Contacts of the helix formed by residues 134 - 163 (chain A) in PDB entry 5OIV
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA 3.7 0.8 + - - -
132A THR 3.6 0.8 - - - -
133A ARG* 1.3 80.9 - - - +
135A ARG* 1.3 60.7 + - - -
136A SER 3.5 2.2 - - - -
137A THR 3.3 3.5 + - - -
138A ARG* 2.9 52.0 + - - +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLY* 1.3 72.3 - - - -
136A SER* 1.3 59.8 + - - +
138A ARG* 3.3 26.7 + - - +
139A ALA* 2.9 59.4 + - + +
142A GLU* 3.4 28.5 + - - -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLY 3.5 0.2 - - - -
135A ARG* 1.3 79.1 - - - +
137A THR* 1.3 68.6 + - - +
139A ALA* 3.4 8.2 + - - +
140A VAL* 3.2 27.7 + - - +
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Residues in contact with THR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.6 36.7 - - + +
130A ALA* 3.8 10.4 - - - +
133A ARG* 3.6 36.3 + - + +
134A GLY 3.3 4.1 + - - -
135A ARG 3.2 0.4 - - - -
136A SER* 1.3 80.9 + - - +
138A ARG* 1.3 65.0 + - - +
140A VAL* 3.1 16.2 + - - +
141A ALA* 3.2 10.0 + - - +
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Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 3.4 23.8 + - + +
131A ARG* 3.5 40.2 + - + +
134A GLY* 2.9 34.5 + - - +
135A ARG* 3.5 43.4 - - - +
137A THR* 1.3 76.5 - - - +
139A ALA* 1.3 57.7 + - - +
141A ALA* 3.2 2.8 + - - +
142A GLU* 2.8 47.7 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 2.9 39.0 + - + +
136A SER* 3.6 9.6 - - - +
138A ARG* 1.3 77.7 - - - +
140A VAL* 1.3 56.5 + - + +
142A GLU* 3.8 3.6 - - - +
143A ALA* 2.9 31.4 + - - +
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.0 15.3 - - + -
57A GLU* 3.8 45.3 - - + +
60A VAL* 4.3 12.7 - - + +
136A SER* 3.2 15.5 + - - +
137A THR* 3.1 11.0 + - - +
139A ALA* 1.3 76.9 - - - +
141A ALA* 1.3 63.6 + - - +
143A ALA* 3.4 4.9 + - - +
144A PHE* 3.1 20.8 + - - +
147A ARG* 5.1 0.7 + - - -
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.5 1.8 - - + -
60A VAL* 4.6 4.0 - - - -
126A ILE* 4.3 14.4 - - + -
127A LEU* 3.9 20.5 - - + +
130A ALA* 3.7 28.7 - - + -
137A THR 3.2 3.2 + - - +
138A ARG* 3.8 4.3 - - - +
140A VAL* 1.3 82.1 - - - +
142A GLU* 1.3 62.6 + - + +
144A PHE* 3.3 11.5 + - - +
145A LEU* 3.1 23.2 + - - +
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 5.3 1.1 - - + -
135A ARG* 3.4 22.5 + - - -
138A ARG* 2.8 34.1 + - - +
139A ALA* 4.0 4.3 - - - +
141A ALA* 1.3 74.3 - - + +
143A ALA* 1.3 61.3 + - - +
145A LEU* 3.2 10.9 + - - +
146A ASP* 3.0 32.7 + - - +
273A TYR* 3.8 36.2 + - + +
275A ARG* 5.4 1.4 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 2.9 19.7 + - - +
140A VAL* 3.8 5.8 - - - +
141A ALA 3.3 0.2 - - - -
142A GLU* 1.3 74.1 - - - +
144A PHE* 1.3 64.4 + - - +
146A ASP* 3.2 12.8 + - - +
147A ARG* 2.9 37.2 + - - +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.6 38.8 - - + -
63A LEU* 3.8 38.1 - - + -
64A ASP* 3.8 15.9 - - - -
67A LEU* 4.2 7.4 - - + -
123A VAL* 3.9 28.7 - - + -
126A ILE* 5.8 4.0 - - + -
127A LEU* 6.5 0.2 - - + -
140A VAL 3.1 14.5 + - - +
141A ALA* 3.4 9.9 - - - +
142A GLU 3.2 0.2 - - - -
143A ALA* 1.3 76.0 - - - +
145A LEU* 1.3 66.3 + - + +
147A ARG* 3.1 11.8 + - - +
148A ARG* 2.8 55.9 + - + +
152A LEU* 4.5 6.7 - - + -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 4.0 20.0 - - + -
127A LEU* 4.2 12.8 - - + -
141A ALA 3.1 15.7 + - - +
142A GLU* 3.2 9.1 + - - +
144A PHE* 1.3 83.3 - - + +
146A ASP* 1.3 64.5 + - - +
149A TRP* 2.9 45.8 + - + +
152A LEU* 5.1 5.8 - - + -
266A LEU* 5.9 0.2 - - + -
269A ILE* 4.0 21.8 - - + -
273A TYR* 3.5 47.1 - - + -
275A ARG* 3.8 13.0 + - - +
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 3.0 19.3 + - - +
143A ALA* 3.2 13.3 + - - +
145A LEU* 1.3 77.5 - - - +
147A ARG* 1.3 62.4 + - - +
149A TRP* 4.5 2.9 + - - +
275A ARG* 2.8 33.0 + - - +
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.3 20.2 - - - +
64A ASP* 2.6 39.7 + - - -
140A VAL 5.1 1.2 + - - -
143A ALA* 2.9 40.9 + - - +
144A PHE* 3.7 12.3 - - - +
146A ASP* 1.3 79.6 - - + +
148A ARG* 1.3 77.2 + - + +
150A GLY 5.1 1.4 + - - -
151A ASP* 4.3 4.9 - - - +
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 2.7 54.3 + - - +
67A LEU* 3.8 37.4 + - + +
68A SER* 4.1 11.9 - - - +
144A PHE* 2.8 40.4 + - + +
147A ARG* 1.3 91.9 + - + +
149A TRP* 1.3 65.7 + - - +
150A GLY 3.2 2.7 - - - -
151A ASP* 2.8 28.8 + - - +
152A LEU* 2.9 25.6 + - + +
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Residues in contact with TRP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 2.9 34.1 + - + +
146A ASP 4.5 2.4 + - - +
147A ARG 3.8 0.6 - - - -
148A ARG* 1.3 75.7 - - - +
150A GLY* 1.3 59.9 + - - +
152A LEU* 3.2 9.2 + - + +
153A MET* 2.9 49.1 + - + +
266A LEU* 3.3 48.9 - - + -
269A ILE* 4.3 4.7 - - + -
270A GLY* 3.5 20.0 - - - -
275A ARG* 3.5 44.2 - - + +
276A PRO* 4.2 4.7 - - + -
279A ASP* 2.8 34.2 + - + -
280A VAL* 4.8 2.5 - - + -
283A LEU* 3.8 13.2 - - + -
503A GOL 4.1 7.4 - - - -
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASP 5.5 1.0 + - - -
147A ARG 5.1 1.4 + - - -
148A ARG 3.2 1.0 - - - -
149A TRP* 1.3 79.2 - - - +
151A ASP* 1.3 59.1 + - - +
153A MET* 3.2 2.8 + - - +
154A ARG* 2.9 36.1 + - - +
503A GOL 3.8 27.2 - - - -
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.3 14.3 - - + +
70A GLN* 2.9 41.6 + - - +
147A ARG 4.3 5.2 + - - +
148A ARG* 2.8 48.4 + - - +
150A GLY* 1.3 76.4 - - - +
152A LEU* 1.3 58.5 + - - +
154A ARG* 3.0 22.8 + - - +
155A TRP* 3.0 12.8 + - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.2 24.7 - - + -
119A HIS* 4.6 21.8 - - + -
120A ALA* 5.4 1.6 - - - +
123A VAL* 4.2 26.9 - - + -
144A PHE* 4.5 12.6 - - + -
145A LEU* 5.1 4.7 - - + -
148A ARG 2.9 22.3 + - - +
149A TRP* 3.6 11.2 - - + +
151A ASP* 1.3 74.8 - - - +
153A MET* 1.3 63.0 + - - +
155A TRP* 3.3 13.8 + - + +
156A HIS* 3.0 28.8 + - - +
266A LEU* 4.1 31.0 - - + -
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Residues in contact with MET 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 2.9 40.0 + - + +
150A GLY 3.2 8.0 + - - +
152A LEU* 1.3 76.8 - - - +
154A ARG* 1.3 57.6 + - - +
156A HIS* 3.3 3.9 + - - +
157A ARG* 2.8 50.5 + - - +
266A LEU* 4.6 2.7 - - + -
279A ASP* 3.7 36.3 - - + +
282A ASP* 4.6 2.9 - - + -
283A LEU* 3.5 32.1 - - + -
286A TRP* 4.1 22.7 - - + -
503A GOL 3.6 14.6 - - - +
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN* 3.2 18.6 + - - +
71A TRP 3.0 27.1 + - - -
72A ARG* 3.2 21.2 + - - +
73A ASN 4.3 2.5 - - - +
74A GLY* 3.6 12.5 - - - +
150A GLY 2.9 21.7 + - - +
151A ASP* 3.0 29.0 + - - +
153A MET* 1.3 75.3 - - - +
155A TRP* 1.3 57.3 + - - +
157A ARG* 3.8 11.7 - - - +
158A TRP* 3.0 29.8 + - - +
503A GOL 3.6 19.3 - - - +
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Residues in contact with TRP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 5.3 0.2 - - - -
70A GLN* 3.4 8.2 - - - +
74A GLY 3.3 13.0 - - - -
76A ILE* 3.4 48.0 - - + +
114A THR* 3.0 28.9 - - - -
115A GLN 3.3 20.6 - - - -
117A PRO* 3.7 27.0 - - + +
119A HIS* 3.1 32.7 + + + +
151A ASP 3.0 13.6 + - - +
152A LEU* 3.4 15.0 - - + +
154A ARG* 1.3 74.1 - - - +
156A HIS* 1.3 84.3 + + - +
158A TRP* 3.3 11.3 + + - +
159A LEU* 3.2 40.1 + - + +
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Residues in contact with HIS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 4.6 4.2 + - + +
120A ALA* 4.4 8.6 + - + +
152A LEU* 3.0 24.6 + - + +
153A MET 3.9 3.1 - - - +
155A TRP* 1.3 97.7 + + - +
157A ARG* 1.3 58.3 + - - +
159A LEU* 3.3 1.6 + - - -
160A ALA* 3.0 25.6 + - - +
259A PHE* 3.3 24.5 - + + -
262A ALA* 3.6 43.1 - - + +
263A CYS* 3.4 18.8 - - - -
266A LEU* 3.9 15.7 - - + +
283A LEU* 3.5 12.3 - - + +
286A TRP* 3.9 15.9 - - + -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 2.8 38.1 + - - +
154A ARG* 3.9 19.0 - - - +
156A HIS* 1.3 74.3 - - - +
158A TRP* 1.3 56.4 + - - +
161A GLU* 2.8 69.0 + - + +
279A ASP* 4.1 3.8 + - - -
282A ASP* 4.8 8.9 + - - -
286A TRP* 3.7 21.9 - - + -
503A GOL 2.8 45.2 + - - -
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Residues in contact with TRP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.3 34.7 - - + +
74A GLY 3.9 4.3 - - - -
75A MET* 3.6 46.2 - - + -
114A THR* 3.8 11.4 - - + -
154A ARG 3.0 19.1 + - - +
155A TRP* 3.3 17.7 + + - +
157A ARG* 1.3 76.2 - - - +
159A LEU* 1.3 87.1 + - + +
161A GLU* 5.1 0.4 - - - -
162A CYS* 2.8 62.9 + - + +
163A ARG* 3.6 39.2 + - + -
239A ASP* 2.9 30.2 + - - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 4.6 1.1 - - + -
117A PRO* 3.7 37.0 - - + -
155A TRP* 3.2 32.2 + - + +
156A HIS* 3.6 6.5 - - - +
157A ARG 3.3 0.2 - - - -
158A TRP* 1.3 102.2 - - + +
160A ALA* 1.3 62.7 + - - +
163A ARG* 3.1 25.7 + - + +
164A ASP 3.4 6.2 + - - -
171A ILE* 3.6 19.3 - - + +
255A PHE* 3.8 27.8 - - + -
259A PHE* 3.8 18.8 - - + -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A HIS 3.0 17.4 + - - +
157A ARG 3.9 2.5 - - - +
159A LEU* 1.3 78.0 - - - +
161A GLU* 1.3 60.5 + - + +
164A ASP* 3.3 27.2 - - - +
167A GLU* 5.6 0.5 - - - +
259A PHE* 4.2 6.5 - - + -
286A TRP* 3.6 42.8 - - + +
289A ARG* 4.5 8.4 + - - +
290A PHE* 4.3 13.0 - - + -
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 2.8 52.4 + - + +
160A ALA* 1.3 79.3 - - + +
162A CYS* 1.3 67.8 + - - +
163A ARG 3.7 0.4 - - - -
164A ASP 4.4 0.9 - - - -
165A ARG* 3.8 22.3 + - - +
286A TRP* 5.3 4.8 - - + +
----------------------------------------------------------
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Residues in contact with CYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.9 1.1 - - - -
158A TRP* 2.8 56.4 + - + +
161A GLU* 1.3 83.7 - - - +
163A ARG* 1.3 63.6 + - - +
164A ASP 3.5 0.7 - - - -
165A ARG* 2.6 52.5 + - - +
174A TYR* 5.2 1.6 + - - -
239A ASP* 4.1 7.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 4.8 5.3 - - - -
112A GLY 5.5 0.8 + - - -
113A ILE* 5.1 2.4 - - - +
114A THR* 4.1 5.7 - - - +
158A TRP* 3.6 45.7 + - + -
159A LEU* 3.1 16.1 + - + +
162A CYS* 1.3 83.1 - - - +
164A ASP* 1.3 60.7 + - - +
165A ARG* 3.8 3.1 - - - +
170A ARG 3.5 2.4 - - - +
171A ILE* 3.6 16.2 - - + +
172A THR* 2.9 64.0 + - - +
173A LEU* 3.8 3.4 - - - +
174A TYR* 3.6 34.3 - - - +
178A GLU* 2.9 41.4 + - - -
239A ASP* 4.9 4.2 + - - -
242A LEU* 4.9 6.1 - - - +
----------------------------------------------------------
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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