Contacts of the helix formed by residues 93 - 120 (chain B) in PDB entry 4P9U
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 ASN 93 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 5.9 0.4 - - - +
90B ASP* 2.4 45.5 + - - +
92B GLU* 1.3 79.2 - - - +
94B ALA* 1.3 56.1 + - - +
95B THR* 2.9 7.9 - - - +
96B SER* 2.8 41.4 + - - +
97B ILE* 3.3 10.7 + - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 3.5 34.9 - - + +
90B ASP 3.5 1.6 + - - -
91B ALA* 2.9 27.9 + - - +
93B ASN* 1.3 79.0 - - - +
95B THR* 1.3 60.9 + - - +
97B ILE* 4.2 4.9 - - - -
98B VAL* 3.2 29.6 + - - +
270B LEU* 6.0 4.7 - - + -
274B PHE* 5.3 4.0 - - + -
275B THR* 4.0 9.4 - - + -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 4.3 0.8 + - - -
92B GLU 4.3 10.3 + - - -
93B ASN* 3.8 3.8 - - - +
94B ALA* 1.3 79.9 - - - +
96B SER* 1.3 62.2 + - - +
98B VAL* 3.8 4.4 + - - +
99B GLU* 3.1 40.3 + - - +
263B TRP* 4.8 6.3 + - - +
267B LYS* 4.6 18.9 - - + +
270B LEU* 5.3 10.7 - - - +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASN* 2.8 30.9 + - - +
95B THR* 1.3 78.5 - - - +
97B ILE* 1.3 74.7 + - - +
99B GLU* 2.9 25.0 + - - +
100B ASP* 3.0 19.6 + - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLN* 5.5 2.7 - - - +
83B LEU* 4.1 20.5 - - + +
86B LEU* 3.8 19.1 - - + +
87B MET* 3.6 57.0 - - + +
90B ASP* 4.5 5.4 - - - +
93B ASN* 3.5 15.9 - - + +
94B ALA* 3.8 2.5 - - - +
95B THR 3.4 0.2 - - - -
96B SER* 1.3 84.1 + - - +
98B VAL* 1.3 63.1 + - - +
100B ASP* 2.9 22.5 + - - +
101B LEU* 3.1 11.1 + - - +
211B LEU* 4.0 20.1 - - + +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 4.1 15.0 - - + -
94B ALA 3.2 17.7 + - - +
95B THR 4.1 2.5 - - - +
96B SER 3.3 0.4 - - - -
97B ILE* 1.3 76.0 - - + +
99B GLU* 1.3 57.7 + - - +
101B LEU* 2.9 10.7 + - + +
102B LEU* 2.9 35.6 + - + +
211B LEU* 5.6 0.4 - - - -
215B VAL* 3.7 39.7 - - + -
263B TRP* 3.5 42.4 - - + +
274B PHE* 4.7 2.9 - - + -
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR* 3.1 39.2 - - - +
96B SER* 2.9 11.1 + - - +
98B VAL* 1.3 76.1 - - - +
100B ASP* 1.3 60.0 + - - +
102B LEU* 4.0 10.1 - - - +
103B ALA* 3.1 26.7 + - - +
263B TRP* 4.3 16.3 + - + +
267B LYS* 3.7 17.7 + - - -
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLY 3.9 14.5 - - - +
198A ASN* 3.3 31.3 + - - +
199A GLN* 3.9 22.6 + - + +
200A ILE* 3.9 7.9 - - + -
83B LEU* 5.8 4.6 - - + +
96B SER* 3.0 18.3 + - - +
97B ILE* 2.9 15.2 + - + +
99B GLU* 1.3 78.8 - - - +
101B LEU* 1.3 66.3 + - - +
103B ALA* 2.9 1.6 + - - +
104B ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 3.8 8.7 - - + +
83B LEU* 6.2 0.2 - - - +
97B ILE 3.1 6.6 + - - +
98B VAL* 2.9 10.4 + - + +
100B ASP* 1.3 75.7 - - - +
102B LEU* 1.3 65.7 + - + +
104B ALA* 4.3 0.7 - - - +
105B ARG* 3.4 23.7 + - + +
205B PHE* 6.5 0.4 - - + -
208B LEU* 3.9 30.7 - - + -
211B LEU* 3.7 41.7 - - + +
212B TYR* 4.0 40.8 - - + -
215B VAL* 4.1 16.8 - - + -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 2.9 27.4 + - + +
99B GLU* 4.2 7.0 - - - +
101B LEU* 1.3 81.7 - - + +
103B ALA* 1.3 56.0 + - - +
105B ARG* 3.7 31.4 + - - +
106B THR* 2.5 36.5 + - - +
215B VAL* 5.4 8.1 - - + -
219B TYR* 6.5 2.2 - - + -
259B SER* 5.3 8.3 - - - +
260B GLY* 5.4 5.8 - - - -
263B TRP* 3.8 39.0 - - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASN* 3.6 11.9 - - - +
99B GLU 3.1 19.5 + - - +
100B ASP* 2.9 5.0 + - - +
102B LEU* 1.3 75.1 - - - +
104B ALA* 1.3 67.6 + - - +
106B THR* 2.9 8.0 + - - -
107B ASN* 2.9 33.3 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASN* 3.6 8.4 - - - +
200A ILE* 3.6 33.9 - - + -
201A TYR* 3.8 19.7 - - + +
100B ASP 2.9 15.2 + - - +
101B LEU 4.3 0.9 - - - +
103B ALA* 1.3 75.0 - - - +
105B ARG* 1.3 59.1 + - - +
107B ASN* 2.9 4.5 + - - +
108B ILE* 2.9 39.6 + - + +
208B LEU* 5.9 0.9 - - + -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.4 18.8 + - + +
102B LEU* 3.8 30.6 + - - +
103B ALA 3.2 0.4 - - - -
104B ALA* 1.3 78.3 - - - +
106B THR* 1.3 60.0 + - - +
108B ILE* 4.3 9.2 - - - +
109B SER* 2.2 47.2 + - - +
185B ASP* 3.7 6.9 + - - -
189B PHE* 3.6 29.4 - - + -
205B PHE* 4.1 12.6 - - + -
212B TYR* 2.5 56.9 + - + -
219B TYR* 6.3 0.8 - - - -
220B PHE* 6.1 0.6 - - - -
255B TYR* 3.9 25.0 + - - -
256B GLY* 6.3 0.6 - - - -
259B SER* 4.7 7.5 + - - -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 2.5 24.5 + - - +
103B ALA* 2.9 8.1 + - - -
105B ARG* 1.3 83.1 + - - +
107B ASN* 1.3 60.2 + - - +
109B SER* 4.4 0.9 - - - -
110B PRO* 3.3 17.8 - - - +
252B ILE* 3.9 23.5 - - + +
253B ARG* 3.7 38.2 + - + +
256B GLY* 4.0 18.4 + - - -
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.7 24.2 - - + +
115A TYR* 3.7 21.3 + - - -
198A ASN* 5.0 0.6 - - - +
201A TYR* 2.8 33.4 + - - +
103B ALA* 2.9 26.6 + - - +
104B ALA* 2.9 3.5 + - - +
106B THR* 1.3 81.4 - - - +
108B ILE* 1.3 60.2 + - - +
109B SER 3.4 0.2 - - - -
110B PRO* 3.3 14.2 - - - +
111B ILE* 3.9 9.4 - - - +
253B ARG* 2.9 32.8 + - - +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 4.4 16.6 - - + -
111A ILE* 5.6 2.5 - - + -
200A ILE* 6.4 0.7 - - + -
201A TYR* 4.2 24.0 - - + +
204A ILE* 5.9 3.6 - - + -
104B ALA* 2.9 25.5 + - + +
105B ARG* 4.2 7.2 - - - +
107B ASN* 1.3 77.5 - - + +
109B SER* 1.3 66.7 + - - +
110B PRO 3.4 1.1 - - - -
111B ILE* 3.0 24.1 + - + +
112B PHE* 3.1 22.9 - - + -
201B TYR* 4.8 12.1 - - + -
204B ILE* 4.6 27.6 - - + -
205B PHE* 4.5 18.6 - - + -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 2.2 29.8 + - - +
106B THR* 4.4 0.3 - - - -
108B ILE* 1.3 74.1 - - - +
110B PRO* 1.3 71.1 - - - +
111B ILE 3.0 2.3 + - - -
112B PHE* 3.6 11.3 - - - -
113B MET* 3.1 39.7 + - - +
189B PHE* 3.6 20.9 - - - -
232B PHE* 6.1 0.2 - - - -
252B ILE* 3.5 22.4 - - - +
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Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR 3.3 17.0 - - - +
107B ASN 3.3 17.3 - - - +
109B SER* 1.3 92.5 - - - +
111B ILE* 1.3 63.3 + - + +
114B ARG* 3.3 24.1 + - - +
248B LEU* 3.6 12.3 - - + +
249B PRO* 4.3 21.3 - - + +
252B ILE* 3.6 23.8 - - + -
253B ARG* 5.3 4.7 - - - +
----------------------------------------------------------
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 3.7 34.8 - - + +
108A ILE* 5.4 1.6 - - + -
111A ILE* 4.9 12.3 - - + -
107B ASN 3.9 7.2 - - - +
108B ILE* 3.2 26.2 - - + +
109B SER 3.0 1.0 - - - -
110B PRO* 1.3 85.6 - - + +
112B PHE* 1.3 62.9 + - - +
114B ARG* 3.6 3.7 - - - +
115B TYR* 3.2 31.1 + - + -
201B TYR* 3.2 32.8 - - + +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.1 31.6 + - + -
109B SER* 3.6 19.3 - - - -
111B ILE* 1.3 76.5 - - - +
113B MET* 1.3 94.7 + - + +
114B ARG 3.1 1.8 - - - -
115B TYR* 3.0 4.8 + - - +
116B ALA* 2.7 36.0 + - - +
189B PHE* 3.8 8.3 - + - -
192B LEU* 3.6 7.9 - - + -
193B ALA* 3.5 28.0 - - + -
196B SER* 3.6 23.1 - - - +
201B TYR* 3.9 31.6 - + + -
205B PHE* 3.8 33.7 - + - -
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Residues in contact with MET 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 3.1 16.6 + - - +
112B PHE* 1.3 98.3 - - + +
114B ARG* 1.3 60.3 + - - +
116B ALA* 4.2 5.4 - - - -
117B PHE* 3.0 41.7 + - + -
188B LEU* 4.4 2.0 - - + -
189B PHE* 3.6 37.5 - - + -
192B LEU* 4.1 23.3 - - + -
232B PHE* 4.9 1.3 - - + -
236B LEU* 3.9 34.1 - - + -
248B LEU* 4.2 9.9 - - + -
252B ILE* 3.7 23.1 - - - -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 5.9 4.4 - - - +
110B PRO 3.3 21.7 + - - +
111B ILE* 3.6 5.8 - - - +
112B PHE 3.1 0.2 - - - -
113B MET* 1.3 77.8 - - - +
115B TYR* 1.3 106.6 + - - +
117B PHE* 3.0 16.0 + - - +
118B LYS* 3.2 33.1 + - + +
245B ARG* 3.5 45.1 - - + +
248B LEU* 4.5 8.2 - - + +
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 4.1 30.6 + - - -
253A ARG* 5.2 7.8 + - - -
111B ILE* 3.2 26.8 + - + -
112B PHE* 3.0 7.6 + - - +
114B ARG* 1.3 111.1 + - - +
116B ALA* 1.3 59.4 + - - +
118B LYS* 3.0 10.4 + - + +
119B LEU* 2.8 48.4 + - + +
196B SER* 3.6 23.6 - - - +
201B TYR* 5.8 2.7 - + - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE 2.7 20.4 + - - +
113B MET* 4.0 7.4 - - - +
115B TYR* 1.3 71.8 - - - +
117B PHE* 1.3 67.6 + - + +
120B ASN* 3.4 29.6 + - - +
124B ALA* 4.0 2.0 - - + +
192B LEU* 3.5 28.5 - - + +
195B HIS* 3.2 28.6 - - + +
196B SER* 3.9 1.0 - - - +
----------------------------------------------------------
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 3.0 30.9 + - + +
114B ARG* 3.0 7.4 + - - +
116B ALA* 1.3 80.8 - - + +
118B LYS* 1.3 59.8 + - + +
121B LYS* 3.5 23.5 - - - +
124B ALA* 4.1 9.6 - - + -
128B MET* 4.0 19.7 - - - -
192B LEU* 4.2 13.7 - - + -
236B LEU* 3.7 32.3 - - + -
239B VAL* 4.0 11.2 - - + -
240B CYS* 3.6 41.4 - - + +
243B GLY* 6.2 0.2 - - - -
245B ARG* 5.4 8.5 - - + -
248B LEU* 3.9 24.9 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.3 43.9 - - - +
115B TYR* 3.0 13.5 + - + +
117B PHE* 1.3 81.7 - - - +
119B LEU* 1.3 73.7 + - + +
121B LYS* 4.5 4.7 + - - +
245B ARG* 3.5 49.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 2.8 44.1 + - + +
118B LYS* 1.3 87.7 - - + +
120B ASN* 1.3 72.1 + - - +
121B LYS 3.8 1.9 + - - -
195B HIS 4.6 5.6 - - - +
196B SER 4.5 10.5 - - - +
197B GLY* 5.4 4.0 - - - +
----------------------------------------------------------
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 3.4 9.0 + - - +
119B LEU* 1.3 87.3 - - - +
121B LYS* 1.3 57.8 + - - +
122B GLU 3.3 3.1 - - - -
123B SER* 3.9 21.1 + - - +
124B ALA* 2.9 29.1 + - - +
195B HIS* 3.5 41.9 + - + +
197B GLY* 5.3 3.2 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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