Contacts of the helix formed by residues 153 - 175 (chain D) in PDB entry 3RKR
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 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D TRP* 3.9 8.5 - - - -
96D PHE* 3.8 21.3 - - - -
150D VAL* 2.8 16.4 + - - +
151D ALA 3.1 1.8 + - - -
152D ASP* 1.3 78.7 - - - +
154D ALA* 1.3 54.2 + - - +
155D ALA 3.5 2.0 - - - -
156D TYR* 3.3 4.9 + - - +
157D THR* 2.7 37.2 + - - -
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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
----------------------------------------------------------
95D TRP* 6.0 1.8 - - - -
98D GLY 5.6 0.4 + - - -
100D LEU* 3.9 39.0 - - + +
150D VAL 3.5 5.3 + - - +
152D ASP 3.7 4.9 - - - +
153D GLY* 1.3 76.4 - - - +
155D ALA* 1.3 58.8 + - - +
157D THR* 3.4 7.5 + - - -
158D ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D TRP* 5.9 1.3 - - + -
100D LEU* 4.4 2.9 - - + +
103D MET* 3.6 38.3 - - + -
108D TRP* 3.7 29.2 - - + -
111D LEU* 3.6 12.0 - - + +
112D ILE* 4.2 2.4 - - + +
153D GLY 3.5 0.2 - - - -
154D ALA* 1.3 75.8 - - - +
156D TYR* 1.3 66.3 + - - +
158D ALA* 3.3 5.6 + - - +
159D SER* 2.9 23.4 + - - -
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Residues in contact with TYR 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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93D VAL 3.5 26.7 - - - -
94D GLY* 4.0 4.5 - - - -
95D TRP 4.3 4.0 + - - +
96D PHE* 3.6 38.4 - + + -
111D LEU* 4.0 13.2 - - + +
115D ASN* 4.0 5.6 - - - -
143D SER* 2.4 32.5 + - - -
144D LEU* 3.8 26.0 - - + -
150D VAL* 4.8 4.5 - - + -
153D GLY* 3.3 13.4 - - - +
154D ALA 3.3 0.2 - - - -
155D ALA* 1.3 78.0 - - - +
157D THR* 1.3 64.3 + - - +
159D SER* 2.7 24.4 + - - -
160D LYS* 3.0 23.6 + - + +
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Residues in contact with THR 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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144D LEU* 3.8 12.3 - - + -
149D PRO* 4.2 17.5 - - + -
150D VAL* 3.2 25.9 + - - +
153D GLY 2.7 22.1 + - - -
154D ALA* 3.4 10.5 - - - -
156D TYR* 1.3 73.2 - - - +
158D ALA* 1.3 63.6 + - - +
160D LYS* 3.0 2.6 + - - -
161D TRP* 2.9 55.8 + - + +
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Residues in contact with ALA 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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108D TRP* 4.9 13.5 - - + -
112D ILE* 5.1 3.6 - - + -
116D LEU* 5.1 2.8 - - - +
154D ALA 2.9 17.3 + - - +
155D ALA* 3.3 12.3 + - - +
157D THR* 1.3 72.7 - - - +
159D SER* 1.3 59.2 + - - +
161D TRP* 4.3 3.9 - - - +
162D GLY* 2.8 28.5 + - - +
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Residues in contact with SER 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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111D LEU* 3.8 9.0 - - - -
112D ILE* 3.9 14.4 - - - -
115D ASN* 3.0 43.7 + - - +
116D LEU* 3.9 12.5 - - - +
155D ALA 2.9 12.8 + - - -
156D TYR* 2.7 19.4 + - - -
158D ALA* 1.3 75.6 - - - +
160D LYS* 1.3 60.8 + - - +
162D GLY 3.9 0.2 - - - -
163D LEU* 2.9 27.4 + - - +
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Residues in contact with LYS 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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91D ALA 5.3 1.6 + - - -
92D GLY* 4.6 11.3 - - - -
93D VAL 5.0 0.4 + - - -
115D ASN* 3.7 36.6 + - + +
141D ILE 4.8 9.9 + - - -
142D SER* 4.1 13.5 - - - +
143D SER* 3.6 28.7 + - - +
144D LEU* 3.8 29.8 - - + -
156D TYR* 3.0 29.2 + - + +
157D THR 3.0 3.8 + - - +
159D SER* 1.3 78.1 - - - +
161D TRP* 1.3 60.6 + - - +
162D GLY 3.1 1.1 - - - -
163D LEU* 3.2 14.2 + - + +
164D ASN* 2.9 35.6 + - - +
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Residues in contact with TRP 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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144D LEU* 4.4 12.4 - - + +
146D GLY* 3.4 53.4 - - - +
147D LYS 3.6 19.3 - - - -
148D ASN 3.7 17.9 + - - -
149D PRO* 4.1 7.9 - - + -
157D THR* 2.9 39.3 + - + +
158D ALA* 4.3 3.4 - - - +
160D LYS* 1.3 74.3 - - - +
162D GLY* 1.3 56.2 + - - +
164D ASN* 3.2 11.3 + - - +
165D GLY* 3.0 25.3 + - - -
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Residues in contact with GLY 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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116D LEU* 3.5 15.8 - - - +
158D ALA 2.8 20.6 + - - -
159D SER 3.9 0.9 - - - -
161D TRP* 1.3 77.7 - - - +
163D LEU* 1.3 50.3 + - - +
165D GLY* 3.1 2.8 + - - -
166D LEU* 2.7 36.0 + - - +
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Residues in contact with LEU 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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89D ASN* 5.8 1.8 - - + +
115D ASN 4.2 9.9 - - - +
116D LEU* 3.4 7.9 - - + +
119D PRO* 3.8 34.8 - - + -
140D ASN* 4.3 14.8 - - + +
141D ILE 4.1 20.0 - - - +
142D SER* 4.2 16.8 - - - +
159D SER 2.9 20.8 + - - +
160D LYS* 3.2 15.2 + - + +
162D GLY* 1.3 74.3 - - - +
164D ASN* 1.3 64.0 + - - +
166D LEU* 3.2 7.8 + - + +
167D MET* 2.9 41.5 + - + +
183D LEU* 4.9 1.1 - - + -
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Residues in contact with ASN 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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142D SER* 2.8 27.3 + - - -
144D LEU 2.9 24.7 + - - -
145D ALA* 3.7 19.2 + - - +
146D GLY* 3.9 3.6 - - - +
160D LYS 2.9 18.2 + - - +
161D TRP* 3.2 12.1 + - - +
163D LEU* 1.3 71.2 - - - +
165D GLY* 1.3 54.9 + - - +
167D MET 4.0 0.2 - - - -
168D THR* 2.6 39.0 + - - +
183D LEU* 3.6 25.9 - - + +
230D GLU* 5.5 2.0 + - - -
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Residues in contact with GLY 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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161D TRP 3.0 14.2 + - - -
162D GLY* 3.6 2.7 - - - -
164D ASN* 1.3 73.7 - - - +
166D LEU* 1.3 67.1 + - - +
168D THR* 3.9 4.9 - - - -
169D SER* 3.0 29.6 + - - -
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Residues in contact with LEU 166 (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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116D LEU* 4.0 24.0 - - + +
120D TYR* 3.9 31.2 - - + +
162D GLY 2.7 21.2 + - - +
163D LEU* 3.5 11.2 - - + +
165D GLY* 1.3 73.8 - - - +
167D MET* 1.3 77.9 + - + +
169D SER* 3.5 4.2 + - - -
170D ALA* 3.0 26.5 + - + +
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Residues in contact with MET 167 (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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89D ASN* 4.1 2.9 - - - +
119D PRO* 3.5 39.3 - - + +
120D TYR* 4.3 0.7 - - - +
123D LEU* 4.0 27.6 - - + -
138D ILE* 4.9 0.9 - - + -
140D ASN* 3.4 46.0 - - + +
163D LEU* 2.9 27.4 + - + +
164D ASN 4.5 0.9 - - - +
166D LEU* 1.3 84.0 - - + +
168D THR* 1.3 60.8 + - - +
169D SER 3.3 0.2 - - - -
170D ALA* 3.8 4.0 - - - +
171D ALA* 3.0 28.8 + - - +
181D VAL* 3.5 14.1 - - + +
182D SER 5.7 0.2 - - - -
183D LEU* 4.8 12.3 - - + -
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Residues in contact with THR 168 (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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187A GLY 5.5 2.2 - - - +
234A ARG* 3.6 25.1 + - - +
164D ASN* 2.6 24.6 + - - +
165D GLY* 3.9 5.2 - - - -
167D MET* 1.3 74.5 - - - +
169D SER* 1.3 62.6 + - - +
171D ALA* 3.5 6.1 - - - +
172D GLU* 3.5 20.9 + - - +
183D LEU* 4.2 13.0 - - - +
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Residues in contact with SER 169 (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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165D GLY 3.0 19.3 + - - -
166D LEU* 3.7 4.7 - - - -
168D THR* 1.3 76.8 - - - +
170D ALA* 1.3 66.0 + - - +
172D GLU* 3.0 21.3 + - - +
173D GLU* 3.2 23.2 + - - +
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Residues in contact with ALA 170 (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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123D LEU* 3.9 29.4 - - + -
166D LEU* 3.0 18.6 + - + +
167D MET* 4.1 9.6 - - - +
168D THR 3.5 0.2 - - - -
169D SER* 1.3 75.2 - - - +
171D ALA* 1.3 58.0 + - - +
173D GLU* 3.0 20.8 + - - +
174D LEU* 2.8 34.4 + - + +
181D VAL* 4.2 4.9 - - + -
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Residues in contact with ALA 171 (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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234A ARG* 3.9 15.5 - - - +
167D MET 3.0 19.2 + - - +
168D THR* 3.5 8.1 - - - +
169D SER 3.1 0.2 - - - -
170D ALA* 1.3 76.3 - - - +
172D GLU* 1.3 58.5 + - - +
174D LEU 3.5 0.9 + - - -
175D ARG* 3.0 31.5 + - - +
179D VAL 4.9 0.7 - - - +
181D VAL* 3.7 34.0 - - + +
227D PHE* 4.0 11.3 - - + -
229D SER* 5.6 0.7 - - - -
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Residues in contact with GLU 172 (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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188A SER* 4.9 2.6 + - - -
189A VAL 5.3 3.1 + - - -
234A ARG* 2.7 34.1 + - - +
168D THR* 3.5 9.4 + - - +
169D SER* 3.0 14.2 + - - +
171D ALA* 1.3 75.4 - - - +
173D GLU* 1.3 66.1 + - + +
174D LEU 3.6 0.2 + - - -
175D ARG* 3.9 17.2 + - - +
176D GLN* 4.6 7.1 + - - -
240D SO4 3.0 15.1 + - - +
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Residues in contact with GLU 173 (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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123D LEU* 6.0 1.7 - - - +
169D SER* 3.2 21.3 + - - +
170D ALA* 3.0 21.6 + - - +
172D GLU* 1.3 80.1 - - + +
174D LEU* 1.3 66.0 + - + +
176D GLN* 3.5 27.5 - - - +
177D HIS* 4.2 4.9 - - - -
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Residues in contact with LEU 174 (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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123D LEU* 4.3 21.5 - - + -
127D ALA* 4.7 9.6 - - + -
131D ILE* 3.9 33.0 - - + -
138D ILE* 4.5 4.5 - - + -
170D ALA* 2.8 16.4 + - + +
171D ALA 3.5 1.5 + - - +
172D GLU 3.3 0.2 - - - -
173D GLU* 1.3 82.4 - - + +
175D ARG* 1.3 62.7 + - - +
176D GLN 3.2 2.5 - - - -
177D HIS* 3.1 20.1 + - + +
179D VAL* 3.0 44.6 + - + +
181D VAL* 3.7 26.0 - - + -
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Residues in contact with ARG 175 (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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234A ARG* 3.9 1.8 - - - +
235A PRO* 2.7 37.8 + - - +
236A THR 3.4 13.3 + - - -
237A LEU* 3.7 26.9 - - + +
238A LYS* 5.1 4.9 + - - +
171D ALA 3.0 23.8 + - - +
172D GLU* 4.0 10.1 - - - +
173D GLU 3.5 1.2 - - - -
174D LEU* 1.3 77.0 - - - +
176D GLN* 1.3 59.3 + - - +
178D GLN* 2.8 23.0 + - - +
179D VAL 3.8 8.1 - - - -
227D PHE* 3.3 33.1 - - + -
240D SO4 2.7 49.6 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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