Contacts of the helix formed by residues 178 - 194 (chain B) in PDB entry 1B3U
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 PRO 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B ASP 3.3 9.6 - - - +
177B THR* 1.3 86.7 - - + +
179B MET* 1.3 65.9 + - - +
181B ARG* 3.1 27.2 + - + +
182B ARG* 2.8 52.6 + - - +
216B GLN* 4.4 18.8 - - + +
219B VAL* 4.2 3.8 - - + +
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Residues in contact with MET 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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140B PHE* 4.0 43.1 - - + -
144B THR* 3.9 6.4 - - + +
177B THR* 3.2 23.1 - - + -
178B PRO* 1.3 88.3 - - - +
180B VAL* 1.3 56.9 + - - +
182B ARG* 3.5 30.1 + - - +
183B ALA* 3.1 26.0 + - - +
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Residues in contact with VAL 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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140B PHE* 4.1 20.4 - - + +
143B ARG* 3.9 21.1 - - + +
144B THR* 4.0 9.9 - - + -
147B CYS* 4.3 1.6 - - - -
172B LEU* 3.8 27.8 - - + +
175B ASP* 3.5 35.4 - - + +
177B THR* 2.9 21.3 + - + +
179B MET* 1.3 74.1 - - - +
181B ARG* 1.3 65.6 + - - +
183B ALA* 3.0 3.8 + - - +
184B ALA* 2.9 21.3 + - - +
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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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172B LEU 4.0 6.5 - - - -
173B CYS 3.3 24.5 - - - +
174B SER* 4.1 3.4 - - - +
175B ASP 2.8 48.4 + - - +
176B ASP* 3.2 21.2 + - - +
177B THR 3.6 3.1 - - - +
178B PRO* 3.1 20.6 + - - +
180B VAL* 1.3 76.3 - - - +
182B ARG* 1.3 57.0 + - - +
184B ALA* 3.4 3.9 + - - +
185B ALA* 3.0 28.8 + - - +
211B LEU* 4.0 9.9 - - + +
214B ASP* 2.9 42.0 + - - -
215B GLU* 5.9 0.8 - - - +
216B GLN* 3.7 19.0 - - - +
219B VAL* 4.4 9.5 - - + +
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Residues in contact with ARG 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 PRO* 2.8 36.3 + - - +
179B MET* 3.6 34.9 - - - +
181B ARG* 1.3 75.0 - - - +
183B ALA* 1.3 64.9 + - - +
185B ALA* 3.4 1.0 + - - -
186B SER* 3.2 20.8 + - - -
218B SER* 3.2 43.5 + - - +
219B VAL* 3.6 16.1 - - + +
222B LEU* 3.4 28.3 - - + +
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Residues in contact with ALA 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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144B THR* 4.1 25.1 - - - +
147B CYS* 3.9 15.3 - - + -
179B MET 3.1 13.9 + - - +
180B VAL 3.0 8.6 + - - +
182B ARG* 1.3 77.6 - - - +
184B ALA* 1.3 61.0 + - - +
186B SER* 2.7 21.7 + - - -
187B LYS* 3.4 15.2 + - - +
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Residues in contact with ALA 184 (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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147B CYS* 3.7 17.2 - - - -
169B PHE* 3.7 11.4 - - + -
172B LEU* 4.2 3.1 - - + -
173B CYS* 3.9 39.3 - - - +
180B VAL 2.9 13.3 + - - +
181B ARG 3.7 7.9 - - - +
182B ARG 3.3 0.2 - - - -
183B ALA* 1.3 76.2 - - - +
185B ALA* 1.3 64.0 + - - +
187B LYS 2.9 13.7 + - - -
188B LEU* 3.0 11.8 + - - +
211B LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 185 (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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181B ARG 3.0 17.9 + - - +
182B ARG* 3.7 5.8 - - - +
184B ALA* 1.3 75.2 - - - +
186B SER* 1.3 61.2 + - - +
187B LYS 3.3 1.0 + - - -
188B LEU* 3.3 16.5 + - - +
189B GLY 4.6 0.9 + - - -
211B LEU* 4.0 29.7 - - + +
219B VAL* 4.8 5.6 - - + +
222B LEU* 4.0 28.3 - - + +
223B ALA* 5.3 1.6 - - - +
225B GLU* 5.2 1.9 - - - +
226B ALA* 4.3 12.4 - - + +
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Residues in contact with SER 186 (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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182B ARG 3.2 9.9 + - - -
183B ALA* 2.7 24.6 + - - -
185B ALA* 1.3 77.5 - - - +
187B LYS* 1.3 73.9 + - - +
188B LEU 3.5 0.2 - - - -
189B GLY 5.1 1.4 + - - -
190B GLU* 5.4 2.3 + - - +
222B LEU* 4.9 12.8 - - - +
225B GLU* 5.3 7.6 - - - +
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Residues in contact with LYS 187 (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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112B ARG* 4.7 4.0 - - - +
147B CYS* 3.6 27.6 - - + +
148B GLY* 3.8 18.3 - - - +
169B PHE* 4.1 7.0 - - + -
183B ALA 3.6 11.0 + - - +
184B ALA 2.9 8.3 + - - +
186B SER* 1.3 91.0 + - - +
188B LEU* 1.3 65.6 + - - +
189B GLY 3.4 2.0 - - - -
190B GLU* 3.5 35.9 + - - +
191B PHE* 3.0 24.1 + - - +
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Residues in contact with LEU 188 (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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169B PHE* 3.7 25.1 - - + -
173B CYS* 4.6 2.9 - - - -
184B ALA 3.0 7.3 + - - +
185B ALA* 3.3 14.3 + - - +
187B LYS* 1.3 75.6 - - - +
189B GLY* 1.3 62.9 + - - +
191B PHE* 3.1 3.3 + - + +
192B ALA* 2.8 31.2 + - - +
204B ILE* 4.1 27.4 - - + -
207B MET* 4.2 14.1 - - + -
208B PHE* 3.9 28.3 - - + +
211B LEU* 3.9 23.1 - - + -
226B ALA* 4.4 15.7 - - + -
230B ILE* 4.6 4.0 - - + -
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Residues in contact with GLY 189 (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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185B ALA 4.6 1.8 + - - -
186B SER 5.1 1.4 + - - -
187B LYS* 3.4 0.4 - - - +
188B LEU* 1.3 77.8 - - - +
190B GLU* 1.3 63.5 + - - +
192B ALA* 3.0 17.9 + - - +
193B LYS* 3.0 20.9 + - - +
225B GLU* 5.6 1.2 + - - -
226B ALA* 4.9 8.0 - - - +
229B ASN* 3.7 33.8 - - - +
230B ILE* 5.4 2.2 - - - -
233B LEU* 5.1 0.2 - - - +
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Residues in contact with GLU 190 (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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112B ARG* 2.9 29.0 + - - +
147B CYS 5.0 0.7 - - - +
148B GLY* 4.3 4.7 - - - +
151B SER* 2.7 36.4 + - - +
186B SER 5.4 2.1 + - - +
187B LYS* 3.5 37.4 + - - +
188B LEU 3.3 0.4 - - - -
189B GLY* 1.3 75.1 - - - +
191B PHE* 1.3 62.6 + - - +
193B LYS* 3.5 20.1 + - - +
194B VAL* 4.0 6.2 + - - +
229B ASN* 4.7 1.8 + - - -
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Residues in contact with PHE 191 (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 PHE* 3.8 29.6 - + + -
151B SER* 4.2 8.7 - - - +
154B TYR* 3.7 32.5 - + + -
166B ARG* 4.2 18.2 - - + -
169B PHE* 3.8 46.7 - + + -
187B LYS* 3.0 18.8 + - + +
188B LEU 3.6 2.9 - - - +
190B GLU* 1.3 77.7 - - + +
192B ALA* 1.3 64.4 - - - +
194B VAL* 3.2 25.9 + - + +
195B LEU* 3.5 29.6 - - + +
204B ILE* 4.2 13.2 - - + -
207B MET* 5.1 3.4 - - + -
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Residues in contact with ALA 192 (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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188B LEU 2.8 17.4 + - - +
189B GLY* 3.4 9.4 - - - +
191B PHE* 1.3 77.9 - - - +
193B LYS* 1.3 61.5 + - - +
195B LEU* 3.0 25.9 + - - +
200B VAL* 3.9 13.2 - - + +
204B ILE* 4.1 28.7 - - + -
230B ILE* 4.9 5.6 - - + -
233B LEU* 4.0 16.8 - - + +
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Residues in contact with LYS 193 (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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189B GLY 3.0 19.1 + - - +
190B GLU* 3.8 14.1 - - - +
191B PHE 3.2 0.6 - - - -
192B ALA* 1.3 76.6 - - - +
194B VAL* 1.3 62.0 + - + +
195B LEU 3.5 3.1 + - - +
229B ASN* 5.7 9.2 - - + +
232B GLN* 6.0 2.0 - - - +
233B LEU* 4.1 31.4 - - + +
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Residues in contact with VAL 194 (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 SER* 4.0 33.4 - - - +
154B TYR* 3.5 32.0 - - + -
155B PRO* 4.2 21.4 - - + +
190B GLU 4.4 6.7 - - - +
191B PHE* 3.2 21.0 + - + +
193B LYS* 1.3 82.1 - - + +
195B LEU* 1.3 61.7 + - + +
196B GLU* 5.3 0.9 - - - -
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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