Contacts of the helix formed by residues 163 - 184 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 2.6 20.1 + - - +
182A ILE* 3.8 13.7 - - - +
86C MET* 3.7 37.6 - - - +
90C ILE* 4.9 0.9 - - - -
127C LYS* 5.2 0.2 - - - +
162C HIS* 1.3 83.9 + - - +
164C PRO* 1.3 76.9 - - - +
165C TYR* 3.5 10.6 + - - +
166C GLY 2.9 21.3 + - - -
167C CYS* 3.0 9.9 + - - -
300C GLU* 5.6 0.9 - - - -
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Residues in contact with PRO 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.7 11.5 + - + +
178A ASP* 3.5 9.2 - - - +
179A TYR* 5.0 3.4 - - + -
182A ILE* 4.2 5.8 - - + -
183A PHE* 4.1 24.2 - - + -
89C SER* 3.5 33.9 - - - +
90C ILE* 4.0 12.6 - - + -
93C PRO* 4.1 13.2 - - + -
96C ASP* 3.0 12.4 - - - +
163C SER* 1.3 87.5 - - - +
165C TYR* 1.3 54.9 + - - +
167C CYS* 3.2 7.8 + - + +
168C SER* 2.9 26.7 + - - -
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Residues in contact with TYR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLN* 3.2 29.4 - - - -
84C VAL* 3.7 23.9 + - - -
85C ALA 4.3 0.4 - - - -
86C MET* 4.0 17.0 - - + -
89C SER* 3.0 22.2 + - - +
96C ASP* 3.6 14.4 - - - -
100C ASN* 4.2 0.2 - - - -
125C THR* 2.8 42.7 - - + +
127C LYS* 4.0 23.8 - - + -
163C SER* 3.6 7.6 - - - +
164C PRO* 1.3 77.1 - - - +
166C GLY* 1.3 63.5 + - - +
168C SER* 3.3 0.9 + - - -
169C LYS* 3.0 42.2 + - + +
1400C NAD 3.3 17.0 + - - -
1401C CDP 6.0 1.1 - - - -
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 5.5 0.2 - - - -
127C LYS* 4.3 17.0 - - - -
128C VAL* 4.4 2.4 - - - +
161C PHE* 3.6 12.6 - - - +
162C HIS 3.3 16.8 - - - -
163C SER* 2.9 11.3 + - - -
165C TYR* 1.3 83.6 - - - +
167C CYS* 1.3 55.6 + - - +
169C LYS* 4.3 2.2 - - - +
170C GLY* 2.8 27.9 + - - -
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Residues in contact with CYS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 5.7 0.5 - - - +
174A GLN* 3.7 20.0 - - + -
175A TYR* 3.6 30.4 - - + -
178A ASP* 3.5 33.2 - - - -
161C PHE* 3.6 24.4 - - + -
163C SER 3.0 11.5 + - - -
164C PRO 3.6 7.2 - - - +
166C GLY* 1.3 78.7 - - - +
168C SER* 1.3 58.9 + - - +
171C ALA* 3.0 29.1 + - - +
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.1 13.2 - - - -
96C ASP* 2.6 32.6 + - - -
100C ASN* 3.0 24.7 + - - +
101C VAL* 3.4 26.5 - - - +
164C PRO 2.9 12.0 + - - -
165C TYR 3.3 3.3 + - - -
167C CYS* 1.3 70.3 - - - +
169C LYS* 1.3 67.8 + - - +
171C ALA 3.4 0.3 + - - -
172C ALA* 3.1 21.3 + - - +
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Residues in contact with LYS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA 5.4 0.6 + - - -
82C GLY* 5.0 0.4 - - - -
83C GLN 4.9 0.2 - - - +
100C ASN* 3.8 22.7 + - - +
122C TYR* 3.3 23.1 + - - +
123C SER* 2.9 24.3 + - - -
124C SER* 4.0 12.1 + - - +
125C THR* 3.4 21.5 - - - +
128C VAL* 4.4 2.0 - - + -
165C TYR* 3.0 41.6 + - + +
166C GLY 4.3 1.6 - - - +
168C SER* 1.3 75.1 + - - +
170C GLY* 1.3 61.1 + - - +
172C ALA* 3.3 2.1 + - - +
173C ASP* 2.9 29.9 + - - +
1400C NAD 2.6 44.1 + - - -
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Residues in contact with GLY 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C VAL* 3.6 15.4 - - - +
161C PHE* 3.3 23.6 - - - -
166C GLY 2.8 19.8 + - - -
169C LYS* 1.3 78.2 - - - +
171C ALA* 1.3 61.1 + - - +
173C ASP* 3.2 3.5 - - - +
174C GLN* 3.0 28.1 + - - +
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Residues in contact with ALA 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 5.4 1.1 - - - -
167A CYS 5.8 0.4 - - - -
171A ALA* 3.6 31.2 - - + -
175A TYR* 5.2 1.3 - - + -
101C VAL* 4.2 19.7 - - + -
161C PHE* 3.6 6.3 - - + -
167C CYS 3.0 19.1 + - - +
168C SER 3.9 3.4 - - - +
169C LYS 3.3 0.2 - - - -
170C GLY* 1.3 76.6 - - - +
172C ALA* 1.3 64.8 + - - +
174C GLN* 3.4 4.3 + - - +
175C TYR* 3.0 32.8 + - + -
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASN 3.5 20.9 - - - +
101C VAL* 4.7 2.5 - - - +
104C THR* 3.7 14.9 - - + +
105C LEU* 5.1 2.9 - - - -
122C TYR* 3.2 32.1 - - + +
168C SER 3.1 12.5 + - - +
169C LYS 3.7 0.7 - - - +
170C GLY 3.3 0.2 - - - -
171C ALA* 1.3 77.5 - - - +
173C ASP* 1.3 55.7 + - - +
175C TYR* 3.3 6.2 + - - +
176C MET* 2.9 33.4 + - - +
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 3.9 11.4 - - - -
124C SER* 2.8 27.2 + - - +
128C VAL* 4.1 6.9 - - - +
159C LEU* 6.1 0.4 - - - -
161C PHE* 6.0 0.4 - - - -
169C LYS 2.9 18.1 + - - +
170C GLY* 3.2 8.5 - - - +
172C ALA* 1.3 75.8 - - - +
174C GLN* 1.3 70.4 + - - +
176C MET* 3.1 6.9 + - - +
177C LEU* 3.1 26.5 + - - +
189C VAL* 3.5 8.4 - - - +
191C ARG* 2.9 45.0 + - - +
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASP* 3.7 12.3 - - - +
161A PHE* 3.1 61.3 + - + +
167A CYS* 3.6 4.9 - - + -
159C LEU* 3.6 17.3 - - - +
161C PHE* 3.9 10.7 - - + -
170C GLY 3.0 15.9 + - - +
171C ALA 3.9 3.4 - - - +
173C ASP* 1.3 97.3 + - - +
175C TYR* 1.3 58.4 + - - +
177C LEU* 3.2 12.0 + - - +
178C ASP* 2.8 31.4 + - - +
181C ARG* 5.5 1.8 + - - -
191C ARG* 3.4 15.2 - - - +
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Residues in contact with TYR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 5.1 2.2 + - + -
96A ASP* 4.2 1.2 + - - -
97A PHE* 3.6 36.4 - + + +
101A VAL* 4.8 2.0 - - + -
164A PRO* 3.8 15.6 + - + -
167A CYS* 3.5 37.2 - - + -
168A SER* 3.3 28.7 + - - -
101C VAL* 5.1 2.0 - - + -
105C LEU* 3.7 34.5 - - + -
108C LEU* 4.0 6.7 - - + -
171C ALA* 3.0 32.3 + - + +
172C ALA 3.6 4.7 - - - +
174C GLN* 1.3 73.0 - - - +
176C MET* 1.3 67.7 + - - +
178C ASP* 5.5 0.2 - - + -
179C TYR* 2.9 53.0 + + - -
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Residues in contact with MET 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C HIS* 4.1 9.2 - - + -
104C THR* 3.6 25.4 - - + -
107C LEU* 4.7 3.4 - - + -
108C LEU* 4.0 21.1 - - + +
120C ILE* 4.1 18.2 - - + +
122C TYR* 3.8 39.3 - - + -
172C ALA 2.9 18.8 + - - +
173C ASP 3.3 8.5 - - - +
175C TYR* 1.3 79.2 - - - +
177C LEU* 1.3 61.9 + - - +
179C TYR* 3.5 0.5 + - - +
180C ALA 3.4 8.7 + - - -
187C THR* 2.8 46.6 + - - +
188C VAL 5.1 0.2 - - - +
189C VAL* 3.6 13.9 - - + -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASP* 6.0 0.2 - - - +
173C ASP* 3.1 27.4 + - - +
174C GLN* 3.8 14.8 - - - +
176C MET* 1.3 81.8 - - - +
178C ASP* 1.3 63.2 + - - +
180C ALA* 3.3 13.8 + - - +
181C ARG* 3.4 35.2 + - - +
187C THR* 4.4 3.6 - - - +
189C VAL* 3.9 13.5 - - + +
191C ARG* 3.8 14.1 - - - +
261C GLY* 3.5 27.8 - - - +
262C ASN* 3.5 23.6 - - - +
263C ALA* 3.7 8.7 - - + +
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE 4.0 0.2 - - - -
162A HIS* 3.5 0.7 - - - -
163A SER* 2.8 48.5 + - - -
164A PRO* 3.2 7.6 - - - +
167A CYS* 3.5 14.4 - - - -
174C GLN 2.8 16.4 + - - +
175C TYR* 4.0 2.5 - - - +
177C LEU* 1.3 74.4 - - - +
179C TYR* 1.3 63.3 + - + +
180C ALA 3.1 2.0 - - - -
181C ARG* 2.7 32.7 + - - +
182C ILE* 2.8 50.4 + - - +
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 3.5 16.6 - - + +
164A PRO* 5.1 2.7 - - + -
105C LEU* 3.9 9.8 - - + +
108C LEU* 3.7 35.2 - - + -
109C GLU* 2.6 34.4 + - - +
112C ARG* 3.9 11.0 - - - -
175C TYR* 2.9 47.2 + + - +
176C MET 4.0 4.0 - - - +
178C ASP* 1.3 78.6 - - + +
180C ALA* 1.3 58.5 + - - +
183C PHE* 3.0 50.0 + + - +
185C LEU* 3.1 42.9 + - + +
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Residues in contact with ALA 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C MET 3.4 2.8 + - - -
177C LEU 3.3 10.4 + - - +
178C ASP 3.1 0.4 - - - -
179C TYR* 1.3 78.9 - - - +
181C ARG* 1.3 58.4 + - - +
184C GLY* 2.9 19.6 + - - -
185C LEU* 3.2 25.5 - - - +
187C THR* 3.3 18.6 + - - +
260C ARG* 3.0 17.7 + - - +
261C GLY* 3.6 22.0 - - - -
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Residues in contact with ARG 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASP* 3.3 20.2 + - - -
161A PHE 3.2 17.6 + - - -
162A HIS* 3.3 30.4 + - - -
300A GLU* 4.7 3.6 - - - +
301A SER* 5.9 0.9 - - - -
174C GLN* 4.9 2.0 + - - -
177C LEU* 3.4 32.0 + - - +
178C ASP* 2.7 46.8 + - - +
180C ALA* 1.3 80.6 - - - +
182C ILE* 1.3 69.5 + - + +
184C GLY* 4.4 1.6 + - - -
261C GLY 5.5 3.4 + - - -
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 4.1 26.0 - - + +
163A SER* 4.1 18.6 - - - +
164A PRO* 4.4 0.9 - - + -
300A GLU* 3.2 32.4 - - + +
301A SER* 4.4 13.7 - - - +
178C ASP* 2.8 40.4 + - - +
181C ARG* 1.3 81.4 - - + +
183C PHE* 1.3 96.5 + - + +
184C GLY 3.5 0.4 + - - -
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Residues in contact with PHE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.5 30.7 - - + -
93A PRO* 3.9 13.9 - - + -
164A PRO* 4.1 14.6 - - + -
112C ARG* 3.7 42.8 - - + -
116C SER* 5.6 2.3 - - - -
178C ASP* 5.8 0.2 - - - -
179C TYR* 3.0 44.9 + + - +
182C ILE* 1.3 105.1 - - + +
184C GLY* 1.3 64.1 + - - +
185C LEU* 3.3 11.4 + - + +
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Residues in contact with GLY 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C SER 4.8 2.9 - - - +
180C ALA 2.9 16.9 + - - -
181C ARG 4.3 1.4 + - - -
182C ILE 3.5 2.2 - - - -
183C PHE* 1.3 78.7 - - - +
185C LEU* 1.3 67.1 + - - +
186C ASN* 3.7 8.1 + - - +
260C ARG* 3.5 9.7 + - - -
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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