Contacts of the helix formed by residues 191 - 213 (chain B) in PDB entry 1LWU
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 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 5.3 10.4 - - - +
187B ARG 3.5 10.6 + - - -
188B SER* 4.4 10.5 - - - -
189B MET 2.8 0.4 - - - -
190B LYS* 1.3 78.8 - - - +
192B VAL* 1.3 54.9 + - - +
194B GLU* 2.9 8.5 + - - +
195B HIS* 2.5 39.3 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 3.5 30.5 - - + -
137A VAL* 4.0 14.8 - - + -
171A ASN* 5.1 4.9 - - - +
174A LEU* 4.0 38.3 - - + +
175A GLU* 4.0 7.6 - - + +
178A ALA* 4.2 4.5 - - + -
188B SER 4.0 14.6 + - - +
189B MET* 3.1 8.8 + - - +
191B SER* 1.3 80.2 - - - +
193B LEU* 1.3 54.9 + - - +
195B HIS* 3.0 7.6 + - - +
196B LEU* 2.7 46.0 + - + +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 5.1 2.7 - - + -
133A ILE* 4.0 23.1 - - + -
136A GLN* 3.6 11.7 - - - +
189B MET 3.0 19.7 + - - +
190B LYS* 4.6 0.2 - - - -
192B VAL* 1.3 77.2 - - - +
194B GLU* 1.3 61.6 + - - +
196B LEU* 4.4 3.4 - - + -
197B ARG* 3.2 7.6 + - - +
109C LEU* 3.6 44.6 - - + +
112C MET* 4.1 20.6 - - + +
113C TRP* 3.5 41.1 - - + -
116C ASN* 3.1 26.1 + - - +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 2.9 50.3 + - - +
191B SER* 2.9 8.8 + - - +
193B LEU* 1.3 78.0 - - - +
195B HIS* 1.3 63.4 - - - +
197B ARG* 3.4 31.5 + - - +
198B ALA* 3.3 21.1 + - - +
112C MET* 4.6 8.5 - - - -
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LYS* 3.6 30.1 - - + +
170A LYS* 3.8 16.9 - - - -
171A ASN* 2.7 44.3 + - + +
174A LEU* 4.1 13.0 - - + -
191B SER* 2.5 20.0 + - - +
192B VAL* 3.4 7.6 - - - +
194B GLU* 1.3 70.9 - - - +
196B LEU* 1.3 67.0 + - - +
198B ALA* 3.2 8.0 + - - +
199B LYS* 3.0 31.3 + - - +
202B ARG* 5.0 7.0 - - - -
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 5.1 1.1 - - + -
136A GLN* 3.1 30.3 - - + +
137A VAL* 3.9 36.8 - - + -
140A ILE* 3.8 26.6 - - + +
171A ASN* 3.8 20.2 - - - +
192B VAL* 2.7 29.7 + - + +
193B LEU* 4.5 4.5 - - + -
195B HIS* 1.3 73.0 + - - +
197B ARG* 1.3 64.0 + - - +
199B LYS* 2.9 20.9 + - + +
200B MET* 3.0 17.6 + - - +
116C ASN* 3.5 11.7 - - - +
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Residues in contact with ARG 197 (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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193B LEU 3.2 7.0 + - - +
194B GLU* 3.4 36.5 + - - +
195B HIS 3.2 0.4 - - - -
196B LEU* 1.3 77.2 - - - +
198B ALA* 1.3 66.4 + - - +
200B MET* 2.7 30.6 + - - +
201B GLN* 2.9 43.2 + - - +
112C MET* 6.0 5.7 - - + +
115C VAL* 5.3 8.7 - - + -
116C ASN* 3.2 26.2 - - - +
119C PHE* 4.2 17.4 - - + -
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Residues in contact with ALA 198 (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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194B GLU 3.3 7.6 + - - +
195B HIS* 3.2 11.7 + - + +
197B ARG* 1.3 89.1 - - - +
199B LYS* 1.3 62.8 + - - +
201B GLN* 3.8 16.5 + - - +
202B ARG* 3.1 39.1 + - - +
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Residues in contact with LYS 199 (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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140A ILE* 3.8 24.2 - - + +
141A LEU* 5.4 6.0 - - - +
144A GLU* 2.9 36.0 + - - +
164A TYR* 4.5 0.7 + - - -
166A LEU* 5.3 0.8 - - - +
167A ASP* 5.7 4.6 - - - +
168A LYS* 4.5 13.1 + - - +
171A ASN* 4.9 12.1 - - - +
195B HIS* 3.0 27.3 + - - +
196B LEU* 2.9 16.9 + - + +
198B ALA* 1.3 77.7 - - - +
200B MET* 1.3 62.2 + - - +
202B ARG* 3.4 28.6 + - - +
203B MET* 3.1 43.5 + - + +
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Residues in contact with MET 200 (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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140A ILE* 3.4 40.2 - - + -
196B LEU 3.2 11.0 - - - +
197B ARG* 2.7 14.4 + - - +
199B LYS* 1.3 69.1 - - - +
201B GLN* 1.3 51.1 + - - -
203B MET* 3.1 10.5 + - - +
204B GLU* 2.6 36.0 + - - +
116C ASN* 3.3 35.7 - - - +
119C PHE* 3.2 53.8 - - + -
120C VAL* 3.6 17.5 - - - -
123C LEU* 3.8 9.7 - - + +
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Residues in contact with GLN 201 (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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197B ARG* 2.9 42.7 + - - +
198B ALA* 3.8 16.0 - - - +
200B MET* 1.3 71.7 - - - +
202B ARG* 1.3 59.0 + - - +
203B MET 2.9 1.3 - - - -
204B GLU* 2.8 4.9 + - - +
205B GLU* 2.7 37.0 + - - +
119C PHE* 3.8 22.6 - - + -
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Residues in contact with ARG 202 (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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144A GLU* 4.8 2.4 + - - -
164A TYR* 3.7 15.7 + - + +
165A ARG 5.3 6.6 + - - -
167A ASP* 4.7 15.2 + - - +
168A LYS* 4.1 21.1 - - - +
195B HIS* 5.0 6.5 - - - -
198B ALA* 3.1 30.8 + - + +
199B LYS* 3.6 42.1 - - - +
201B GLN* 1.3 78.1 - - + +
203B MET* 1.3 57.0 + - - +
205B GLU* 3.2 13.1 - - + +
206B ALA* 3.1 27.2 + - - +
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Residues in contact with MET 203 (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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140A ILE* 4.1 10.8 - - + +
143A VAL* 4.6 1.1 - - - -
144A GLU* 3.4 37.9 - - + +
147A ILE* 3.8 23.1 - - + -
164A TYR* 3.1 27.6 - - + +
199B LYS* 3.1 52.4 + - + +
200B MET* 3.2 14.4 - - - +
201B GLN 2.8 1.4 + - - -
202B ARG* 1.3 74.7 - - - +
204B GLU* 1.3 66.8 + - - +
205B GLU 3.1 1.6 - - - -
206B ALA* 3.0 3.3 + - - +
207B ILE* 2.9 28.3 + - - +
123C LEU* 3.9 14.1 - - + -
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Residues in contact with GLU 204 (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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200B MET 2.6 19.9 + - - +
201B GLN* 2.8 6.3 + - - +
203B MET* 1.3 71.4 - - - +
205B GLU* 1.3 60.6 + - - +
207B ILE* 3.3 2.8 + - - +
208B LYS* 3.0 37.9 + - + +
119C PHE* 3.1 25.0 - - + -
122C ARG* 2.7 33.3 + - - -
123C LEU* 3.6 12.3 - - + +
126C GLN* 3.1 27.4 + - - +
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Residues in contact with GLU 205 (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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201B GLN 2.7 17.4 + - - +
202B ARG* 3.2 20.2 - - + +
204B GLU* 1.3 70.4 - - - +
206B ALA* 1.3 74.4 + - - +
207B ILE 3.0 0.3 + - - -
208B LYS* 3.0 8.1 + - - +
209B THR* 2.9 37.1 + - - -
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Residues in contact with ALA 206 (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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151A LEU* 4.0 13.5 - - + +
164A TYR* 3.2 40.6 - - + -
202B ARG 3.1 8.7 + - - +
203B MET 3.0 5.9 + - - +
205B GLU* 1.3 89.9 - - - +
207B ILE* 1.3 59.4 + - - +
209B THR* 3.8 4.8 + - - +
210B GLN* 3.3 22.7 + - - +
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Residues in contact with ILE 207 (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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147A ILE* 3.4 26.7 - - + -
151A LEU* 3.2 40.4 - - + -
203B MET 2.9 20.9 + - - +
204B GLU* 3.6 6.7 - - - +
206B ALA* 1.3 74.1 - - - +
208B LYS* 1.3 69.3 + - - +
209B THR 3.1 1.3 - - - -
210B GLN* 3.2 2.4 + - - +
211B LYS* 2.8 29.9 + - + +
123C LEU* 4.9 1.3 - - + -
126C GLN* 3.7 41.3 - - + +
130C ILE* 4.6 17.0 - - + +
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Residues in contact with LYS 208 (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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204B GLU* 3.0 25.4 + - + +
205B GLU* 3.0 6.9 + - - +
207B ILE* 1.3 83.7 - - - +
209B THR* 1.3 58.6 + - - +
211B LYS* 3.4 32.1 + - + +
212B GLU* 3.0 30.1 + - - +
126C GLN* 3.3 32.1 + - - +
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Residues in contact with THR 209 (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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162A LEU* 4.1 20.4 - - + -
205B GLU* 2.9 30.9 + - - +
206B ALA* 3.9 5.6 - - - +
208B LYS* 1.3 77.1 - - - +
210B GLN* 1.3 63.7 + - + +
212B GLU* 3.3 6.9 + - - +
213B LEU* 3.1 45.1 + - + +
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Residues in contact with GLN 210 (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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151A LEU* 4.0 32.1 - - + +
154A CYS* 3.3 28.1 - - + +
160A ARG 3.7 9.6 + - - +
161A TYR* 3.2 19.0 - - + +
162A LEU* 2.8 38.9 - - + +
163A GLU 5.6 0.9 - - - +
206B ALA 3.3 11.6 + - - +
207B ILE 3.2 4.2 + - - +
209B THR* 1.3 76.3 - - - +
211B LYS* 1.3 68.5 + - - +
213B LEU* 3.1 12.0 + - - +
214B CYS* 3.1 26.0 + - - -
130C ILE* 4.5 5.4 - - + -
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Residues in contact with LYS 211 (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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207B ILE* 2.8 22.5 + - + +
208B LYS* 3.4 31.0 - - - +
210B GLN* 1.3 71.3 - - - +
212B GLU* 1.3 64.7 + - - +
214B CYS* 3.0 20.9 + - + +
215B SER* 3.8 3.6 + - - -
129C ASP* 4.6 17.2 + - - +
130C ILE* 4.4 15.4 - - + +
133C THR* 4.8 16.9 - - + +
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Residues in contact with GLU 212 (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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208B LYS 3.0 17.7 + - - +
209B THR* 3.5 8.1 - - - +
210B GLN 3.2 0.2 - - - -
211B LYS* 1.3 77.4 - - - +
213B LEU* 1.3 63.6 + - + +
214B CYS 3.1 5.0 + - - -
215B SER* 3.3 26.7 + - - -
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Residues in contact with LEU 213 (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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158A CYS* 3.3 14.6 - - - +
159A ALA* 3.8 4.0 + - - +
160A ARG* 3.1 71.7 + - + +
162A LEU* 3.3 33.9 - - + -
209B THR* 3.1 28.2 + - + +
210B GLN* 3.1 14.1 + - - +
212B GLU* 1.3 80.3 - - + +
214B CYS* 1.4 54.7 + - - +
215B SER* 3.5 2.9 - - - -
216B ALA 4.0 2.1 - - - +
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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