.8 0.7 - - - +
68C GLY* 3.2 28.7 - - - +
71C LEU* 3.6 2.3 - - + +
72C GLY* 3.8 5.2 - - - +
91D MET 2.8 15.7 + - - +
92D GLY 3.6 4.9 - - - +
94D GLY* 1.3 74.1 - - - +
96D ALA* 1.3 57.3 + - - +
98D THR* 2.5 24.1 + - - -
99D ILE* 3.3 16.8 - - - +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 4.0 11.4 - - + -
92D GLY 2.8 16.0 + - - +
93D GLY* 3.5 8.3 - - - +
94D GLY 3.1 0.4 - - - -
95D ALA* 1.3 74.2 - - - +
97D ALA* 1.3 63.9 + - - +
98D THR 3.1 2.3 + - - -
99D ILE* 3.4 13.7 + - + +
100D ALA 3.6 6.9 + - - -
121D GLY 5.1 0.9 - - - -
125D GLY* 4.3 1.6 - - - -
214D THR 5.1 0.2 - - - +
217D ALA* 4.0 28.5 - - + -
218D VAL* 4.4 10.5 - - + +
221D GLU* 3.7 18.2 - - + +
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Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLY 3.0 7.2 + - - +
94D GLY* 3.1 11.2 + - - +
96D ALA* 1.3 75.8 - - - +
98D THR* 1.3 57.8 + - + +
100D ALA* 3.5 2.0 + - - +
101D ALA* 3.1 20.3 + - - +
122D GLY* 4.0 13.0 - - - +
125D GLY* 3.8 0.6 - - - -
126D SER* 3.3 42.4 - - - +
129D PHE* 6.3 0.2 - - + -
184D PHE* 3.3 16.8 - - + -
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Residues in contact with THR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 4.7 2.8 - - - +
52C VAL* 5.6 2.2 - - - -
64C ILE* 3.6 39.0 - - + +
65C GLY* 5.4 2.0 - - - -
67C LEU* 4.9 2.2 - - + -
68C GLY* 3.7 17.2 - - - +
71C LEU* 4.5 4.9 - - + -
94D GLY 3.0 19.4 + - - +
95D ALA* 2.5 27.4 + - - -
97D ALA* 1.3 75.2 - - - +
99D ILE* 1.3 61.0 + - - +
100D ALA 3.2 0.2 - - - -
101D ALA* 3.0 21.0 + - - +
102D VAL* 3.1 20.4 + - - +
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 4.0 18.6 - - + -
48C GLY* 4.2 19.7 - - - +
49C ALA* 4.2 13.9 - - - +
52C VAL* 4.9 11.4 - - + -
95D ALA 3.3 18.2 - - - +
96D ALA* 3.4 8.6 + - - +
98D THR* 1.3 77.9 + - - +
100D ALA* 1.3 61.0 + - - +
102D VAL* 4.9 0.3 - - - +
103D GLU* 3.7 26.4 + - + +
218D VAL* 6.5 0.4 - - - -
221D GLU* 3.5 22.3 - - + +
225D VAL* 3.9 27.0 - - + +
230D LEU* 4.1 20.0 - - + -
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA 3.6 1.6 + - - +
97D ALA 3.5 9.8 + - - +
98D THR 3.2 0.4 - - - -
99D ILE* 1.3 79.8 - - - +
101D ALA* 1.3 58.4 + - - +
103D GLU* 4.0 1.7 + - - +
104D LEU* 3.2 33.9 + - + +
109D PHE* 5.9 0.2 - - - -
118D ALA* 3.3 18.3 - - - +
119D ILE* 5.0 2.7 - - - -
122D GLY* 3.7 14.4 - - - -
183D PHE* 6.2 0.2 - - + -
184D PHE* 4.1 8.1 - - + -
221D GLU* 3.2 27.6 + - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.6 20.0 - - + -
97D ALA 3.1 13.3 + - - +
98D THR* 3.0 13.7 + - - +
100D ALA* 1.3 76.7 - - - +
102D VAL* 1.3 64.9 + - + +
104D LEU* 3.5 11.1 + - - +
105D LEU* 3.6 19.5 + - + +
180D ILE* 4.7 4.6 - - + +
184D PHE* 3.6 24.2 - - + -
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Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 3.9 34.3 - - + +
55C HIS 5.9 0.9 - - - +
56C ALA* 5.3 3.1 - - + -
61C GLU* 4.1 42.6 - - + +
64C ILE* 4.5 13.0 - - + -
65C GLY* 4.4 16.6 - - - +
98D THR 3.1 15.2 + - - +
101D ALA* 1.3 71.7 - - + +
103D GLU* 1.3 59.3 + - - +
104D LEU 3.1 8.7 + - - -
105D LEU* 3.3 17.8 + - + +
106D LYS* 3.6 18.4 + - + +
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 3.4 29.7 - - + +
55C HIS* 5.1 6.4 - - - +
99D ILE* 3.7 17.0 + - + +
100D ALA 4.2 1.1 - - - +
101D ALA 3.4 0.6 - - - -
102D VAL* 1.3 76.6 - - - +
104D LEU* 1.3 59.8 + - - +
106D LYS* 4.4 20.7 - - - -
107D GLY 4.9 0.7 - - - -
108D ALA* 3.6 32.9 + - - +
109D PHE* 3.2 38.3 - - + -
225D VAL* 4.9 15.9 - - + -
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ALA* 3.2 26.4 + - + +
101D ALA 3.5 5.3 + - - +
102D VAL 3.1 0.8 - - - -
103D GLU* 1.3 82.7 - - - +
105D LEU* 1.3 62.4 + - - +
106D LYS 3.4 1.6 - - - -
107D GLY* 3.9 11.2 + - - +
109D PHE* 4.4 14.4 - - + -
115D MET* 3.8 29.6 - - + -
118D ALA* 5.3 1.8 - - + -
119D ILE* 3.8 31.6 - - + +
171D LEU* 4.8 13.5 - - + -
175D ASP* 4.3 14.2 - - + +
180D ILE* 3.4 33.5 - - + +
183D PHE* 5.8 2.7 - - + -
184D PHE* 5.0 6.1 - - + -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 5.0 7.9 - - + +
61C GLU* 3.7 36.0 - - + +
64C ILE* 4.8 16.8 - - + -
101D ALA* 3.6 17.0 + - + +
102D VAL* 3.3 9.8 + - + +
104D LEU* 1.3 78.9 - - - +
106D LYS* 1.3 58.6 - - - +
107D GLY 3.4 0.2 - - - -
177D THR* 3.8 33.0 + - + +
180D ILE* 4.0 16.8 - - + -
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C HIS* 3.4 29.0 + - - +
57C GLU* 4.5 15.7 + - + +
61C GLU* 3.4 28.5 - - - +
102D VAL* 3.6 18.1 + - + +
103D GLU* 4.4 19.5 - - - +
104D LEU 3.4 0.2 - - - -
105D LEU* 1.3 79.1 - - - +
107D GLY* 1.3 60.8 + - - +
108D ALA* 4.1 19.1 - - + -
----------------------------------------------------------
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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