Contacts of the helix formed by residues 147 - 169 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ARG* 4.5 1.4 + - - +
140A SER* 3.7 17.9 - - - -
145A GLN 4.2 4.4 + - - +
146A LEU* 1.3 75.0 - - - +
148A MET* 1.3 66.5 + - - +
149A PHE* 2.8 33.7 + - - +
150A THR* 2.9 28.3 + - - +
151A LEU* 3.4 6.8 + - - +
337A ASP* 3.4 29.8 + - + -
340A SER* 3.8 9.2 - - - -
344A VAL* 4.6 1.0 - - - +
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Residues in contact with MET 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASN* 1.3 75.8 - - - +
149A PHE* 1.3 91.3 + - + +
151A LEU* 3.4 3.2 + - - +
152A ILE* 3.0 34.4 + - + +
198A VAL* 5.1 2.7 - - - -
202A GLN* 4.4 9.6 - - - +
205A GLU* 5.4 4.0 - - - +
334A ARG* 6.3 2.2 - - - -
336A ALA* 4.4 13.9 - - + +
337A ASP* 3.4 22.6 + - - +
340A SER* 3.7 21.8 - - - +
386A LEU* 3.3 40.4 - - + +
387A GLY* 4.6 10.3 - - - -
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.5 32.8 - + + +
136A ARG* 3.5 56.5 - - + -
137A GLY* 3.5 6.3 - - - +
147A ASN* 2.8 21.3 + - - +
148A MET* 1.3 107.3 - - + +
150A THR* 1.3 58.5 + - - +
152A ILE* 4.6 3.4 - - + +
153A ALA* 2.9 33.1 + - - +
198A VAL* 5.0 4.7 - - + -
202A GLN* 3.8 25.4 - - - -
337A ASP* 5.5 2.9 - - - -
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 3.9 10.8 - - - -
140A SER* 2.8 28.7 - - - +
141A LEU* 5.8 0.7 - - - -
146A LEU* 3.6 17.8 - - + +
147A ASN* 2.9 29.4 + - - +
149A PHE* 1.3 72.6 - - - +
151A LEU* 1.3 64.6 + - - +
153A ALA* 4.3 1.2 - - - +
154A MET* 3.0 29.3 + - - +
344A VAL* 3.5 26.4 - - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASN 3.4 4.3 + - - +
148A MET 3.6 7.9 - - - +
150A THR* 1.3 80.9 + - - +
152A ILE* 1.3 63.5 + - + +
154A MET* 3.0 21.4 + - + +
155A GLY 3.0 20.8 + - - -
340A SER* 4.1 8.3 - - - +
343A PHE* 3.3 37.7 - - + -
344A VAL* 3.6 28.7 - - + -
347A VAL* 5.1 0.2 - - + -
381A ALA* 5.0 4.0 - - + -
382A CYS* 3.5 5.8 - - - -
383A PRO* 3.8 29.4 - - + -
386A LEU* 3.8 20.0 - - + -
686A PHE* 4.0 5.6 - - + -
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 4.2 25.6 - - + -
148A MET* 3.0 19.0 + - + +
149A PHE* 4.6 3.8 - - + +
151A LEU* 1.3 77.6 - - + +
153A ALA* 1.3 67.9 + - - +
156A ILE* 3.0 43.7 + - + +
194A ILE* 4.7 4.7 - - + -
198A VAL* 3.3 39.3 - - + -
382A CYS* 3.2 16.1 - - - -
383A PRO* 4.5 9.6 - - + +
384A CYS 5.5 0.2 - - - +
386A LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.2 27.1 - - - +
134A PHE* 3.5 26.7 - - + +
137A GLY* 4.2 7.6 - - - -
149A PHE 2.9 23.1 + - - +
150A THR* 4.3 1.3 - - - +
152A ILE* 1.3 80.0 - - - +
154A MET* 1.3 56.4 + - - +
156A ILE* 4.6 2.2 - - - -
157A GLY* 3.0 23.0 + - - -
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Residues in contact with MET 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR 3.0 22.0 + - - +
151A LEU* 3.1 32.1 - - + +
153A ALA* 1.3 74.0 - - - +
155A GLY* 1.3 73.9 + - - +
157A GLY* 2.9 13.5 + - - -
158A VAL* 3.0 17.1 + - + +
344A VAL* 4.8 10.3 - - + -
347A VAL* 5.3 2.0 - - + -
348A ILE* 4.5 17.9 - - - -
378A LEU* 3.8 52.9 - - + +
381A ALA* 5.0 4.0 - - + -
382A CYS* 5.6 0.9 - - - +
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU 3.0 9.9 + - - -
154A MET* 1.3 78.8 - - - +
156A ILE* 1.3 59.1 + - - +
158A VAL* 3.4 10.1 - - - +
159A ALA* 2.8 31.5 + - - +
378A LEU 4.0 11.9 - - - -
379A ILE* 3.9 5.7 - - - +
382A CYS* 3.8 23.3 - - - -
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.5 30.2 - - + +
133A PHE* 5.9 1.1 - - + -
134A PHE* 3.8 10.8 - - + -
152A ILE* 3.0 34.6 + - + +
153A ALA* 4.1 3.4 - - - +
155A GLY* 1.3 73.7 - - - +
157A GLY* 1.3 66.5 + - - +
159A ALA* 3.4 3.9 + - + +
160A TRP* 3.0 23.2 + - - +
191A ALA* 3.6 11.7 - - + +
194A ILE* 3.4 42.2 - - + -
195A THR* 3.6 26.9 - - + -
382A CYS* 4.7 0.7 - - - -
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.8 16.8 - - - -
153A ALA 3.0 12.1 + - - -
154A MET 2.9 7.6 + - - -
156A ILE* 1.3 73.8 - - - +
158A VAL* 1.3 64.1 + - - -
160A TRP* 3.0 7.7 + - - +
161A ILE* 3.0 36.8 + - - +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MET* 3.0 20.5 + - + +
155A GLY* 3.4 15.5 - - - +
157A GLY* 1.3 71.6 - - - +
159A ALA* 1.3 61.4 + - - +
161A ILE* 3.8 9.9 - - - +
162A TYR* 3.0 28.1 + - - +
375A VAL* 3.6 40.6 - - + +
378A LEU* 4.0 28.0 - - + -
379A ILE 4.6 3.8 - - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLY 2.8 23.8 + - - +
156A ILE* 3.5 7.4 - - + +
158A VAL* 1.3 79.2 - - - +
160A TRP* 1.3 57.7 + - - +
162A TYR* 4.0 3.7 - - - +
163A SER* 3.0 32.8 + - - -
187A TYR* 4.8 9.8 - - + +
191A ALA* 4.4 13.9 - - + -
375A VAL* 5.9 0.4 - - - -
379A ILE* 3.4 29.2 - - + -
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Residues in contact with TRP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA 4.7 0.7 - - - -
123A THR* 3.4 42.0 - - - +
126A VAL* 4.1 20.4 - - + -
127A LEU* 3.9 29.8 - - + -
134A PHE* 6.5 0.7 - + - -
156A ILE 3.0 17.9 + - - +
157A GLY* 3.0 4.9 + - - +
159A ALA* 1.3 75.8 - - - +
161A ILE* 1.3 70.8 + - + +
163A SER* 4.5 0.2 - - - -
164A MET* 2.6 72.2 + - + +
188A PHE* 3.7 25.4 - + - -
191A ALA* 4.9 4.7 - - + +
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY* 3.0 29.2 + - - +
158A VAL* 4.0 7.4 - - + +
160A TRP* 1.3 99.7 - - + +
162A TYR* 1.3 62.0 + - - +
164A MET* 4.0 3.1 - - + -
165A VAL* 3.0 36.0 + - + +
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A VAL 3.0 17.1 + - - +
159A ALA* 4.0 2.7 - - - +
161A ILE* 1.3 76.8 - - - +
163A SER* 1.3 62.4 + - - +
165A VAL* 4.1 1.9 - - - +
166A ALA* 3.0 28.9 + - - +
173A PHE* 3.7 32.1 - + - -
177A PHE* 3.2 33.5 - + - -
185A ALA* 3.6 17.1 - - - +
187A TYR* 3.1 44.0 + + - -
372A ILE* 4.2 22.2 - - + +
375A VAL* 3.4 34.1 - - + -
376A SER* 6.3 1.6 - - - -
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ALA 3.0 18.1 + - - -
162A TYR* 1.3 82.3 - - - +
164A MET* 1.3 63.6 + - - +
166A ALA* 3.2 5.4 + - - +
167A VAL* 3.0 27.9 + - - +
186A VAL* 2.9 16.9 - - - +
187A TYR 3.8 17.9 - - - +
188A PHE* 2.8 38.3 - - - -
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.5 28.7 - - + -
123A THR* 5.0 1.3 - - - -
160A TRP* 2.6 66.6 + - + +
161A ILE* 3.9 6.1 - - + +
163A SER* 1.3 78.5 + - - +
165A VAL* 1.3 63.8 + - + +
167A VAL* 3.4 2.3 - - - +
168A LEU* 3.0 41.2 + - + +
188A PHE* 3.2 25.5 - - + -
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.0 24.7 + - + +
162A TYR* 4.1 2.5 - - - +
164A MET* 1.3 75.7 - - + +
166A ALA* 1.3 68.5 + - - +
168A LEU* 4.4 4.5 - - - -
169A TRP* 2.9 56.8 + - + +
172A VAL* 4.6 10.8 - - + -
173A PHE* 3.8 20.9 - - + -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 3.0 20.6 + - + +
163A SER 3.2 5.8 + - - +
165A VAL* 1.3 81.0 - - - +
167A VAL* 1.3 63.0 + - - +
170A PRO* 3.1 26.2 - - - +
173A PHE* 3.2 23.1 - - + -
184A VAL* 3.3 21.4 - - + +
185A ALA 3.9 16.4 - - - +
186A VAL* 5.6 1.3 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLY 3.8 3.6 - - - +
115A SER* 3.7 29.4 - - - +
116A TRP* 3.3 39.6 + - + +
119A LEU* 3.4 24.5 - - + -
163A SER 3.1 16.4 - - - +
164A MET 3.4 5.2 - - - +
166A ALA* 1.3 79.2 - - - +
168A LEU* 1.3 66.2 - - - +
170A PRO* 4.0 8.3 - - - +
184A VAL* 3.9 6.7 - - + +
186A VAL* 5.6 3.4 - - + -
188A PHE* 3.8 13.2 - - + -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TRP* 3.5 34.8 - - + -
119A LEU* 5.2 5.4 - - + -
164A MET* 3.0 34.8 + - + +
165A VAL* 3.9 1.3 - - - +
167A VAL* 1.3 79.8 - - + +
169A TRP* 1.3 96.7 + - + +
170A PRO* 4.3 0.7 - - - +
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Residues in contact with TRP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A VAL* 2.9 45.1 + - + +
168A LEU* 1.3 120.4 - - + +
170A PRO* 1.3 61.7 - - - +
171A GLY* 3.1 9.5 + - - +
172A VAL* 3.3 30.8 - - + +
173A PHE* 4.7 0.2 - - - -
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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