Contacts of the helix formed by residues 163 - 184 (chain B) in PDB entry 1ORR
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 SER 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B MET* 3.5 34.2 - - - +
90B ILE* 4.8 1.3 - - - -
162B HIS* 1.3 77.9 + - - +
164B PRO* 1.3 71.6 - - - +
165B TYR* 3.4 5.4 + - - +
166B GLY 3.1 12.3 + - - -
167B CYS* 2.8 27.5 + - - -
301B SER* 3.9 14.2 + - - -
178D ASP* 2.8 20.2 + - - +
182D ILE* 4.1 7.7 - - - +
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Residues in contact with PRO 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 3.3 34.8 - - - +
90B ILE* 3.8 16.6 - - + -
93B PRO* 4.1 13.0 - - + -
96B ASP* 3.0 11.7 - - - +
163B SER* 1.3 90.6 - - - +
165B TYR* 1.3 50.3 + - - +
167B CYS* 3.1 7.6 + - + +
168B SER* 2.7 32.2 + - - -
175D TYR* 3.8 12.4 + - + +
178D ASP* 3.6 9.2 - - - +
179D TYR* 5.3 2.0 - - + -
182D ILE* 4.3 5.2 - - + -
183D PHE* 4.2 20.2 - - + -
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLN* 3.1 28.9 - - - -
84B VAL* 3.7 24.8 + - - +
86B MET* 4.0 16.4 - - + -
89B SER* 3.2 23.6 + - - +
96B ASP* 3.4 13.7 - - - -
125B THR* 3.5 36.1 + - + -
127B LYS* 4.1 16.8 - - + -
163B SER* 3.1 8.0 - - - +
164B PRO* 1.3 77.0 - - - +
166B GLY* 1.3 57.1 + - - +
169B LYS* 2.9 54.8 + - + +
1300B NAD 3.3 26.0 + - - -
1301B CDP 5.6 3.5 + - - -
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 5.0 0.2 - - - -
127B LYS* 4.3 22.2 - - - -
128B VAL* 4.4 2.3 - - - +
161B PHE* 3.6 12.6 - - - +
162B HIS 3.5 17.0 - - - -
163B SER* 3.1 11.3 + - - -
165B TYR* 1.3 76.8 - - - +
167B CYS* 1.3 58.6 + - - +
169B LYS* 4.2 2.4 - - - +
170B GLY* 2.8 27.9 + - - -
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Residues in contact with CYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 3.7 24.4 - - + -
163B SER 2.8 16.0 + - - +
164B PRO 3.4 7.2 - - - +
166B GLY* 1.3 79.0 - - - +
168B SER* 1.3 61.1 + - - +
171B ALA* 3.0 24.6 + - - +
171D ALA* 5.8 0.5 - - - -
174D GLN* 3.7 19.5 - - + -
175D TYR* 3.6 30.6 - - + -
178D ASP* 3.5 28.7 - - - -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP* 2.6 30.3 + - - -
100B ASN* 3.1 25.1 + - - +
101B VAL* 3.4 25.9 - - - +
164B PRO 2.7 10.1 + - - -
165B TYR 3.2 4.5 + - - -
167B CYS* 1.3 72.0 - - - +
169B LYS* 1.3 67.8 + - - +
171B ALA 3.4 0.5 + - - -
172B ALA* 3.1 22.7 + - - +
175D TYR* 3.2 16.4 + - - -
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA 5.4 0.6 + - - -
82B GLY* 5.1 0.4 - - - -
100B ASN* 3.5 26.8 + - - +
122B TYR* 3.3 26.7 + - - +
123B SER 2.9 21.7 + - - -
124B SER* 4.2 9.6 - - - +
125B THR* 3.5 17.3 - - + -
165B TYR* 2.9 45.8 + - + +
168B SER* 1.3 80.7 + - - +
170B GLY* 1.4 57.2 + - - +
172B ALA* 3.3 2.4 + - - +
173B ASP* 2.9 31.0 + - - +
1300B NAD 2.8 40.3 + - - +
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B VAL* 3.7 16.0 - - - +
161B PHE* 3.5 22.2 - - - -
166B GLY 2.8 22.9 + - - -
169B LYS* 1.4 75.3 - - - +
171B ALA* 1.3 60.5 + - - +
173B ASP* 3.3 3.8 + - - +
174B GLN* 3.0 28.8 + - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.1 19.1 - - + -
161B PHE* 3.8 6.3 - - + -
167B CYS 3.0 19.0 + - - +
168B SER 3.8 3.8 - - - +
169B LYS 3.3 0.2 - - - -
170B GLY* 1.3 75.7 - - - +
172B ALA* 1.3 63.8 + - - +
174B GLN* 3.3 5.7 + - - +
175B TYR* 2.9 31.6 + - + -
161D PHE* 5.4 1.6 - - - -
167D CYS 5.7 0.7 - - - -
171D ALA* 3.6 30.1 - - + -
175D TYR* 5.3 1.6 - - + -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ASN 3.6 16.4 - - - +
101B VAL* 4.8 3.7 - - - +
104B THR* 3.8 12.6 - - - +
105B LEU* 5.4 0.2 - - - -
122B TYR* 3.2 33.9 - - + +
168B SER 3.1 12.6 + - - +
169B LYS 3.5 3.4 - - - +
171B ALA* 1.3 76.6 - - - +
173B ASP* 1.3 63.8 + - - +
175B TYR* 3.1 8.7 + - - +
176B MET* 2.8 28.1 + - - +
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Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.8 10.3 - - - -
124B SER* 2.8 28.0 + - - +
128B VAL* 4.2 5.0 - - - +
161B PHE* 6.2 0.4 - - - -
169B LYS 2.9 17.7 + - - +
170B GLY* 3.4 7.9 - - - +
172B ALA* 1.3 76.0 - - - +
174B GLN* 1.3 71.7 + - - +
176B MET* 3.2 6.4 + - - +
177B LEU* 3.1 25.5 + - - +
189B VAL* 3.5 9.3 - - - +
191B ARG* 2.8 46.1 + - - +
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 3.8 15.3 - - - +
161B PHE* 4.1 7.2 - - + -
170B GLY 3.0 16.7 + - - +
171B ALA 3.8 3.4 - - - +
173B ASP* 1.3 96.6 + - - +
175B TYR* 1.3 57.8 + - - +
177B LEU* 3.3 13.2 + - - +
178B ASP* 2.9 31.0 + - - +
181B ARG* 4.8 1.0 + - - -
191B ARG* 3.4 15.0 - - - +
160D ASP* 3.7 12.3 + - - +
161D PHE* 3.1 65.0 + - + +
167D CYS* 3.7 5.1 - - + -
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.8 3.6 - - + -
105B LEU* 3.4 39.3 - - + -
108B LEU* 3.9 8.1 - - + -
171B ALA* 2.9 30.2 + - + +
172B ALA* 3.5 4.7 - - - +
174B GLN* 1.3 76.5 - - - +
176B MET* 1.3 58.1 + - - +
178B ASP* 3.7 0.4 - - - -
179B TYR* 2.8 59.3 + + - +
93D PRO* 5.1 2.2 + - + -
96D ASP* 4.3 1.2 + - - -
97D PHE* 3.5 31.5 - + + +
101D VAL* 4.8 2.2 - - + -
164D PRO* 3.9 14.2 + - + -
167D CYS* 3.6 37.9 - - + -
168D SER* 3.2 27.4 - - - -
171D ALA* 5.3 0.2 - - + -
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Residues in contact with MET 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B HIS* 4.1 9.4 - - + -
104B THR* 3.4 26.2 - - + -
107B LEU* 4.7 4.0 - - + -
108B LEU* 3.9 26.2 - - + +
120B ILE* 4.0 22.2 - - + -
122B TYR* 3.8 34.1 - - + -
172B ALA 2.8 17.0 + - - +
173B ASP 3.3 9.2 - - - +
175B TYR* 1.3 77.3 - - - +
177B LEU* 1.3 63.0 + - - +
179B TYR* 3.5 6.1 + - - +
180B ALA 3.5 2.6 + - - -
187B THR* 2.8 41.2 + - - +
188B VAL 5.2 0.2 - - - +
189B VAL* 3.5 14.4 - - + -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ASP* 3.1 15.1 + - - +
174B GLN* 3.8 14.4 - - - +
176B MET* 1.3 83.2 - - - +
178B ASP* 1.3 61.3 + - - +
180B ALA* 3.3 14.2 + - - +
181B ARG* 3.4 37.8 + - - +
187B THR* 4.3 3.4 - - - +
188B VAL 5.2 0.2 - - - -
189B VAL* 3.6 19.1 - - + +
191B ARG* 3.9 24.5 - - - +
261B GLY* 3.6 16.9 - - - +
262B ASN 3.5 31.2 - - - +
263B ALA* 4.0 9.0 - - + +
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLN 2.9 17.8 + - - +
175B TYR* 3.2 3.1 + - + +
177B LEU* 1.3 73.6 - - - +
179B TYR* 1.3 65.1 + - + +
181B ARG* 2.9 29.6 + - - +
182B ILE* 2.8 49.3 + - - +
161D PHE 4.1 0.2 - - - -
162D HIS* 3.4 1.4 - - - +
163D SER* 2.7 52.0 + - - -
164D PRO* 3.1 7.4 - - - +
167D CYS* 3.5 13.5 - - - -
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 3.7 10.3 - - + +
108B LEU* 3.8 34.8 - - + -
109B GLU* 2.5 37.4 + - - +
112B ARG* 3.9 5.2 - - - -
175B TYR* 2.8 49.0 + + - +
176B MET 4.0 4.0 - - - +
177B LEU 3.3 0.2 - - - -
178B ASP* 1.3 83.9 - - + +
180B ALA* 1.4 56.8 + - - +
183B PHE* 3.0 57.9 + + - +
184B GLY 3.1 5.9 + - - -
185B LEU* 3.1 35.4 + - + -
187B THR* 5.1 0.2 - - + -
93D PRO* 3.4 15.8 - - + +
164D PRO* 5.2 2.9 - - + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B MET 3.5 3.2 + - - -
177B LEU 3.3 9.4 + - - +
178B ASP 3.2 0.6 - - - -
179B TYR* 1.4 77.1 - - - +
181B ARG* 1.3 60.1 + - + +
184B GLY* 3.0 19.6 + - - -
185B LEU* 3.2 25.1 - - - +
187B THR* 3.4 17.9 + - - +
260B ARG* 3.0 18.8 + - - +
261B GLY* 3.5 22.9 - - - -
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLN* 4.8 1.0 + - - -
177B LEU* 3.4 36.2 + - - +
178B ASP* 2.9 39.7 + - - +
180B ALA* 1.3 82.4 - - + +
182B ILE* 1.3 69.8 + - + +
184B GLY* 4.3 1.2 + - - -
261B GLY 5.0 5.9 + - - -
160D ASP* 3.6 14.5 + - - -
161D PHE 3.3 17.6 + - - -
162D HIS* 3.5 33.2 + - - -
300D GLU* 4.5 5.2 - - - +
301D SER* 4.5 4.7 - - - -
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP* 2.8 45.1 + - - +
181B ARG* 1.3 83.0 - - + +
183B PHE* 1.3 94.3 + - + +
184B GLY 3.4 0.4 + - - -
90D ILE* 4.0 22.7 - - + -
163D SER* 4.1 15.7 - - - +
164D PRO* 4.5 0.9 - - + -
300D GLU* 3.4 39.2 - - + +
301D SER* 5.6 4.7 - - - +
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Residues in contact with PHE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG* 3.4 35.7 - - + -
116B SER* 5.7 1.6 - - - -
179B TYR* 3.0 56.2 + + - +
182B ILE* 1.3 101.9 - - + +
184B GLY* 1.3 65.0 + - - +
185B LEU* 3.3 12.7 + - + +
90D ILE* 3.5 31.4 - - + -
93D PRO* 3.8 16.4 - - + -
164D PRO* 4.2 11.4 - - + -
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Residues in contact with GLY 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B SER 4.8 2.8 - - - +
180B ALA 3.0 19.1 + - - -
181B ARG 4.3 1.4 + - - -
182B ILE 3.4 2.4 + - - -
183B PHE* 1.3 78.3 - - - +
185B LEU* 1.3 66.5 + - - +
186B ASN* 3.8 8.1 + - - +
260B ARG* 3.5 10.5 + - - -
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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
------------------------------------------------------------
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