Contacts of the helix formed by residues 139 - 165 (chain D) in PDB entry 4O46
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 THR 139 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL 4.5 5.8 - - - +
138D ALA* 1.3 78.8 - - - +
140D GLY* 1.3 67.8 + - - +
142D LYS* 3.4 11.3 + - - +
143D ARG* 3.2 16.8 + - - +
163E GLU* 2.9 41.1 + - - +
164E HIS* 4.0 12.2 + - + -
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Residues in contact with GLY 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 1.3 73.2 - - - +
141D GLU* 1.3 61.2 + - - -
143D ARG* 3.3 13.8 + - - +
144D ALA* 3.3 12.0 + - - +
163E GLU* 3.9 22.3 - - - +
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR 3.6 0.2 + - - -
140D GLY* 1.3 69.2 - - - -
142D LYS* 1.3 63.1 + - - +
144D ALA* 3.3 10.3 + - + +
145D THR* 2.9 29.5 + - - +
163E GLU* 5.5 0.6 + - - -
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Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ALA* 4.3 9.6 - - + +
139D THR 3.4 10.0 + - - +
140D GLY 3.3 0.2 - - - -
141D GLU* 1.3 77.0 - - - +
143D ARG* 1.4 61.6 + - - +
145D THR* 3.5 8.2 + - - -
146D VAL* 3.3 26.0 + - - +
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ALA* 3.7 17.6 + - - +
138D ALA* 3.4 36.9 + - + +
139D THR* 3.2 12.3 + - - +
140D GLY 3.4 10.8 - - - +
141D GLU 3.2 0.2 - - - -
142D LYS* 1.4 73.1 - - - +
144D ALA* 1.3 65.6 + - - +
145D THR 3.2 0.3 + - - -
146D VAL* 3.3 3.5 - - - +
147D VAL* 3.0 48.1 + - + +
185D GLU 4.8 1.8 + - - -
186D ILE* 2.8 47.1 + - - +
187D GLN* 5.8 0.2 + - - -
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLY 3.3 9.7 + - - +
141D GLU* 3.5 13.7 - - - +
143D ARG* 1.3 78.1 - - - +
145D THR* 1.3 61.7 + - - +
147D VAL* 3.6 6.3 + - - +
148D GLU* 3.2 25.1 + - - +
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Residues in contact with THR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D GLU* 2.9 14.2 + - - +
142D LYS* 3.6 10.8 - - - -
144D ALA* 1.3 74.4 - - - +
146D VAL* 1.3 64.0 + - + +
148D GLU* 3.3 14.3 + - - +
149D SER* 3.1 33.1 + - - +
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 3.6 34.7 - - + +
134D LEU* 3.9 19.7 - - + -
135D ALA* 3.7 27.4 - - - +
138D ALA* 4.2 4.0 - - + -
142D LYS 3.3 12.3 + - - +
143D ARG* 3.3 17.3 - - - +
145D THR* 1.3 79.3 - - + +
147D VAL* 1.4 58.5 + - - +
149D SER* 3.4 8.0 + - - -
150D SER* 2.9 29.8 + - - -
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ALA* 3.8 11.9 - - + -
143D ARG* 3.0 43.3 + - - +
144D ALA* 3.8 6.5 - - - +
146D VAL* 1.4 71.7 - - - +
148D GLU* 1.3 60.0 + - - +
150D SER* 3.4 5.6 + - - -
151D GLU* 3.0 28.6 + - - +
182D PHE* 3.5 9.9 - - + -
186D ILE* 3.6 23.6 - - + -
187D GLN* 3.3 34.5 - - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ALA 3.2 15.3 + - - +
145D THR* 3.4 16.0 - - - +
147D VAL* 1.3 76.1 - - - +
149D SER* 1.4 55.1 + - - +
151D GLU* 3.4 7.9 + - + +
152D LYS* 3.0 30.6 + - + +
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LYS* 5.5 1.4 - - - -
131D TYR* 3.6 40.2 + - - -
145D THR* 3.1 19.2 + - - +
146D VAL 3.6 8.3 - - - -
147D VAL 3.3 0.2 - - - -
148D GLU* 1.4 72.4 - - - +
150D SER* 1.4 58.5 + - - +
152D LYS* 3.4 8.2 + - - +
153D ALA* 3.1 28.6 + - - +
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Residues in contact with SER 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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128D GLY* 2.8 27.7 + - - -
131D TYR* 3.7 13.2 - - - +
132D ARG* 3.7 7.0 + - - +
146D VAL 2.9 17.5 + - - -
147D VAL* 3.6 5.8 - - - -
149D SER* 1.4 71.1 - - - +
151D GLU* 1.3 59.4 + - - +
153D ALA* 3.3 3.3 + - - +
154D TYR* 3.0 48.5 + - - -
182D PHE* 3.4 16.9 - - - -
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Residues in contact with GLU 151 (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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147D VAL 3.0 18.5 + - - +
148D GLU* 3.6 7.4 - - - +
149D SER 3.4 0.2 - - - -
150D SER* 1.3 75.6 - - - +
152D LYS* 1.4 54.3 + - - +
154D TYR* 3.4 3.1 + - - +
155D SER* 2.8 44.4 + - - -
179D TYR* 2.7 26.5 + - - -
182D PHE* 3.7 20.0 - - + -
183D TYR* 3.8 15.0 + - - -
187D GLN* 3.4 23.1 + - - +
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Residues in contact with LYS 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 GLU* 3.0 17.7 + - + +
149D SER* 3.6 9.0 - - - +
151D GLU* 1.4 76.6 - - - +
153D ALA* 1.4 61.0 + - - +
155D SER* 4.0 4.9 - - - -
156D GLU* 3.3 24.3 + - - +
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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
----------------------------------------------------------
124D LEU* 3.4 34.0 - - + +
127D LYS* 3.8 22.0 - - + -
128D GLY* 3.5 15.9 - - - +
149D SER 3.1 16.6 + - - +
150D SER 3.7 2.0 - - - +
151D GLU 3.3 0.2 - - - -
152D LYS* 1.4 74.3 - - - +
154D TYR* 1.4 63.3 + - - +
156D GLU* 3.5 2.3 + - - +
157D ALA* 3.1 23.2 + - - +
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Residues in contact with TYR 154 (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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125D LYS* 3.6 19.5 - - + -
128D GLY* 3.4 10.1 - - - -
129D ASP* 2.6 33.2 + - - -
132D ARG* 2.8 19.8 + - - -
150D SER* 3.0 41.2 + - - +
151D GLU 4.0 0.4 - - - +
153D ALA* 1.4 74.5 - - - +
155D SER* 1.4 52.3 + - - +
157D ALA* 3.3 2.8 + - - +
158D HIS* 2.8 36.0 + - - +
175D LEU* 3.7 22.3 - - + +
178D ASN* 3.9 16.2 - - + +
179D TYR* 3.5 39.8 - + + -
182D PHE* 3.7 23.3 - + + -
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Residues in contact with SER 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 GLU* 2.8 30.3 + - - -
152D LYS* 4.0 6.1 - - - -
154D TYR* 1.4 71.2 - - - +
156D GLU* 1.4 60.6 + - - +
158D HIS* 3.4 3.6 + - - +
159D GLU* 3.1 23.6 + - - +
179D TYR* 3.8 20.2 + - - -
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Residues in contact with GLU 156 (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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124D LEU* 3.7 31.4 - - + -
152D LYS 3.3 17.0 + - - +
153D ALA 3.8 4.5 - - - +
154D TYR 3.4 0.2 - - - -
155D SER* 1.4 76.7 - - - +
157D ALA* 1.4 61.0 + - - +
159D GLU* 3.3 7.3 + - + +
160D ILE* 3.2 36.7 + - + +
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Residues in contact with ALA 157 (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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121D VAL* 3.7 21.5 - - + +
124D LEU* 3.7 23.4 - - + +
125D LYS 4.2 2.5 - - - +
153D ALA 3.1 17.0 + - - +
154D TYR 3.6 4.7 - - - +
156D GLU* 1.4 73.9 - - - +
158D HIS* 1.3 57.9 + - - +
160D ILE* 3.5 0.8 + - - -
161D SER* 3.0 31.4 + - - -
175D LEU* 3.5 23.1 - - + +
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Residues in contact with HIS 158 (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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154D TYR 2.8 17.5 + - - +
155D SER* 3.6 5.8 - - - +
156D GLU 3.3 0.2 - - - -
157D ALA* 1.3 75.2 - - - +
159D GLU* 1.3 59.0 + - - +
161D SER* 4.0 2.0 - - - -
162D LYS* 3.1 61.4 + - + +
172D ARG* 5.9 4.4 + - + -
175D LEU* 3.5 16.8 - - + +
176D ALA* 5.3 6.8 - - + +
179D TYR* 4.0 22.1 - + + -
196D LEU* 3.5 30.3 - - + +
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Residues in contact with GLU 159 (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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155D SER 3.1 13.4 + - - +
156D GLU* 3.3 10.7 + - + +
158D HIS* 1.3 77.6 + - - +
160D ILE* 1.4 61.5 + - + +
162D LYS* 3.9 7.4 - - - +
163D GLU* 3.3 23.7 + - - +
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Residues in contact with ILE 160 (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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117D TYR* 4.3 18.4 - - + +
120D LYS* 4.5 12.8 - - + -
121D VAL* 3.7 20.2 - - + -
124D LEU* 3.8 24.9 - - + -
156D GLU* 3.2 27.2 + - + +
157D ALA* 4.7 1.1 - - - -
158D HIS 3.4 0.2 - - - -
159D GLU* 1.4 74.1 - - + +
161D SER* 1.4 58.6 + - - +
163D GLU* 3.2 2.8 + - - -
164D HIS* 2.9 49.3 + - + +
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Residues in contact with SER 161 (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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121D VAL* 3.8 9.8 - - - +
157D ALA 3.0 18.4 + - - -
158D HIS* 4.0 4.3 - - - -
159D GLU 3.5 0.2 - - - -
160D ILE* 1.4 74.9 - - - +
162D LYS* 1.4 57.7 + - - +
165D MET* 2.9 56.3 + - - +
172D ARG* 3.6 26.6 - - - -
175D LEU* 4.2 7.2 - - - -
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Residues in contact with LYS 162 (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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158D HIS* 3.1 53.8 + - + +
159D GLU* 3.9 6.7 - - - +
161D SER* 1.4 76.7 - - - +
163D GLU* 1.3 61.2 + - - +
165D MET 4.2 2.1 - - - +
172D ARG* 4.0 32.8 + - - +
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Residues in contact with GLU 163 (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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159D GLU 3.3 16.2 + - - +
160D ILE* 3.2 5.0 + - - +
162D LYS* 1.3 81.2 - - - +
164D HIS* 1.3 83.6 + - + +
165D MET 5.2 0.2 - - - -
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Residues in contact with HIS 164 (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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114D GLU 6.2 0.2 - - - -
117D TYR* 4.0 23.7 - - + +
160D ILE* 2.9 39.2 + - + +
163D GLU* 1.3 97.2 - - + +
165D MET* 1.3 62.2 + - + +
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Residues in contact with MET 165 (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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117D TYR* 4.9 5.6 - - + +
118D GLU* 3.8 22.7 - - + -
121D VAL* 3.8 30.3 - - - -
161D SER* 2.9 26.1 + - - +
162D LYS 4.2 3.1 - - - +
164D HIS* 1.3 86.1 - - + +
166D GLN* 1.3 60.2 + - - +
167D PRO* 4.3 0.3 - - - +
169D HIS* 3.4 44.6 - - + +
171D ILE* 3.7 17.5 - - + -
172D ARG* 2.8 36.0 + - - +
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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) + - + + + + + -
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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