Contacts of the helix formed by residues 134 - 160 (chain D) in PDB entry 3IKM
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 134 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLY 4.2 0.2 - - - -
133D ASP* 1.3 82.2 - - - +
135D LEU* 1.3 68.5 + - - +
136D ASP* 2.7 27.7 + - - +
137D GLN* 2.4 51.1 + - + +
138D HIS* 2.7 12.5 + - - +
1166D TYR* 5.5 5.4 - - - +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN* 3.9 41.6 - - + +
87D ILE* 3.3 31.9 - - + -
133D ASP 4.1 0.6 - - - +
134D ASN* 1.3 83.4 - - - +
136D ASP* 1.3 56.3 + - + +
138D HIS* 2.6 7.7 + - - +
139D PHE* 2.6 44.0 + - + -
1159D LEU* 3.9 11.4 - - + +
1162D CYS* 3.7 3.4 - - + -
1163D MET* 3.0 43.5 - - + +
1166D TYR* 4.2 14.1 - - + -
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Residues in contact with ASP 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ASN* 3.2 25.4 + - - +
135D LEU* 1.3 80.3 - - + +
137D GLN* 1.3 69.0 + - - +
139D PHE* 2.8 13.2 + - - +
140D ARG* 2.4 48.5 + - - +
1163D MET* 4.0 22.9 - - + -
1167D LYS* 2.5 32.9 - - + +
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ASP* 4.5 18.5 + - - +
134D ASN* 2.4 41.3 + - + +
136D ASP* 1.3 81.3 + - - +
138D HIS* 1.3 65.6 + - + +
140D ARG* 3.4 9.3 + - - +
141D LEU* 2.7 31.2 + - + +
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Residues in contact with HIS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN* 3.2 9.5 + - - +
131D TYR* 2.7 43.9 - + + +
132D GLY* 2.7 32.1 + - - -
133D ASP 4.9 0.8 + - - -
134D ASN 2.7 6.2 + - - +
135D LEU* 2.6 16.2 + - - +
137D GLN* 1.3 78.7 + - + +
139D PHE* 1.3 53.1 + - - -
141D LEU* 3.2 26.1 + - + +
142D LEU* 2.5 50.2 + - + +
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 2.6 27.7 + - + -
136D ASP* 2.8 7.7 + - - +
138D HIS* 1.3 70.4 - - - +
140D ARG* 1.3 69.9 + - - +
142D LEU* 3.5 16.0 - - + +
143D ALA* 2.8 27.9 + - - +
422D VAL* 4.3 14.5 - - + +
1111D LEU* 3.6 31.6 - - + -
1114D VAL* 4.1 11.7 - - + -
1115D ALA* 3.8 19.1 - - + -
1159D LEU* 4.5 9.2 - - + -
1160D THR* 3.6 29.4 - - - -
1163D MET* 3.4 43.1 - - + -
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Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 2.4 57.4 + - - +
137D GLN* 3.4 12.1 - - - +
139D PHE* 1.3 81.8 - - - +
141D LEU* 1.3 49.1 + - - +
144D GLN* 2.6 43.8 + - - +
420D HIS* 4.2 16.5 + - - -
421D PRO* 3.8 28.0 - - + +
422D VAL* 5.0 4.2 - - - +
1020D ILE* 5.8 0.8 - - - +
1163D MET* 5.4 0.8 - - - +
1167D LYS* 3.4 22.5 - - - +
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLN* 2.7 35.4 + - + +
138D HIS* 3.2 34.0 + - + +
139D PHE 3.1 0.6 - - - -
140D ARG* 1.3 76.9 - - - +
142D LEU* 1.3 60.3 + - + +
144D GLN* 2.9 9.1 + - - +
145D LYS* 2.6 42.6 + - + +
1118D TRP* 5.3 1.1 - - + -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 5.9 6.1 - - + -
138D HIS* 2.5 42.8 + - + +
139D PHE* 3.5 32.1 - - + +
141D LEU* 1.3 83.3 - - + +
143D ALA* 1.3 54.0 - - - +
145D LYS 3.3 3.5 + - - -
146D GLN* 2.7 32.4 + - - +
1114D VAL* 3.7 13.7 - - + -
1115D ALA* 4.4 9.2 - - + -
1118D TRP* 3.3 50.3 - - + +
1119D LEU* 6.2 1.3 - - + -
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE 2.8 16.3 + - - +
142D LEU* 1.3 74.0 - - - +
144D GLN* 1.3 51.8 + - - +
146D GLN* 3.2 11.8 - - - +
147D SER* 2.7 40.2 + - - -
421D PRO* 3.0 39.0 - - + +
422D VAL* 3.4 12.6 - - + +
425D ALA* 3.3 4.5 - - + +
1114D VAL* 3.9 10.4 - - + +
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Residues in contact with GLN 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ARG* 2.6 27.9 + - - +
141D LEU* 2.9 14.6 + - - +
143D ALA* 1.3 77.9 - - - +
145D LYS* 1.3 51.1 + - + +
147D SER* 2.8 10.9 + - - -
148D LEU* 2.7 55.7 + - + +
421D PRO* 4.2 10.6 - - - +
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Residues in contact with LYS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 2.6 16.5 + - + +
144D GLN* 1.3 69.7 - - + +
146D GLN* 1.3 54.4 + - - +
148D LEU* 4.6 6.5 - - + -
149D PRO* 2.4 41.9 - - + +
1118D TRP* 2.9 40.6 - - + -
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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 LEU 2.7 28.0 - - - +
143D ALA* 3.2 12.8 - - - +
145D LYS* 1.3 77.2 - - - +
147D SER* 1.3 61.4 + - - +
149D PRO* 3.3 4.7 - - - +
150D TYR* 3.3 19.0 + - - +
290D ARG* 5.9 1.0 + - - -
425D ALA* 4.6 12.9 + - + +
428D LEU* 5.4 4.4 - - + +
429D GLU* 4.8 6.0 + - - +
1114D VAL* 3.6 21.2 - - - +
1117D LYS* 3.8 25.8 - - - +
1118D TRP* 2.9 29.0 - - + -
1121D GLU* 3.8 13.7 + - - +
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA 2.7 28.1 + - - -
144D GLN* 2.8 24.8 + - - +
146D GLN* 1.3 72.9 - - - +
148D LEU* 1.3 48.0 + - - -
150D TYR* 3.0 12.3 - - - +
151D LEU* 2.5 54.2 + - - +
420D HIS 6.0 0.2 - - - -
421D PRO* 4.7 7.2 + - - +
424D LEU* 5.9 2.0 - - - -
425D ALA* 3.6 21.0 - - - +
428D LEU* 5.4 0.4 - - - -
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D GLN* 2.7 46.0 + - + +
145D LYS* 4.0 5.6 - - + +
147D SER* 1.3 72.7 + - - +
149D PRO* 1.3 64.9 - - + +
151D LEU* 2.8 17.6 + - + +
152D GLU* 2.7 48.4 + - + +
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Residues in contact with PRO 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LYS* 2.4 33.7 - - + +
146D GLN* 3.3 5.2 - - - +
148D LEU* 1.3 88.0 - - + +
150D TYR* 1.3 64.9 + - - +
152D GLU* 3.7 6.4 + - + +
153D ALA* 3.7 16.3 + - - +
263D GLU* 5.8 2.8 - - - +
264D GLN 4.9 2.9 + - - +
290D ARG* 6.3 0.9 - - - +
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Residues in contact with TYR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLN 3.3 11.5 + - - +
147D SER* 3.0 16.8 - - - +
149D PRO* 1.3 80.1 - - - +
151D LEU* 1.3 84.9 - - + +
153D ALA* 3.5 6.0 + - - +
154D ALA* 3.4 13.7 + - + -
264D GLN 5.6 2.7 - - - -
266D VAL* 3.2 43.9 - - + +
290D ARG* 4.2 13.5 - - + +
292D LEU* 3.1 42.7 - - + +
297D MET* 5.1 0.9 - - - +
424D LEU* 5.4 7.0 - - + -
425D ALA* 6.1 0.7 - - - -
428D LEU* 3.3 35.9 - - + -
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D GLN* 6.0 3.1 - - - +
147D SER* 2.5 39.7 + - - +
148D LEU* 2.8 20.4 + - + +
150D TYR* 1.3 87.1 - - + +
152D GLU* 1.3 58.1 + - - +
153D ALA 2.9 2.0 - - - -
154D ALA* 2.4 41.3 + - + +
155D ASN* 3.1 17.9 + - - +
416D GLU* 6.0 1.3 - - - +
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 2.7 30.0 + - + +
149D PRO* 4.2 6.1 - - + +
151D LEU* 1.3 71.9 - - - +
153D ALA* 1.3 59.3 + - - +
154D ALA 3.6 0.2 + - - -
155D ASN* 3.2 22.4 + - - +
156D LEU* 3.4 24.7 + - - +
263D GLU* 5.2 4.0 - - + +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D PRO 3.7 6.0 + - - +
150D TYR 3.5 9.1 + - - +
151D LEU 2.7 5.1 + - - -
152D GLU* 1.3 75.8 - - - +
154D ALA* 1.3 64.0 + - - +
156D LEU* 3.8 13.8 - - - +
157D LEU* 3.8 11.1 + - - +
193D ARG* 5.1 2.7 - - - +
194D ALA* 4.1 13.1 - - - +
263D GLU* 4.6 12.2 + - + +
264D GLN 3.3 30.3 - - - +
265D LEU* 3.9 11.6 - - + +
266D VAL* 4.4 2.9 - - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D TYR* 3.4 9.0 + - + +
151D LEU* 2.4 36.7 + - + +
153D ALA* 1.3 68.4 - - - +
155D ASN* 1.3 67.4 + - - +
157D LEU* 2.9 15.1 + - - +
158D LEU* 2.8 30.7 + - + +
266D VAL* 3.6 24.7 - - + +
408D GLN* 6.0 0.4 - - - +
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Residues in contact with ASN 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 3.1 15.2 + - - +
152D GLU* 3.2 45.7 + - - +
154D ALA* 1.3 75.6 - - - +
156D LEU* 1.3 67.1 + - + +
158D LEU* 2.9 20.4 + - - +
159D GLN* 2.9 17.6 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLU* 3.4 19.5 - - - +
153D ALA* 3.8 9.9 - - - +
154D ALA 3.1 0.4 + - - -
155D ASN* 1.3 78.6 - - + +
157D LEU* 1.3 71.9 + - + +
159D GLN* 3.6 5.9 + - - +
160D ALA* 3.6 17.7 + - - +
193D ARG* 4.2 19.7 - - + -
194D ALA* 5.8 0.7 - - + -
263D GLU* 3.6 24.5 - - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ALA 3.8 2.7 + - - +
154D ALA* 2.9 10.5 + - - +
156D LEU* 1.3 81.5 - - + +
158D LEU* 1.3 69.9 + - + +
160D ALA* 3.5 19.6 + - + +
193D ARG* 5.8 2.0 - - + -
194D ALA* 2.9 53.8 - - + +
195D LEU* 3.7 8.7 - - - +
196D VAL* 5.3 5.4 - - + -
215D ILE* 4.8 15.3 - - + +
216D SER* 5.5 4.0 - - - +
265D LEU* 3.4 17.3 - - + -
408D GLN* 5.3 8.5 - - - +
409D GLN* 4.1 2.6 + - - -
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ALA* 2.8 46.6 + - + +
155D ASN* 2.9 11.7 + - - +
157D LEU* 1.3 71.3 - - + +
159D GLN* 1.3 63.9 + - - +
408D GLN* 4.1 27.4 - - + +
409D GLN* 2.6 43.7 + - + +
412D PRO* 3.5 40.8 - - + -
413D LEU* 5.7 1.8 - - + -
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ASN 2.9 16.3 + - - +
156D LEU* 3.9 6.5 - - - +
158D LEU* 1.3 76.7 - - - +
160D ALA* 1.3 63.7 + - - +
161D GLN* 3.5 12.0 + - - +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D LEU 3.6 8.9 + - - +
157D LEU* 3.5 15.3 + - + +
158D LEU 3.0 1.5 + - - +
159D GLN* 1.3 78.6 - - - +
161D GLN* 1.3 62.8 + - - +
162D LEU* 3.7 7.0 - - + +
215D ILE* 6.5 1.3 - - + -
409D GLN* 2.6 32.2 + - - -
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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