Contacts of the helix formed by residues 160 - 184 (chain B) in PDB entry 4LEY
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 LYS 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ARG 4.3 7.9 - - - +
159B LEU* 1.3 79.3 - - - +
161B ARG* 1.3 61.6 + - - +
162B LYS* 3.1 6.5 + - + +
163B ASP* 3.1 30.4 + - - +
164B ILE* 2.9 27.6 + - - +
209B PRO* 5.7 0.6 - - - +
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Residues in contact with ARG 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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159B LEU 4.2 1.2 + - - -
160B LYS* 1.3 71.6 - - - +
162B LYS* 1.3 59.4 + - + +
164B ILE* 3.7 18.3 - - + +
165B SER* 2.9 27.9 + - - -
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS* 3.1 4.6 - - + +
161B ARG* 1.3 80.2 - - + +
163B ASP* 1.3 74.9 + - - +
165B SER* 3.1 6.0 + - - -
166B GLU* 2.3 67.4 + - + +
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS* 3.1 36.2 + - - +
162B LYS* 1.3 84.9 + - - +
164B ILE* 1.3 63.6 + - - +
166B GLU* 3.4 12.6 + - - +
167B ALA* 3.0 28.1 + - - +
209B PRO* 3.7 24.5 - - + +
302B GLU* 5.5 2.4 - - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 3.8 36.6 - - + +
160B LYS 2.9 20.8 + - - +
161B ARG* 3.7 16.8 - - + +
163B ASP* 1.3 75.1 - - - +
165B SER* 1.3 58.2 + - - +
167B ALA* 4.1 0.3 - - - +
168B ALA* 2.9 35.3 + - + +
200B TYR* 3.3 26.3 + - + +
209B PRO* 3.8 15.2 - - + +
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ARG 2.9 20.6 + - - -
162B LYS* 3.4 7.4 - - - -
164B ILE* 1.3 78.1 - - - +
166B GLU* 1.3 59.3 + - - +
168B ALA* 3.8 3.8 - - - +
169B GLU* 2.9 43.8 + - - +
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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
----------------------------------------------------------
162B LYS* 2.3 56.7 + - + +
163B ASP* 4.0 11.3 - - - +
165B SER* 1.3 74.1 - - - +
167B ALA* 1.3 67.8 + - - +
169B GLU* 3.0 26.0 + - - +
170B THR* 3.1 17.3 + - - -
300B ASN* 4.0 13.7 - - - +
302B GLU* 4.5 13.2 - - - +
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Residues in contact with ALA 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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163B ASP 3.0 19.1 + - - +
164B ILE 4.1 1.6 - - - +
166B GLU* 1.3 76.0 - - - +
168B ALA* 1.3 58.1 + - - +
170B THR* 3.4 1.8 + - - -
171B VAL* 2.9 36.3 + - - +
209B PRO* 3.6 26.9 - - + +
212B PHE* 4.1 7.9 - - + -
300B ASN* 4.2 2.6 + - - -
302B GLU* 5.0 3.1 + - + +
304B ILE* 3.7 24.0 - - + -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 2.9 23.0 + - + +
165B SER* 3.8 4.0 - - - +
167B ALA* 1.3 73.4 - - - +
169B GLU* 1.3 66.4 + - - +
171B VAL* 4.3 4.9 - - - -
172B ASN* 2.9 42.7 + - - +
200B TYR* 3.8 17.9 - - + +
212B PHE* 4.3 7.5 - - + -
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B SER* 2.9 31.2 + - - +
166B GLU* 3.0 17.2 + - - +
168B ALA* 1.3 78.2 - - - +
170B THR* 1.3 65.7 + - - +
172B ASN* 3.7 5.1 - - - +
173B LYS* 3.0 41.0 + - - +
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Residues in contact with THR 170 (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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166B GLU 3.1 6.8 + - - -
167B ALA* 3.9 5.4 - - - -
169B GLU* 1.3 77.9 - - - +
171B VAL* 1.3 64.7 + - - +
173B LYS* 3.0 23.1 + - - +
174B VAL* 3.0 13.6 + - - +
280B ILE* 3.5 41.2 - - + +
298B ILE* 3.7 17.0 - - + -
300B ASN* 2.4 36.5 + - - +
304B ILE* 5.4 0.9 - - - -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA 2.9 22.0 + - - +
168B ALA* 3.9 3.8 - - - +
170B THR* 1.3 77.5 - - - +
172B ASN* 1.3 66.4 + - - +
174B VAL* 3.3 1.7 + - - +
175B VAL* 2.9 46.1 + - + +
201B TYR* 4.6 5.4 - - - +
212B PHE* 3.7 51.4 - - + -
214B VAL* 5.5 0.7 - - + -
298B ILE* 4.5 12.1 - - + -
304B ILE* 4.1 10.1 - - + -
306B VAL* 4.0 15.7 - - + -
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Residues in contact with ASN 172 (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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168B ALA* 2.9 42.7 + - - +
169B GLU* 3.7 5.2 - - - +
171B VAL* 1.3 79.4 - - - +
173B LYS* 1.3 63.6 + - - +
175B VAL* 3.9 6.1 - - - +
176B GLU* 3.0 26.3 + - - +
194B GLN* 6.0 0.3 + - - -
196B ASN* 5.7 2.3 + - - -
201B TYR* 4.7 7.3 + - - -
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 3.0 34.4 + - - +
170B THR* 3.0 14.6 + - - +
172B ASN* 1.3 78.8 - - - +
174B VAL* 1.3 65.9 + - + +
176B GLU* 3.5 7.1 - - - +
177B ARG* 3.0 27.5 + - - +
279B ASP* 5.1 10.1 + - - +
280B ILE* 4.5 18.3 - - + +
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR 3.0 11.9 + - - +
171B VAL 3.8 4.9 - - - +
173B LYS* 1.3 74.6 - - - +
175B VAL* 1.3 65.5 + - + +
177B ARG* 3.2 8.5 + - - +
178B LEU* 3.0 46.7 + - + +
274B VAL* 5.3 0.4 - - + -
277B ILE* 4.3 15.9 - - + -
280B ILE* 4.1 25.8 - - + -
282B VAL* 4.4 13.5 - - + -
296B LEU* 3.8 16.8 - - + -
298B ILE* 4.0 20.9 - - + -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 2.9 36.0 + - + +
172B ASN* 3.9 7.4 - - - +
174B VAL* 1.3 75.7 - - + +
176B GLU* 1.3 63.2 - - - +
178B LEU* 3.3 9.4 + - + +
179B LEU* 2.9 24.1 + - + +
194B GLN* 3.3 36.1 - - - +
214B VAL* 4.2 24.2 - - + -
216B PHE* 4.2 9.3 - - + -
296B LEU* 6.1 0.4 - - + -
306B VAL* 4.6 10.8 - - + -
308B ILE* 4.7 4.9 - - + -
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Residues in contact with GLU 176 (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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172B ASN 3.0 19.6 + - - +
173B LYS* 3.2 7.9 + - - +
175B VAL* 1.3 76.5 - - - +
177B ARG* 1.3 79.7 + - - +
179B LEU* 3.8 6.4 - - - +
180B ARG* 2.9 63.7 + - + +
194B GLN* 6.1 0.4 - - - -
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Residues in contact with ARG 177 (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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173B LYS* 3.0 17.9 + - + +
174B VAL* 3.5 8.5 - - - +
176B GLU* 1.3 88.4 + - - +
178B LEU* 1.3 56.8 + - - +
180B ARG* 3.8 4.0 - - - +
181B ARG* 3.0 31.2 + - - +
273B GLU* 2.4 35.2 + - + +
276B GLU* 3.3 34.3 + - - +
277B ILE* 3.7 35.2 - - + +
278B LYS 5.1 0.6 - - - +
279B ASP* 5.4 3.9 + - - -
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Residues in contact with LEU 178 (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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174B VAL* 3.0 30.4 + - + +
175B VAL* 3.7 5.4 - - - +
177B ARG* 1.3 74.8 - - + +
179B LEU* 1.3 60.1 + - - +
181B ARG* 3.4 5.9 + - - +
182B MET* 2.9 35.3 + - + +
216B PHE* 4.1 12.1 - - + -
270B ILE* 3.8 36.1 - - + +
273B GLU* 4.4 12.1 - - + -
274B VAL* 3.9 15.7 - - + -
277B ILE* 5.1 2.0 - - + -
296B LEU* 3.6 28.9 - - + -
308B ILE* 4.3 18.6 - - + -
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Residues in contact with LEU 179 (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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175B VAL* 2.9 18.5 + - + +
176B GLU* 3.8 5.8 - - - +
178B LEU* 1.3 75.1 - - - +
180B ARG* 1.3 59.9 + - - +
182B MET* 2.9 19.7 + - - +
183B GLN* 3.0 28.6 + - + +
192B VAL* 3.6 32.3 - - + +
193B GLU* 4.4 10.5 - - - -
194B GLN* 3.8 27.1 - - + +
216B PHE* 3.7 25.4 - - + -
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Residues in contact with ARG 180 (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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176B GLU* 2.9 40.9 + - - +
177B ARG* 3.8 5.4 - - - +
179B LEU* 1.3 77.3 - - - +
181B ARG* 1.3 50.6 + - - +
183B GLN* 3.0 10.1 + - + +
184B LYS* 2.6 78.6 + - + +
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Residues in contact with ARG 181 (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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177B ARG 3.0 17.7 + - - +
178B LEU* 3.7 4.3 - - - +
180B ARG* 1.3 74.3 - - - +
182B MET* 1.3 63.1 + - + +
183B GLN 3.1 1.6 + - - -
184B LYS* 3.3 16.2 + - - +
185B ARG* 3.5 61.0 + - - +
187B SER* 4.4 9.9 - - - -
268B LYS* 5.8 1.0 - - - +
269B ILE* 3.7 44.7 + - + +
272B GLU* 3.4 24.4 + - - +
273B GLU* 3.4 37.5 + - + +
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Residues in contact with MET 182 (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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178B LEU* 2.9 19.6 + - + +
179B LEU* 2.9 15.8 + - - +
181B ARG* 1.3 77.1 - - + +
183B GLN* 1.3 58.0 + - - +
187B SER* 3.1 21.0 + - - -
189B PHE* 3.3 47.4 - - + +
190B LYS* 3.5 2.3 - - - -
192B VAL* 3.9 17.0 - - + -
216B PHE* 4.3 11.0 - - + -
266B PHE* 4.0 20.2 - - + -
269B ILE* 3.9 28.9 - - + -
270B ILE* 3.8 29.4 - - + -
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Residues in contact with GLN 183 (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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179B LEU* 3.0 27.7 + - + +
180B ARG* 3.5 7.4 - - + +
181B ARG 3.8 0.2 - - - -
182B MET* 1.3 81.1 - - - +
184B LYS* 1.3 68.5 + - + +
185B ARG 4.5 2.4 - - - +
186B GLU* 4.5 0.2 - - - -
190B LYS* 2.7 34.2 + - - +
191B GLY* 2.9 30.4 + - - -
192B VAL* 2.7 45.3 + - - +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ARG* 2.6 69.5 + - + +
181B ARG* 3.3 9.0 + - - +
183B GLN* 1.3 75.9 - - - +
185B ARG* 1.3 61.4 + - + +
186B GLU* 2.6 23.7 + - - +
190B LYS* 3.8 6.2 + - - +
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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
------------------------------------------------------------
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