Contacts of the helix formed by residues 127 - 154 (chain D) in PDB entry 2ONK
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 ALA 127 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 5.9 0.2 - - + -
123D LYS* 3.4 28.5 - - + +
124D PHE 2.8 8.5 + - - +
125D VAL 2.6 9.3 + - - +
126D ASP* 1.3 74.7 - - - +
128D LEU* 1.3 68.3 + - - +
129D PRO* 3.2 5.4 - - + -
130D GLY* 2.8 14.9 + - - -
131D ILE* 3.4 8.2 + - - +
207D ALA* 3.6 1.5 - - - +
210D PRO* 3.8 7.6 - - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D THR* 4.6 12.6 - - + -
56D TYR* 4.1 29.8 - - + +
57D ALA* 4.2 21.8 - - + -
60D ILE* 4.4 11.2 - - + -
127D ALA* 1.3 71.0 - - - +
129D PRO* 1.3 65.3 - - + +
131D ILE* 2.7 38.1 + - + +
132D VAL* 3.0 18.5 + - + +
210D PRO* 4.3 6.6 - - + +
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Residues in contact with PRO 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 3.6 33.9 - - + -
123D LYS 3.9 4.9 - - - +
124D PHE* 3.2 29.4 - - + -
127D ALA* 3.3 11.9 - - + -
128D LEU* 1.3 97.6 - - + +
130D GLY* 1.3 62.9 + - - +
131D ILE 3.3 0.2 + - - -
132D VAL* 3.3 8.3 + - + +
133D VAL* 3.0 27.9 + - - +
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Residues in contact with GLY 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PHE* 6.1 0.4 - - - -
124D PHE* 3.4 15.4 + - - +
127D ALA 2.8 13.8 + - - -
129D PRO* 1.3 75.4 - - - +
131D ILE* 1.3 57.9 + - - +
133D VAL* 3.8 3.8 - - - +
134D ALA* 2.9 28.8 + - - +
206D ILE* 3.4 35.0 - - - +
207D ALA* 5.1 0.7 - - - -
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D THR* 4.6 3.4 - - + -
57D ALA* 3.6 14.4 - - + -
127D ALA 3.4 6.9 + - - +
128D LEU* 2.7 35.1 + - + +
130D GLY* 1.3 69.2 - - - +
132D VAL* 1.3 54.5 + - - +
134D ALA* 3.0 7.2 + - - +
135D MET* 2.8 46.0 + - + +
203D VAL* 4.2 13.7 - - + -
207D ALA* 4.0 11.4 - - + -
210D PRO* 3.0 36.1 - - + +
212D ILE* 3.1 35.9 - - + -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA* 3.9 17.7 - - - +
60D ILE* 3.8 27.8 - - + -
61D SER* 4.3 7.9 - - - -
64D ILE* 3.5 31.6 - - + -
128D LEU* 3.0 21.9 + - + +
129D PRO* 3.6 10.1 - - + +
131D ILE* 1.3 73.4 - - - +
133D VAL* 1.3 61.6 + - + +
134D ALA 2.8 1.2 + - - -
135D MET* 2.8 6.6 + - - -
136D LEU* 2.6 37.6 + - + +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.4 26.6 - - + -
106D LEU* 3.3 38.5 - - + +
110D PHE* 3.9 34.8 - - + -
124D PHE* 4.6 5.6 - - + -
129D PRO 3.0 16.5 + - - +
130D GLY* 3.9 5.6 - - - +
132D VAL* 1.3 84.1 - - + +
134D ALA* 1.3 63.8 + - - +
136D LEU* 4.0 2.9 - - + -
137D PHE 3.3 14.7 + - - -
206D ILE* 4.8 1.6 - - + -
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 3.4 12.2 - - - +
130D GLY 2.9 16.7 + - - +
131D ILE* 3.1 9.4 - - - +
132D VAL 2.8 1.0 + - - -
133D VAL* 1.3 79.9 - - - +
135D MET* 1.3 61.2 + - - +
137D PHE* 3.5 1.7 + - - +
138D VAL* 2.8 29.0 + - - +
202D ALA* 4.1 2.2 - - - -
203D VAL* 3.5 30.7 - - + +
206D ILE* 3.5 15.0 - - + -
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Residues in contact with MET 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D THR* 4.2 2.5 - - + +
57D ALA 3.7 6.7 - - - +
58D ALA* 3.3 36.1 - - + +
61D SER* 3.9 8.5 - - - -
131D ILE* 2.8 30.5 + - + +
132D VAL 2.8 2.6 + - - +
134D ALA* 1.3 70.6 - - - +
136D LEU* 1.3 69.9 + - - +
138D VAL* 3.1 8.4 + - - +
139D SER* 2.8 22.4 + - - -
196D GLY* 2.9 44.2 - - - +
197D ILE* 3.9 4.3 - - - +
199D GLU* 4.8 2.0 - - + -
203D VAL* 4.2 12.1 - - + -
212D ILE* 3.4 33.9 - - + -
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 5.0 4.9 - - + -
19C PHE* 3.4 33.2 - - + -
61D SER* 3.3 36.4 - - - +
64D ILE* 3.9 26.0 - - + -
65D ALA* 4.1 13.5 - - + +
132D VAL* 2.6 22.9 + - + +
133D VAL* 3.9 4.0 - - + +
135D MET* 1.3 69.1 - - - +
137D PHE* 1.3 57.0 + - - +
139D SER* 2.7 28.9 + - - +
140D VAL* 2.8 36.7 + - + -
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Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.4 14.8 - + + -
20C VAL* 3.6 41.8 - - + +
23C PRO* 4.2 7.6 - - + -
24C VAL* 3.9 20.4 - - + -
94D PRO* 3.0 55.9 - - + +
97D ILE* 3.9 12.3 - - + -
102D ALA* 3.7 33.7 - - + -
105D ALA* 6.2 1.1 - - + -
106D LEU* 4.0 20.6 - - + -
133D VAL 3.3 16.4 + - - +
134D ALA 3.7 3.6 - - - +
136D LEU* 1.3 78.9 - - - +
138D VAL* 1.3 65.0 + - + +
139D SER 3.7 0.2 + - - -
140D VAL* 4.4 3.4 - - - +
141D PRO* 3.8 3.3 - - - +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D PRO* 4.5 12.6 - - - +
99D HIS* 4.7 6.1 - - - +
102D ALA* 5.3 2.0 - - + -
134D ALA 2.8 23.3 - - - +
135D MET* 3.7 5.8 - - - +
136D LEU 2.7 4.9 + - - -
137D PHE* 1.3 85.3 - - + +
139D SER* 1.3 57.8 + - - +
141D PRO* 3.9 11.7 - - - +
142D ILE* 4.7 3.3 - - - +
195D ARG* 2.7 53.9 + - + +
199D GLU* 4.0 9.0 - - + +
202D ALA* 3.9 20.2 - - + -
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D SER* 3.9 8.1 + - - -
65D ALA* 5.9 0.2 - - - -
135D MET 2.8 18.4 + - - -
136D LEU* 2.7 15.9 + - - +
138D VAL* 1.3 71.9 - - - +
140D VAL* 1.3 66.4 + - - +
141D PRO* 3.3 3.8 - - - -
142D ILE* 2.9 16.7 + - - +
143D TYR* 3.1 9.0 + - - +
192D SER* 3.4 37.0 + - - -
195D ARG* 3.6 18.2 - - - -
196D GLY 4.4 1.8 + - - -
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.9 25.6 - - + -
19C PHE* 4.7 2.7 - - + -
20C VAL* 4.3 12.3 - - + -
65D ALA* 5.0 8.5 - - + +
69D GLY* 6.0 0.9 - - - -
91D VAL* 5.3 2.9 - - - +
136D LEU* 2.8 55.0 + - + +
137D PHE* 4.3 4.9 - - - +
139D SER* 1.3 70.7 + - - +
141D PRO* 1.3 73.1 - - + +
143D TYR* 3.1 7.8 + - - +
144D ILE* 3.0 42.8 + - + +
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Residues in contact with PRO 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D VAL* 3.1 35.7 - - + +
92D ASP* 4.5 4.9 - - - +
94D PRO* 3.6 27.1 - - + -
95D VAL* 4.1 21.8 - - + -
137D PHE 3.8 4.3 - - - +
138D VAL 3.9 10.8 - - - +
139D SER 3.3 1.1 - - - -
140D VAL* 1.3 96.3 - - + +
142D ILE* 1.3 71.9 + - + +
143D TYR 3.0 0.5 + - - -
144D ILE* 3.7 0.2 - - - +
145D ASN* 3.0 28.7 + - - +
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 6.0 6.1 - - + -
95D VAL* 6.3 1.6 - - + -
138D VAL 4.7 3.4 - - - +
139D SER* 2.9 16.2 + - - +
141D PRO* 1.3 85.0 - - + +
143D TYR* 1.3 61.5 + - - +
145D ASN* 4.3 3.6 - - - +
146D GLN* 3.6 18.2 + - - +
188D GLY 4.8 0.2 - - - +
191D MET* 3.9 19.7 - - + +
192D SER* 3.8 25.4 - - - +
195D ARG* 4.0 33.2 - - + +
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Residues in contact with TYR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ALA* 4.1 22.7 - - + -
66D VAL* 3.6 24.6 - - + +
69D GLY* 4.0 4.7 - - - -
70D THR* 2.5 42.6 + - - -
139D SER 3.1 4.9 + - - +
140D VAL 3.1 8.2 + - - +
142D ILE* 1.3 74.7 - - - +
144D ILE* 1.3 80.9 + - + +
146D GLN* 2.8 15.9 + - - +
147D ALA* 2.8 25.4 + - + +
185D ILE* 3.1 46.9 - - + +
188D GLY* 3.4 25.4 - - - -
189D ALA* 3.4 5.8 - - - -
192D SER* 4.1 14.6 - - - -
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Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 5.5 2.5 - - + -
69D GLY* 4.1 24.9 - - - +
72D LEU* 3.5 27.4 - - + -
73D ALA* 3.7 12.1 - - + +
76D LEU* 4.3 19.5 - - + -
91D VAL* 3.9 26.2 - - + -
140D VAL* 3.0 36.0 + - + +
141D PRO 3.7 3.4 - - - +
143D TYR* 1.3 82.9 - - + +
145D ASN* 1.3 55.9 + - - +
147D ALA* 3.0 6.4 + - - +
148D LYS* 2.7 36.0 + - + +
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C MET* 5.5 9.3 - - - +
91D VAL* 4.2 10.7 - - - +
92D ASP* 3.9 23.1 + - - +
141D PRO 3.0 16.4 + - - +
142D ILE* 4.3 4.5 - - - +
144D ILE* 1.3 80.7 - - - +
146D GLN* 1.3 62.3 + - - +
148D LYS* 3.2 24.3 + - - +
149D GLU* 3.1 29.2 + - - +
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ILE 3.6 7.4 + - - +
143D TYR 2.8 11.5 + - - +
145D ASN* 1.3 75.5 - - - +
147D ALA* 1.3 63.6 + - - +
149D GLU* 3.3 24.3 + - - +
150D GLY 3.1 16.1 + - - -
184D HIS* 3.7 35.6 + - - +
187D ALA* 4.1 8.8 - - - +
188D GLY* 3.5 16.8 - - - -
191D MET* 3.3 35.1 - - + +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 4.9 0.9 - - - -
73D ALA* 3.4 22.7 - - + -
143D TYR* 2.8 39.5 + - + +
144D ILE 3.4 3.4 - - - +
146D GLN* 1.3 77.3 - - - +
148D LYS* 1.3 63.3 + - - +
150D GLY* 3.1 10.1 + - - -
151D PHE* 3.0 27.4 + - + -
181D SER* 5.2 0.5 - - - -
184D HIS 4.6 6.4 + - - -
185D ILE* 4.9 8.4 - - + +
188D GLY* 5.1 0.2 - - - -
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Residues in contact with LYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ALA* 3.7 25.3 - - + +
76D LEU* 4.2 27.6 - - + +
77D ALA* 3.9 16.3 - - + +
88D GLU* 4.1 17.4 + - - +
144D ILE* 2.7 16.9 + - - +
145D ASN* 3.3 29.5 + - - +
147D ALA* 1.3 69.1 - - - +
149D GLU* 1.3 66.5 + - + +
150D GLY 2.8 5.3 + - - -
151D PHE* 3.0 4.3 + - - +
152D ALA* 2.7 26.3 + - + +
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLU* 4.0 26.2 - - - +
145D ASN* 3.1 13.8 + - - +
146D GLN* 3.7 27.0 + - - +
148D LYS* 1.3 80.0 - - + +
150D GLY* 1.3 64.0 + - - +
152D ALA* 3.6 10.4 - - + +
153D SER* 3.0 20.6 + - - -
184D HIS* 4.2 13.8 + - + +
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Residues in contact with GLY 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLN 3.1 6.5 + - - -
147D ALA 3.1 5.9 + - - -
148D LYS 2.8 2.8 + - - -
149D GLU* 1.3 75.4 - - - +
151D PHE* 1.3 57.5 + - - -
153D SER* 2.6 31.5 + - - -
154D VAL 3.6 1.6 + - - -
181D SER* 3.4 12.3 - - - -
184D HIS* 3.2 34.9 - - - -
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Residues in contact with PHE 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 3.8 18.2 - - + -
73D ALA* 3.8 11.9 - - + -
74D TYR* 3.5 59.7 - + + -
77D ALA* 3.6 16.6 - - + -
78D ARG* 2.9 30.7 + - - +
147D ALA* 3.0 27.2 + - + -
148D LYS 3.0 1.8 + - - +
150D GLY* 1.3 72.5 - - - +
152D ALA* 1.3 63.3 + - - +
154D VAL* 3.1 8.4 + - + +
173D PHE* 3.8 1.1 - + - -
177D SER* 4.3 7.4 - - - -
178D LEU* 3.4 36.8 - - + -
181D SER* 3.5 19.6 - - - -
185D ILE* 4.4 5.8 - - + -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ALA* 3.9 13.4 - - + +
78D ARG* 4.7 5.3 + - - +
148D LYS* 2.7 25.0 + - + +
149D GLU* 3.6 12.1 - - + +
151D PHE* 1.3 74.0 - - - +
153D SER* 1.3 61.6 + - - +
154D VAL 3.4 4.9 + - - +
----------------------------------------------------------
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Residues in contact with SER 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D GLU 3.0 11.4 + - - -
150D GLY 2.6 19.5 + - - -
152D ALA* 1.3 78.8 - - - +
154D VAL* 1.3 64.3 + - - +
155D ASP 3.5 2.4 + - - -
180D LEU 4.9 3.6 + - - -
184D HIS* 3.7 20.8 + - - -
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 3.2 23.3 + - - +
150D GLY 4.2 5.8 - - - +
151D PHE* 3.1 5.1 + - - +
152D ALA 4.1 4.0 - - - +
153D SER* 1.3 82.3 + - - +
155D ASP* 1.3 72.8 + - - +
156D VAL* 3.0 5.7 + - - +
158D LEU* 4.2 5.6 - - + -
159D GLU* 3.8 17.3 - - - +
176D VAL* 4.7 3.4 - - + -
177D SER* 4.0 12.8 - - - +
180D LEU* 3.4 54.3 - - + +
181D SER* 4.3 2.2 - - - +
----------------------------------------------------------
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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