Contacts of the helix formed by residues 170 - 186 (chain B) in PDB entry 4WLU
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 THR 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B VAL* 4.7 1.8 - - + -
168B GLY 3.1 12.8 + - - +
169B VAL* 1.3 73.7 - - - +
171B THR* 1.3 65.6 + - - +
172B LEU* 3.1 3.8 - - - -
173B ASP* 2.9 33.9 + - - +
174B ILE* 3.6 9.1 - - - +
196B VAL* 5.3 0.8 + - - -
199B GLY 4.8 2.0 - - - -
200B HIS* 4.1 27.6 - - + +
275B CYS 3.6 18.5 + - - -
276B SER* 3.8 1.2 - - - -
277B PHE* 4.0 20.2 - - + +
289B SER* 3.7 17.6 + - - +
402B NAD 5.2 1.1 - - - -
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Residues in contact with THR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.4 7.8 - - - +
170B THR* 1.3 78.3 + - - +
172B LEU* 1.3 59.0 + - - +
174B ILE* 3.1 13.3 + - + +
175B VAL* 3.0 26.5 + - + +
254B ALA* 3.5 29.6 - - + +
257B ARG* 3.7 34.5 - - + +
258B PHE* 3.4 32.1 - - - +
274B GLU* 4.5 5.8 + - - +
275B CYS 4.4 4.4 + - - -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 5.0 1.1 - - + -
169B VAL 5.4 0.2 + - - -
170B THR 3.0 1.2 + - - -
171B THR* 1.3 79.9 - - - +
173B ASP* 1.3 56.9 + - - +
175B VAL* 4.2 11.7 - - + -
176B ARG* 2.9 73.7 + - + +
247B ALA* 4.3 1.6 - - + -
250B SER* 3.7 41.5 - - - +
251B MET* 4.0 31.4 - - + +
254B ALA* 3.6 15.3 - - + +
401B LMR 4.0 7.4 - - - +
402B NAD 4.3 9.4 - - + +
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Residues in contact with ASP 173 (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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170B THR* 2.9 21.4 + - - +
172B LEU* 1.3 76.9 - - - +
174B ILE* 1.3 57.7 + - + +
176B ARG* 3.5 15.7 + - - +
177B ALA* 3.0 29.3 + - - +
196B VAL* 3.8 24.5 - - + +
199B GLY 4.1 2.6 - - - +
200B HIS* 2.8 42.3 + - - +
205B ILE* 3.8 28.2 - - + +
230B ILE* 4.2 7.0 - - + +
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR* 3.6 22.0 - - - +
171B THR* 3.1 12.8 + - + +
173B ASP* 1.3 73.6 - - + +
175B VAL* 1.3 61.4 + - - +
177B ALA* 3.2 2.1 + - - +
178B ASN* 2.9 50.1 + - - +
193B ASN* 4.3 7.2 - - - +
194B VAL 3.6 21.5 - - - +
195B PRO* 4.9 0.2 - - + -
196B VAL* 3.8 28.3 - - + +
257B ARG* 3.9 21.8 - - - +
274B GLU* 5.8 1.8 - - - +
275B CYS* 3.7 32.3 - - + +
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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
----------------------------------------------------------
70A HIS 3.4 17.0 - - - +
71A ILE* 4.0 5.2 - - + -
72A GLU* 3.7 34.8 - - + +
171B THR* 3.0 34.5 + - + +
172B LEU* 3.7 15.9 - - + +
174B ILE* 1.3 76.7 - - - +
176B ARG* 1.3 58.7 + - - +
178B ASN* 3.5 2.8 + - - +
179B THR* 3.0 28.1 + - - -
253B TYR* 3.9 30.3 - - + -
254B ALA* 4.2 3.4 - - + -
257B ARG* 4.1 4.5 - - - +
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Residues in contact with ARG 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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70A HIS* 3.4 42.7 + - + +
110B ARG* 4.6 1.2 - - - +
172B LEU* 2.9 46.5 + - + +
173B ASP* 3.7 19.7 + - - +
175B VAL* 1.3 73.9 - - - +
177B ALA* 1.3 60.2 + - - +
179B THR* 3.1 2.9 + - - -
180B PHE* 2.9 47.1 + - + -
200B HIS* 4.4 0.6 - - - -
230B ILE* 4.9 8.3 + - + -
233B ALA* 3.5 16.6 + - + +
234B GLY* 3.5 24.6 - - - +
237B VAL* 4.5 0.8 - - - +
247B ALA* 3.8 9.9 - - - +
250B SER* 4.8 0.2 + - - -
401B LMR 2.7 43.9 + - - -
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Residues in contact with ALA 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 ASP 3.0 18.4 + - - +
174B ILE 3.5 4.3 - - - +
176B ARG* 1.3 74.9 - - - +
178B ASN* 1.3 58.6 + - - +
180B PHE* 4.1 0.6 - - - +
181B VAL* 3.0 35.5 + - - +
194B VAL* 3.7 28.0 - - + -
196B VAL* 4.1 8.1 - - + -
230B ILE* 3.7 29.5 - - + +
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Residues in contact with ASN 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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72A GLU* 2.9 27.5 + - + +
174B ILE* 2.9 33.9 + - - +
175B VAL 3.7 4.9 - - - +
176B ARG 3.2 0.2 - - - -
177B ALA* 1.3 75.9 - - - +
179B THR* 1.3 61.9 + - - +
182B ALA* 3.0 26.5 + - - +
189B PRO* 4.3 8.7 - - - +
192B VAL* 3.2 35.0 + - + +
193B ASN* 3.3 5.5 + - - +
194B VAL* 2.7 31.2 + - - +
257B ARG* 4.0 3.8 - - - +
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER 3.4 24.9 - - - +
70A HIS* 2.7 25.1 + - - +
71A ILE 4.2 4.9 - - - +
72A GLU* 3.3 15.2 - - - -
73A THR 5.8 0.7 - - - +
175B VAL 3.0 6.1 + - - -
176B ARG* 3.1 9.0 + - - -
178B ASN* 1.3 78.8 - - - +
180B PHE* 1.3 63.0 + - + +
182B ALA* 3.3 5.9 + - - +
183B GLU* 2.9 44.1 + - + +
189B PRO* 4.6 10.2 - - + +
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 3.6 43.5 - + - -
176B ARG* 2.9 31.7 + - + +
177B ALA 4.1 1.3 - - - +
179B THR* 1.3 78.0 - - + +
181B VAL* 1.3 65.5 + - - +
183B GLU* 3.4 23.8 + - - +
184B LEU* 3.2 29.0 + - + +
226B LEU* 3.7 19.1 - - + -
229B ARG* 3.8 58.8 - - + +
230B ILE* 3.8 18.2 - - + -
233B ALA* 4.1 4.5 - - + -
236B GLU* 4.9 0.7 - - - -
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Residues in contact with VAL 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 ALA* 3.0 22.6 + - - +
178B ASN 4.1 2.0 - - - +
180B PHE* 1.3 76.8 - - - +
182B ALA* 1.3 63.2 + - - +
184B LEU* 3.4 1.4 + - - +
185B LYS* 3.2 25.1 + - + +
187B LEU* 5.2 1.1 - - + -
192B VAL* 4.1 19.3 - - + -
194B VAL* 3.9 14.4 - - + -
209B ILE* 4.2 11.7 - - + -
212B CYS* 4.2 13.5 - - - -
216B VAL* 4.2 22.4 - - + -
218B PHE* 4.7 10.1 - - + -
226B LEU* 4.0 24.9 - - + -
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Residues in contact with ALA 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 ASN 3.0 20.4 + - - +
179B THR 3.6 3.8 - - - +
181B VAL* 1.3 75.3 - - - +
183B GLU* 1.3 55.7 + - - +
186B GLY* 2.8 31.9 + - - -
187B LEU* 2.9 34.5 + - - +
189B PRO* 3.7 25.4 - - + -
192B VAL* 4.0 9.0 - - + -
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Residues in contact with GLU 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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69A SER* 4.4 6.8 - - - +
179B THR* 2.9 35.4 + - + +
180B PHE* 3.6 26.0 - - - +
181B VAL 3.3 0.4 - - - -
182B ALA* 1.3 77.3 - - - +
184B LEU* 1.3 64.7 + - + +
185B LYS 3.4 0.2 + - - -
186B GLY* 3.4 8.5 + - - -
229B ARG* 4.8 8.4 + - - -
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Residues in contact with LEU 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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180B PHE* 3.2 17.3 + - + +
181B VAL 4.0 2.0 - - - +
182B ALA 3.4 0.2 - - - -
183B GLU* 1.3 83.3 - - + +
185B LYS* 1.3 62.4 + - - +
186B GLY 3.9 0.3 + - - -
218B PHE* 3.7 35.4 - - + -
222B GLN* 4.8 12.1 - - - +
226B LEU* 4.0 26.5 - - + -
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Residues in contact with LYS 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 VAL 3.2 17.6 + - - +
184B LEU* 1.3 80.2 - - - +
186B GLY* 1.3 63.6 + - - +
187B LEU* 3.3 24.9 + - + +
216B VAL* 4.1 22.4 - - + +
217B ASP* 2.7 33.5 + - - +
218B PHE* 3.5 31.6 - - + -
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Residues in contact with GLY 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 ALA 2.8 10.1 + - - -
183B GLU* 3.4 9.3 + - - -
184B LEU 3.5 0.8 + - - -
185B LYS* 1.3 79.3 - - - +
187B LEU* 1.3 61.4 + - - +
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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