Contacts of the helix formed by residues 147 - 169 (chain B) in PDB entry 3RFU
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 ASN 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 4.5 1.8 + - - +
140B SER* 3.7 17.9 - - - -
145B GLN 4.2 4.8 + - - +
146B LEU* 1.3 74.2 - - - +
148B MET* 1.3 66.8 + - - +
149B PHE* 2.8 34.4 + - - +
150B THR* 2.9 28.6 + - - +
151B LEU* 3.4 6.6 + - - +
337B ASP* 3.4 29.4 + - + -
340B SER* 3.8 9.8 - - - -
341B GLY 4.6 0.2 - - - +
344B VAL* 4.6 0.9 - - - +
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASN* 1.3 75.9 - - - +
149B PHE* 1.3 90.0 + - + +
151B LEU* 3.4 3.4 + - - +
152B ILE* 3.0 34.3 + - + +
198B VAL* 5.1 2.5 - - - -
202B GLN* 4.4 10.3 - - - +
205B GLU* 5.4 4.3 - - - +
334B ARG* 6.4 1.8 - - - -
336B ALA* 4.4 12.6 - - + +
337B ASP* 3.4 22.1 + - - +
340B SER* 3.7 22.4 - - - +
386B LEU* 3.3 40.4 - - + +
387B GLY* 4.6 10.5 - - - -
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.5 31.9 - + - +
136B ARG* 3.5 54.3 - - + -
137B GLY* 3.5 6.1 - - - +
147B ASN* 2.8 21.3 + - - +
148B MET* 1.3 109.2 - - + +
150B THR* 1.3 58.6 + - - +
152B ILE* 4.6 4.0 - - + +
153B ALA* 2.9 33.2 + - - +
198B VAL* 5.0 4.3 - - + -
202B GLN* 3.8 25.6 - - - -
337B ASP* 5.5 2.7 - - - -
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY* 3.9 11.4 - - - -
140B SER* 2.8 27.8 - - - +
141B LEU* 5.8 0.7 - - - -
146B LEU* 3.6 17.5 - - + +
147B ASN* 2.9 29.3 + - - +
149B PHE* 1.3 73.2 - - - +
151B LEU* 1.3 62.9 + - - +
153B ALA* 4.3 0.8 - - - +
154B MET* 2.9 30.3 + - - +
344B VAL* 3.5 26.4 - - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASN 3.4 4.5 + - - +
148B MET 3.6 7.2 - - - +
150B THR* 1.3 80.1 + - - +
152B ILE* 1.3 63.8 + - + +
154B MET* 3.0 22.0 + - + +
155B GLY 3.0 20.1 + - - -
340B SER* 4.1 9.0 - - - +
343B PHE* 3.3 37.2 - - + -
344B VAL* 3.6 28.7 - - + -
347B VAL* 5.1 0.7 - - + -
381B ALA* 5.0 4.3 - - + +
382B CYS* 3.4 5.3 - - - -
383B PRO* 3.8 29.4 - - + -
386B LEU* 3.8 19.1 - - + -
686B PHE* 4.0 6.1 - - + -
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 4.2 25.6 - - + -
148B MET* 3.0 18.5 + - + +
149B PHE* 4.6 3.4 - - + +
151B LEU* 1.3 77.6 - - + +
153B ALA* 1.3 68.2 + - - +
154B MET 3.1 0.2 + - - -
156B ILE* 3.0 44.0 + - + +
194B ILE* 4.8 4.3 - - + -
198B VAL* 3.3 38.6 - - + -
382B CYS* 3.2 15.9 - - - -
383B PRO* 4.5 9.4 - - + +
384B CYS 5.5 0.2 - - - +
386B LEU* 3.8 29.2 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.2 27.8 - - - +
134B PHE* 3.5 26.4 - - + +
137B GLY* 4.2 7.4 - - - -
149B PHE 2.9 23.1 + - - +
150B THR* 4.3 1.6 - - - +
152B ILE* 1.3 78.8 - - - +
154B MET* 1.3 62.3 + - - +
156B ILE* 4.6 1.8 - - - -
157B GLY* 3.0 18.4 + - - -
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Residues in contact with MET 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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150B THR 2.9 21.7 + - - +
151B LEU* 3.1 33.9 - - + +
152B ILE 3.0 0.2 - - - -
153B ALA* 1.3 74.7 - - - +
155B GLY* 1.3 73.3 + - - +
157B GLY* 2.9 13.0 + - - -
158B VAL* 3.0 16.6 + - + +
344B VAL* 4.8 10.3 - - + +
347B VAL* 5.3 1.8 - - + -
348B ILE* 4.5 17.5 - - - -
378B LEU* 3.9 54.5 - - + +
381B ALA* 5.0 4.0 - - + -
382B CYS* 5.6 0.4 - - - -
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Residues in contact with GLY 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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151B LEU 3.0 10.5 + - - -
154B MET* 1.3 77.2 - - - +
156B ILE* 1.3 58.2 + - - +
158B VAL* 3.4 10.4 - - - +
159B ALA* 2.8 31.9 + - - +
378B LEU 4.0 11.7 - - - -
379B ILE* 3.9 4.9 - - - +
382B CYS* 3.7 24.0 - - - -
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Residues in contact with ILE 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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126B VAL* 3.5 30.3 - - + -
130B GLY* 6.4 0.2 - - - -
133B PHE* 5.9 0.9 - - + -
134B PHE* 3.8 10.5 - - + -
152B ILE* 3.0 33.3 + - + +
153B ALA* 4.1 3.6 - - - +
155B GLY* 1.3 75.2 - - - +
157B GLY* 1.3 65.4 + - - +
159B ALA* 3.4 4.0 + - + +
160B TRP* 3.0 22.7 + - - +
191B ALA* 3.6 12.6 - - + +
194B ILE* 3.4 41.7 - - + -
195B THR* 3.5 26.0 - - + -
382B CYS* 4.7 0.7 - - - -
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Residues in contact with GLY 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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134B PHE* 3.8 15.9 - - - -
153B ALA 3.0 12.7 + - - -
154B MET 2.9 7.2 + - - -
156B ILE* 1.3 74.2 - - - +
158B VAL* 1.3 65.4 + - - -
160B TRP* 3.0 8.0 + - - +
161B ILE* 3.0 36.7 + - - +
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Residues in contact with VAL 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 MET* 3.0 21.4 + - + +
155B GLY* 3.4 15.9 - - - +
157B GLY* 1.3 71.0 - - - +
159B ALA* 1.3 58.1 + - - +
161B ILE* 3.9 10.0 - - - +
162B TYR* 3.0 28.4 + - - +
375B VAL* 3.6 42.3 - - + +
378B LEU* 4.0 28.0 - - + -
379B ILE* 4.6 3.8 - - - +
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Residues in contact with ALA 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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155B GLY 2.8 23.2 + - - +
156B ILE* 3.5 8.1 - - - +
157B GLY 3.0 0.4 - - - -
158B VAL* 1.3 79.0 - - - +
160B TRP* 1.3 56.7 + - - +
162B TYR* 4.0 4.3 - - - +
163B SER* 3.0 32.5 + - - -
187B TYR* 4.8 9.6 - - + +
191B ALA* 4.4 13.5 - - + -
379B ILE* 3.4 30.1 - - + -
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Residues in contact with TRP 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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122B ALA 4.7 2.0 - - - -
123B THR* 3.4 42.3 - - - +
126B VAL* 4.1 19.7 - - + -
127B LEU* 3.9 30.3 - - + -
134B PHE* 6.5 0.4 - + - -
156B ILE 3.0 17.2 + - - +
157B GLY* 3.0 4.2 + - - +
159B ALA* 1.3 75.6 - - - +
161B ILE* 1.3 70.7 + - + +
163B SER* 4.5 0.4 - - - -
164B MET* 2.6 72.1 + - + +
188B PHE* 3.6 24.9 - + - -
191B ALA* 4.9 4.7 - - + +
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Residues in contact with ILE 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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157B GLY* 3.0 29.2 + - - +
158B VAL* 4.0 8.3 - - - +
160B TRP* 1.3 99.5 - - + +
162B TYR* 1.3 61.1 + - - +
163B SER 3.3 0.2 - - - -
164B MET* 3.9 4.4 - - + +
165B VAL* 3.0 36.1 + - + +
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Residues in contact with TYR 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 VAL 3.0 18.4 + - - +
159B ALA* 4.0 2.7 - - - +
161B ILE* 1.3 76.0 - - - +
163B SER* 1.3 62.9 + - - +
165B VAL* 4.0 2.7 - - - +
166B ALA* 3.0 28.9 + - - +
173B PHE* 3.7 30.9 - + - -
177B PHE* 3.2 33.5 - + - -
185B ALA* 3.6 15.8 - - - +
187B TYR* 3.1 43.9 + + + -
372B ILE* 4.2 22.4 - - + +
375B VAL* 3.4 33.7 - - + -
376B SER* 6.1 1.6 - - - -
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Residues in contact with SER 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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159B ALA 3.0 18.8 + - - -
162B TYR* 1.3 83.2 - - - +
164B MET* 1.3 64.6 + - - +
166B ALA* 3.2 5.5 + - - +
167B VAL* 3.0 27.9 + - - +
186B VAL* 2.9 17.3 - - - +
187B TYR 3.8 17.9 - - - +
188B PHE* 2.8 37.1 - - - -
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Residues in contact with MET 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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119B LEU* 3.5 29.2 - - + -
123B THR* 5.3 0.7 - - - -
160B TRP* 2.6 67.8 + - + +
161B ILE* 3.9 5.8 - - + +
163B SER* 1.3 77.4 - - - +
165B VAL* 1.3 63.6 + - + +
167B VAL* 3.4 2.3 - - - +
168B LEU* 3.0 41.6 + - + +
188B PHE* 3.2 24.4 - - + -
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Residues in contact with VAL 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 ILE* 3.0 26.3 + - + +
162B TYR* 4.1 2.0 - - - +
164B MET* 1.3 74.9 - - + +
166B ALA* 1.3 69.0 + - - +
168B LEU* 4.4 4.0 - - - -
169B TRP* 2.9 56.8 + - + +
172B VAL* 4.6 11.0 - - + -
173B PHE* 3.8 20.9 - - + -
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Residues in contact with ALA 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 TYR* 3.0 20.2 + - + +
163B SER 3.3 6.1 - - - +
165B VAL* 1.3 79.9 - - - +
167B VAL* 1.3 64.1 + - - +
170B PRO* 3.1 26.7 - - - +
173B PHE* 3.2 22.9 - - + -
177B PHE* 6.1 0.2 - - + -
184B VAL* 3.3 21.5 - - + +
185B ALA 3.9 16.4 - - - +
186B VAL* 5.6 1.1 - - + -
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Residues in contact with VAL 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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111B GLY 3.8 2.9 - - - +
115B SER* 3.7 30.5 - - - +
116B TRP* 3.3 38.4 + - + +
119B LEU* 3.4 25.4 - - + -
163B SER 3.1 15.5 - - - +
164B MET 3.4 4.7 - - - +
166B ALA* 1.3 79.9 - - - +
168B LEU* 1.3 65.7 + - - +
170B PRO* 4.0 8.9 - - - +
184B VAL* 3.9 6.5 - - + +
186B VAL* 5.6 2.9 - - + +
188B PHE* 3.8 13.5 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 3.5 35.2 - - + -
119B LEU* 5.2 5.2 - - + -
164B MET* 3.0 36.1 + - + +
165B VAL* 3.9 1.1 - - - +
167B VAL* 1.3 81.1 - - + +
169B TRP* 1.3 95.6 + - + +
170B PRO* 4.3 1.2 - - - +
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Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 2.9 44.4 + - + +
168B LEU* 1.3 120.6 - - + +
170B PRO* 1.3 62.4 - - - +
171B GLY* 3.1 9.3 + - - +
172B VAL* 3.3 31.3 - - + +
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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