Contacts of the helix formed by residues 146 - 168 (chain B) in PDB entry 1PR9
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 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ALA* 6.1 0.4 - - + -
88B LEU 5.9 0.7 - - - -
89B LEU* 3.6 43.4 - - + +
143B VAL* 3.1 28.5 + - + +
144B THR 2.8 26.5 + - - -
145B ASN* 1.3 81.8 - - + +
147B SER* 1.3 64.6 + - - +
148B VAL 3.3 2.7 - - - -
149B TYR* 3.9 20.2 - + + -
150B CYS* 2.8 36.6 + - - +
190B THR* 5.6 0.6 - - + +
191B TRP* 4.2 13.9 + + - -
196B LYS* 5.9 4.0 - - - -
1247B 2HP 3.4 25.6 + - - -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLN 4.5 2.1 + - - -
92B PHE* 3.9 28.3 - - - -
95B VAL* 3.7 22.2 - - - +
143B VAL 4.4 1.2 + - - -
145B ASN* 3.6 3.4 + - - +
146B HIS* 1.3 76.3 - - - +
148B VAL* 1.3 62.6 + - - +
150B CYS* 4.0 2.1 - - - +
151B SER* 2.7 34.5 + - - -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU 4.7 10.9 + - - +
90B GLN* 5.2 2.2 + - - +
95B VAL* 3.8 37.4 - - + +
99B ALA* 4.3 2.5 - - + +
100B PHE* 4.2 26.0 - - + +
103B SER* 3.4 35.0 - - - +
104B PHE* 4.3 10.5 - - + -
146B HIS 3.3 0.4 - - - -
147B SER* 1.3 77.4 + - - +
149B TYR* 1.3 65.0 + - - +
151B SER* 3.2 6.3 + - - -
152B THR* 3.1 21.7 + - - +
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Residues in contact with TYR 149 (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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85B ALA* 4.9 0.7 - - + -
86B VAL 3.5 26.9 - - - -
87B ALA* 3.9 18.4 - - + -
88B LEU 4.9 5.8 + - - +
89B LEU* 4.3 17.7 - - + -
103B SER* 5.6 1.3 - - - -
107B ASN* 4.0 6.5 - - - +
136B SER* 4.0 3.2 - - - -
138B CYS* 3.7 21.3 - - - -
146B HIS* 3.4 18.2 + + + +
148B VAL* 1.3 81.7 - - - +
150B CYS* 1.3 61.5 + - - +
152B THR* 2.7 25.2 + - - -
153B LYS* 3.2 25.7 + - + +
186B MET* 4.2 5.0 - - - -
1245B NAP 2.6 41.5 + - - -
1246B K 3.6 24.3 - - - -
1247B 2HP 4.0 2.9 - - - -
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Residues in contact with CYS 150 (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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138B CYS* 2.3 59.0 - - - +
139B SER* 4.4 0.5 - - - +
141B ARG 4.1 7.6 - - - +
142B ALA* 4.7 3.4 - - - -
143B VAL 4.2 9.6 - - - -
146B HIS* 2.8 41.2 + - - +
147B SER* 4.3 2.2 - - - +
149B TYR* 1.3 73.4 - - - +
151B SER* 1.3 56.0 + - - +
153B LYS* 3.3 2.2 + - - +
154B GLY* 2.8 26.5 + - - -
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Residues in contact with SER 151 (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 PHE* 6.2 0.4 - - - -
104B PHE* 3.9 17.3 - - - -
147B SER* 2.7 25.7 + - - -
148B VAL* 3.2 6.3 + - - -
150B CYS* 1.3 76.3 - - - +
152B THR* 1.3 56.9 + - - +
154B GLY* 4.4 1.3 - - - +
155B ALA* 2.9 29.6 + - - +
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Residues in contact with THR 152 (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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103B SER* 4.0 15.9 - - - +
104B PHE* 3.6 36.6 - - + -
107B ASN* 3.2 40.8 + - - +
108B LEU* 4.1 4.7 - - - +
148B VAL 3.1 15.2 + - - +
149B TYR 2.7 17.2 + - - -
151B SER* 1.3 76.3 - - - +
153B LYS* 1.3 62.4 + - - +
155B ALA* 3.3 3.1 + - - +
156B LEU* 2.8 27.6 + - - +
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Residues in contact with LYS 153 (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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84B ALA 5.3 0.6 + - - -
85B ALA* 3.9 9.8 - - - +
107B ASN* 4.9 5.6 + - + +
134B VAL 2.7 25.2 + - - -
135B SER* 3.8 19.1 - - - +
136B SER* 3.8 13.0 - - - -
138B CYS* 4.7 0.4 - - - -
139B SER* 3.4 31.0 - - - +
149B TYR* 3.2 32.5 + - + +
150B CYS* 3.9 5.4 - - - +
151B SER 3.3 0.2 - - - -
152B THR* 1.3 83.8 + - - +
154B GLY* 1.3 67.7 + - - +
156B LEU* 3.6 13.8 - - + +
157B ASP* 3.0 21.1 + - - +
1245B NAP 3.0 34.0 + - - -
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Residues in contact with GLY 154 (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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139B SER* 3.6 21.0 - - - +
150B CYS 2.8 16.0 + - - -
151B SER* 3.9 2.5 - - - -
153B LYS* 1.3 79.6 - - - +
155B ALA* 1.3 60.6 + - - +
157B ASP* 3.4 5.2 + - - +
158B MET* 3.4 18.9 + - - +
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Residues in contact with ALA 155 (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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104B PHE* 4.4 5.6 - - + -
108B LEU* 3.7 26.1 - - + +
151B SER 2.9 19.1 + - - +
152B THR* 3.4 7.2 - - - +
154B GLY* 1.3 76.2 - - - +
156B LEU* 1.3 56.2 + - - +
158B MET* 3.4 6.8 + - - +
159B LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 156 (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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82B ASN 5.5 0.9 - - - +
107B ASN 4.2 7.4 - - - +
108B LEU* 3.8 16.2 - - + -
111B VAL* 3.9 38.8 - - + -
133B ASN* 4.2 19.7 - - + +
134B VAL 3.5 28.3 - - - +
135B SER* 4.0 15.3 - - - +
152B THR 2.8 19.4 + - - +
153B LYS* 3.2 18.1 + - + +
155B ALA* 1.3 71.6 - - - +
157B ASP* 1.3 58.8 + - - +
159B LEU* 3.6 5.4 - - + +
160B THR* 2.8 34.5 + - - +
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Residues in contact with ASP 157 (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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135B SER* 2.8 27.0 + - - -
139B SER* 2.5 28.1 + - - +
140B GLN* 3.1 18.9 - - - +
153B LYS 3.0 11.5 + - - -
154B GLY* 3.8 7.6 - - - +
155B ALA 3.4 0.2 - - - -
156B LEU* 1.3 74.8 - - - +
158B MET* 1.3 63.8 + - - +
160B THR* 3.2 19.6 - - - +
161B LYS* 3.3 24.0 + - - +
176B ALA* 4.2 1.4 - - - +
178B ASN* 3.3 5.4 + - - -
234B THR* 3.5 21.9 - - + +
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Residues in contact with MET 158 (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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154B GLY 3.4 10.0 + - - +
155B ALA* 3.8 8.5 - - - +
156B LEU 3.2 0.4 - - - -
157B ASP* 1.3 78.2 - - - +
159B LEU* 1.3 66.3 + - - +
161B LYS* 3.0 42.5 + - + +
162B VAL* 3.1 35.7 + - + +
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Residues in contact with LEU 159 (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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108B LEU* 3.8 22.7 - - + -
111B VAL* 3.9 24.0 - - + -
112B ILE* 3.9 34.1 - - + -
133B ASN* 5.1 0.2 - - - +
155B ALA 2.9 17.9 + - - +
156B LEU* 3.6 8.5 - - + +
158B MET* 1.3 75.8 - - - +
160B THR* 1.3 66.3 + - - +
162B VAL* 3.2 9.0 + - + +
163B MET* 2.9 43.2 + - + +
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Residues in contact with THR 160 (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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133B ASN* 3.1 28.0 + - - +
156B LEU 2.8 20.0 + - - -
157B ASP* 3.2 14.1 - - - +
159B LEU* 1.3 77.7 - - - +
161B LYS* 1.3 58.2 + - - +
163B MET* 3.7 2.2 - - - +
164B ALA* 3.0 28.9 + - - +
174B VAL* 3.7 27.2 - - + +
175B ASN* 3.8 20.6 - - - -
176B ALA* 3.9 8.3 - - + +
232B GLY* 4.4 5.8 - - - +
233B SER 4.1 7.0 - - - +
234B THR* 5.7 0.4 - - + -
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Residues in contact with LYS 161 (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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140B GLN* 5.6 2.4 + - - -
157B ASP* 3.3 24.9 + - - +
158B MET* 3.0 38.7 + - + +
160B THR* 1.3 75.0 - - - +
162B VAL* 1.3 62.1 + - - +
164B ALA* 3.4 7.7 + - - +
165B LEU* 3.0 26.2 + - - +
232B GLY* 3.5 25.4 - - - +
234B THR* 5.2 8.7 - - - +
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Residues in contact with VAL 162 (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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158B MET* 3.1 33.2 + - + +
159B LEU* 3.2 8.9 + - + +
161B LYS* 1.3 73.1 - - - +
163B MET* 1.3 67.3 + - - +
165B LEU* 3.1 14.1 + - + +
166B GLU* 2.9 47.7 + - + +
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Residues in contact with MET 163 (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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111B VAL* 4.9 1.6 - - - +
112B ILE* 5.9 1.8 - - - -
115B SER* 3.4 36.6 - - - +
131B ILE* 4.0 20.2 - - + -
133B ASN* 4.1 15.0 - - - +
159B LEU* 2.9 48.8 + - + +
160B THR 3.7 4.0 - - - +
162B VAL* 1.3 76.7 - - - +
164B ALA* 1.3 54.0 + - - +
166B GLU* 3.2 2.6 + - - -
167B LEU* 2.7 52.2 + - + +
174B VAL* 4.0 18.6 - - + -
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Residues in contact with ALA 164 (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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160B THR 3.0 18.9 + - - +
161B LYS 3.5 5.4 - - - +
163B MET* 1.3 77.0 - - - +
165B LEU* 1.3 56.6 + - - +
168B GLY* 3.0 28.2 + - - +
172B ILE 4.9 1.1 - - - +
174B VAL* 3.9 10.2 - - - +
231B THR* 3.5 21.5 + - + +
232B GLY* 3.5 30.3 - - - +
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Residues in contact with LEU 165 (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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161B LYS 3.0 13.8 + - - +
162B VAL* 3.1 16.4 + - + +
164B ALA* 1.3 80.1 - - - +
166B GLU* 1.3 72.4 + - + +
168B GLY* 4.3 0.2 - - - -
169B PRO* 3.5 16.1 - - - +
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Residues in contact with GLU 166 (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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162B VAL* 2.9 37.0 + - + +
163B MET* 4.2 2.9 - - - +
165B LEU* 1.3 86.7 - - + +
167B LEU* 1.3 70.4 + - + +
168B GLY 3.5 0.2 - - - -
169B PRO* 3.6 9.8 - - - +
170B HIS* 4.0 11.1 + - - -
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Residues in contact with LEU 167 (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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115B SER* 5.8 0.4 - - - +
119B ALA* 4.2 25.1 - - + -
123B ILE* 5.0 4.9 - - + -
131B ILE* 4.3 7.9 - - + -
163B MET* 2.7 39.0 + - + +
166B GLU* 1.3 84.1 - - + +
168B GLY* 1.3 63.2 + - - +
169B PRO 3.4 0.9 - - - -
170B HIS* 3.0 25.5 + - + +
172B ILE* 3.4 43.7 + - + +
174B VAL* 4.2 16.2 - - + -
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Residues in contact with GLY 168 (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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164B ALA 3.0 20.0 + - - -
165B LEU 4.3 0.7 - - - -
167B LEU* 1.3 76.9 - - - +
169B PRO* 1.3 61.4 - - - +
171B LYS* 3.0 22.5 + - - +
172B ILE 4.0 8.5 + - - -
231B THR* 6.0 3.1 - - - -
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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