Contacts of the helix formed by residues 162 - 184 (chain D) 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 HIS 162 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP* 3.4 2.7 - - - +
181B ARG* 3.5 27.0 - - - -
182B ILE* 6.1 0.2 - - + -
127D LYS* 3.9 12.9 + - - +
130D GLY* 3.7 11.2 - - - -
131D ASP* 3.8 25.4 + - - -
160D ASP* 2.7 52.1 + - - -
161D PHE* 1.3 72.5 - - - +
163D SER* 1.3 79.0 + - - +
166D GLY* 3.4 8.3 - - - -
301D SER* 2.4 44.6 + - - +
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Residues in contact with SER 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 2.7 21.4 + - - +
182B ILE* 4.1 13.0 - - - +
86D MET* 3.3 38.5 - - - +
89D SER* 4.4 0.2 - - - -
127D LYS* 5.0 0.7 - - - +
162D HIS* 1.3 82.4 + - - +
164D PRO* 1.3 73.3 - - - +
165D TYR* 3.5 2.1 + - - -
166D GLY 2.9 13.2 + - - -
167D CYS* 2.8 27.7 + - - -
300D GLU* 5.4 3.8 - - - -
301D SER* 5.3 1.1 - - - -
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Residues in contact with PRO 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 3.9 12.0 + - + -
178B ASP* 3.1 10.1 - - - +
179B TYR* 5.2 2.2 - - + -
182B ILE* 4.3 4.5 - - + -
183B PHE* 4.2 22.4 - - + -
89D SER* 3.5 35.4 - - - +
90D ILE* 3.8 13.5 - - + -
93D PRO* 4.1 12.6 - - + +
96D ASP* 2.9 11.8 - - - +
163D SER* 1.3 90.4 - - - +
165D TYR* 1.3 55.6 + - - +
167D CYS* 3.1 7.9 + - + +
168D SER* 2.8 27.4 + - - -
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Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D GLN* 3.1 30.7 - - - -
84D VAL* 3.5 24.2 + - - -
85D ALA 4.2 0.2 - - - -
86D MET* 3.8 13.7 - - + -
89D SER* 3.0 23.6 + - - +
96D ASP* 3.4 14.1 - - - -
125D THR* 3.7 28.2 + - + -
127D LYS* 3.7 36.5 + - + -
163D SER* 3.7 4.5 - - - +
164D PRO* 1.3 76.2 - - - +
166D GLY* 1.3 64.8 + - - +
168D SER* 3.2 1.0 + - - -
169D LYS* 2.9 48.7 + - + +
1500D NAD 3.4 22.8 + - - -
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Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D THR* 5.1 0.7 - - - -
127D LYS* 4.4 16.4 - - - -
128D VAL* 4.5 2.3 - - - +
161D PHE* 3.5 12.9 - - - +
162D HIS 3.4 16.6 - - - -
163D SER* 2.9 11.3 + - - -
165D TYR* 1.3 83.3 - - - +
167D CYS* 1.3 56.3 + - - +
169D LYS* 4.3 2.4 - - - +
170D GLY* 2.8 27.3 + - - -
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Residues in contact with CYS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA* 5.5 0.7 - - - +
174B GLN* 3.7 19.1 - - + -
175B TYR* 3.6 30.4 - - + -
178B ASP* 3.5 29.4 - - - -
161D PHE* 3.7 24.1 - - + -
163D SER 2.8 15.7 + - - +
164D PRO 3.5 7.2 - - - +
166D GLY* 1.3 77.7 - - - +
168D SER* 1.3 58.4 + - - +
171D ALA* 2.9 29.8 + - - +
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 3.2 14.6 + - - -
96D ASP* 2.5 34.5 + - - -
97D PHE* 4.1 0.2 - - - -
100D ASN* 3.1 24.3 + - - +
101D VAL* 3.4 27.0 - - - +
164D PRO 2.8 10.4 + - - -
165D TYR 3.2 2.6 + - - -
167D CYS* 1.3 70.5 - - - +
169D LYS* 1.3 67.4 + - - +
171D ALA 3.4 0.5 + - - -
172D ALA* 3.1 22.5 + - - +
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLY* 5.2 0.8 - - - -
100D ASN* 3.7 24.7 + - - +
122D TYR* 3.4 24.9 + - - +
123D SER 2.7 29.4 + - - -
124D SER* 4.0 12.1 - - - +
125D THR* 3.6 17.3 - - + -
128D VAL* 4.6 1.1 - - - -
165D TYR* 2.9 47.5 + - + +
166D GLY 4.3 0.2 - - - +
168D SER* 1.3 77.8 + - - +
170D GLY* 1.3 58.1 + - - +
172D ALA* 3.3 3.1 + - - +
173D ASP* 2.9 30.5 + - - +
1500D NAD 2.8 34.3 + - - -
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Residues in contact with GLY 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D VAL* 3.8 15.4 - - - +
161D PHE* 3.5 22.4 - - - -
166D GLY 2.8 21.3 + - - -
169D LYS* 1.3 77.6 - - - +
171D ALA* 1.3 60.9 + - - +
173D ASP* 3.3 3.2 + - - +
174D GLN* 3.0 28.9 + - - +
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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
----------------------------------------------------------
161B PHE* 5.3 2.2 - - - -
167B CYS 5.8 0.2 - - - -
171B ALA* 3.6 29.6 - - + -
175B TYR* 5.3 1.6 - - + -
101D VAL* 4.1 20.2 - - + -
161D PHE* 3.8 5.9 - - - -
167D CYS 2.9 18.7 + - - +
168D SER 3.8 3.6 - - - +
169D LYS 3.4 0.2 - - - -
170D GLY* 1.3 77.3 - - - +
172D ALA* 1.3 63.4 + - - +
174D GLN* 3.4 4.4 + - - +
175D TYR* 2.9 32.6 + - + -
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Residues in contact with ALA 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASN 3.6 17.3 - - - +
101D VAL* 4.7 4.4 - - - +
104D THR* 3.8 14.4 - - - +
105D LEU* 5.5 0.7 - - - -
122D TYR* 3.4 29.8 - - + +
168D SER 3.1 17.0 + - - +
169D LYS 3.5 0.7 - - - +
171D ALA* 1.3 76.2 - - - +
173D ASP* 1.3 56.0 + - - +
175D TYR* 3.3 7.1 + - - +
176D MET* 2.9 32.2 + - - +
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Residues in contact with ASP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D TYR* 3.9 10.7 - - - -
124D SER* 2.8 25.3 + - - +
128D VAL* 4.2 6.6 - - - +
159D LEU* 6.2 0.4 - - - -
161D PHE* 6.1 0.7 - - - -
169D LYS 2.9 16.5 + - - +
170D GLY* 3.4 7.2 - - - +
172D ALA* 1.3 75.4 - - - +
174D GLN* 1.3 69.6 + - - +
176D MET* 3.3 5.2 + - - +
177D LEU* 3.2 26.5 + - - +
189D VAL* 3.5 12.2 - - - +
191D ARG* 2.7 45.7 + - - +
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Residues in contact with GLN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 3.6 13.7 - - - +
161B PHE* 3.0 65.9 + - + +
167B CYS* 3.7 3.5 - - + -
159D LEU* 3.7 15.9 - - - +
161D PHE* 4.1 6.7 - - + -
170D GLY 3.0 20.4 + - - +
171D ALA 3.9 3.6 - - - +
173D ASP* 1.3 99.0 + - - +
175D TYR* 1.3 57.1 + - - +
177D LEU* 3.4 13.1 + - - +
178D ASP* 2.9 31.0 + - - +
181D ARG* 5.8 0.2 + - - -
191D ARG* 3.4 14.8 - - - +
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 4.9 2.6 + - + -
96B ASP* 4.3 1.0 + - - -
97B PHE* 3.6 36.8 - + + +
101B VAL* 4.8 2.2 - - + -
164B PRO* 3.8 14.8 + - + +
167B CYS* 3.6 39.0 - - + -
168B SER* 3.2 27.9 + - - -
101D VAL* 5.0 2.5 - - + -
105D LEU* 3.6 25.1 - - + -
108D LEU* 4.0 13.2 - - + -
171D ALA* 2.9 31.1 + - + +
172D ALA* 3.7 4.9 - - - +
174D GLN* 1.3 77.8 - - - +
176D MET* 1.3 58.1 + - - +
178D ASP* 4.6 0.4 - - + -
179D TYR* 2.9 61.6 + + - -
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Residues in contact with MET 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D HIS* 4.1 10.3 - - + -
104D THR* 3.5 26.7 - - + -
107D LEU* 4.6 4.7 - - + -
108D LEU* 3.9 27.1 - - + +
120D ILE* 4.0 21.1 - - + -
122D TYR* 3.7 34.3 - - + -
172D ALA 2.9 18.3 + - - +
173D ASP 3.3 8.0 + - - +
175D TYR* 1.3 77.9 - - - +
177D LEU* 1.3 59.3 + - - +
179D TYR* 3.5 1.0 + - - +
180D ALA 3.4 8.3 + - - -
187D THR* 2.8 42.3 + - - +
188D VAL 5.3 0.2 - - - +
189D VAL* 3.5 13.9 - - + -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 6.1 0.9 - - - +
173D ASP* 3.2 27.2 + - - +
174D GLN* 3.7 16.4 - - - +
175D TYR 3.3 0.2 - - - -
176D MET* 1.3 77.7 - - - +
178D ASP* 1.3 60.1 + - - +
180D ALA* 3.3 13.9 + - - +
181D ARG* 3.3 34.3 + - - +
187D THR* 4.4 3.8 - - - +
188D VAL 5.5 0.2 - - - -
189D VAL* 3.8 14.4 - - + +
191D ARG* 3.9 13.7 - - - +
261D GLY* 3.6 26.4 - - - +
262D ASN 3.6 21.8 - - - +
263D ALA* 3.9 9.9 - - + +
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE 4.0 1.3 - - - -
162B HIS* 3.2 1.9 - - - +
163B SER* 2.8 50.3 + - - -
164B PRO* 3.4 5.4 - - - +
167B CYS* 3.5 12.3 - - - -
174D GLN 2.9 18.0 + - - +
175D TYR* 4.0 2.0 - - + +
177D LEU* 1.3 73.6 - - - +
179D TYR* 1.3 59.1 + - + +
180D ALA 3.0 1.8 - - - -
181D ARG* 2.9 30.8 + - - +
182D ILE* 2.7 51.3 + - - +
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Residues in contact with TYR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 3.4 16.7 - - + +
164B PRO* 5.3 3.4 - - + -
105D LEU* 3.7 12.1 - - + +
108D LEU* 3.8 33.7 - - + -
109D GLU* 2.7 31.0 + - - -
112D ARG* 3.8 13.0 - - - -
175D TYR* 2.9 47.4 + + - +
176D MET 3.9 5.2 - - - +
177D LEU 3.4 0.2 - - - -
178D ASP* 1.3 79.5 - - + +
180D ALA* 1.3 58.5 + - - +
183D PHE* 2.9 50.7 + + - +
185D LEU* 3.2 41.3 + - + -
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D MET 3.4 3.0 + - - -
177D LEU 3.3 12.0 + - - +
178D ASP 3.0 0.4 - - - -
179D TYR* 1.3 80.2 - - - +
181D ARG* 1.3 58.7 + - + +
184D GLY* 3.0 20.3 + - - -
185D LEU* 3.3 24.4 - - - +
187D THR* 3.4 17.3 - - - +
260D ARG* 3.0 17.8 + - - +
261D GLY* 3.6 22.9 - - - -
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Residues in contact with ARG 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 3.9 6.7 + - - -
161B PHE 3.1 19.6 + - - -
162B HIS* 3.2 36.8 + - - +
174D GLN* 5.8 0.2 + - - -
177D LEU* 3.3 27.4 + - - +
178D ASP* 2.9 40.5 + - - +
180D ALA* 1.3 82.8 - - + +
182D ILE* 1.3 65.5 + - + +
184D GLY* 4.4 1.7 + - - -
261D GLY* 5.3 7.3 + - - +
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 4.1 26.4 - - + +
162B HIS* 6.0 0.4 - - + -
163B SER* 4.1 19.3 - - - +
164B PRO* 4.4 1.8 - - + -
300B GLU 6.0 0.7 - - - -
301B SER* 4.4 17.9 - - - +
178D ASP* 2.7 46.2 + - - +
181D ARG* 1.3 79.0 - - + +
183D PHE* 1.3 93.7 + - + +
184D GLY 3.5 0.6 + - - -
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Residues in contact with PHE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.4 32.8 - - + -
93B PRO* 3.8 16.2 - - + -
164B PRO* 4.2 8.5 - - + -
112D ARG* 3.5 43.5 - - + -
116D SER* 5.6 2.1 - - - -
179D TYR* 2.9 45.0 + + - +
182D ILE* 1.3 104.5 - - + +
184D GLY* 1.3 63.7 + - - +
185D LEU* 3.2 13.7 + - + +
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Residues in contact with GLY 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D SER 4.8 3.3 - - - +
180D ALA 3.0 15.7 + - - -
181D ARG 4.4 1.4 + - - -
182D ILE 3.5 2.2 - - - -
183D PHE* 1.3 77.4 - - - +
185D LEU* 1.3 67.6 + - - +
186D ASN* 3.7 8.1 + - - +
260D ARG* 3.5 10.7 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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