Contacts of the helix formed by residues 170 - 185 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C VAL* 4.9 1.1 - - + -
168C GLY 3.1 12.2 + - - +
169C VAL* 1.3 74.1 - - - +
171C THR* 1.3 54.8 + - - +
172C LEU* 3.1 3.6 - - - -
173C ASP* 2.8 44.0 + - - +
174C ILE* 3.7 9.7 - - - +
196C VAL* 5.9 0.4 - - - -
199C GLY 4.8 5.6 - - - +
200C HIS* 4.2 21.8 - - + -
275C CYS 3.4 20.8 + - - -
276C SER* 3.6 6.1 - - - -
277C PHE* 3.9 20.9 - - + +
289C SER* 3.6 14.2 + - - +
402C NAD 5.2 0.7 - - - -
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Residues in contact with THR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C VAL* 3.4 8.9 - - - +
170C THR* 1.3 78.0 + - - +
172C LEU* 1.3 58.2 + - - +
174C ILE* 3.1 14.3 + - + +
175C VAL* 3.0 26.0 + - + +
254C ALA* 3.5 30.5 - - + +
257C ARG* 3.8 34.5 - - + +
258C PHE* 3.3 31.8 - - - +
274C GLU* 4.7 5.2 + - - +
275C CYS 4.4 4.7 + - - -
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR 3.0 1.2 + - - -
171C THR* 1.3 78.4 - - - +
173C ASP* 1.3 58.2 + - - +
175C VAL* 4.1 14.1 - - + -
176C ARG* 2.9 74.1 + - + +
200C HIS* 5.5 0.2 - - + -
247C ALA* 4.2 3.1 - - + -
250C SER* 3.6 40.6 - - - +
251C MET* 3.9 29.7 - - - +
254C ALA* 3.5 14.7 - - + +
401C LMR 3.9 8.7 - - - +
402C NAD 4.6 5.6 - - - +
70D HIS* 5.0 1.1 - - + -
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR* 2.8 18.3 + - - +
172C LEU* 1.3 77.2 - - - +
174C ILE* 1.3 58.3 + - + +
176C ARG* 3.8 15.9 + - - +
177C ALA* 3.0 28.9 + - - +
196C VAL* 3.8 23.1 - - + +
199C GLY 4.0 5.5 - - - +
200C HIS* 2.7 43.3 + - - +
205C ILE* 3.7 29.0 - - + +
230C ILE* 4.1 7.3 - - - +
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR* 3.7 22.4 - - - +
171C THR* 3.1 10.5 + - + +
173C ASP* 1.3 73.5 - - + +
175C VAL* 1.3 61.8 + - - +
177C ALA* 3.2 2.9 + - - +
178C ASN* 2.8 50.2 + - - +
193C ASN* 4.4 7.0 - - - +
194C VAL 3.7 21.8 - - - +
196C VAL* 3.7 30.1 - - + +
257C ARG* 3.9 22.9 - - - +
274C GLU* 5.8 1.8 - - - +
275C CYS* 3.8 29.8 - - + +
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C THR* 3.0 33.2 + - + +
172C LEU* 3.7 16.4 - - + +
174C ILE* 1.3 76.5 - - - +
176C ARG* 1.3 56.0 + - - +
178C ASN* 3.3 3.6 + - - +
179C THR* 3.0 31.4 + - - -
253C TYR* 3.9 20.2 - - + -
254C ALA* 4.3 3.4 - - + -
257C ARG* 4.1 3.6 - - - +
70D HIS 3.4 17.5 - - - +
71D ILE* 3.9 4.9 - - + -
72D GLU* 3.6 45.0 - - + +
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Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ARG* 4.4 1.0 - - - +
172C LEU* 2.9 45.7 + - + +
173C ASP* 3.8 20.0 + - - +
175C VAL* 1.3 74.6 - - - +
177C ALA* 1.3 60.6 + - - +
179C THR* 3.2 2.6 + - - -
180C PHE* 2.9 49.0 + - + -
200C HIS* 4.4 0.6 - - - -
205C ILE* 6.0 0.6 - - - +
230C ILE* 4.8 6.6 + - + -
233C ALA* 3.5 17.9 + - + +
234C GLY* 3.5 24.5 - - - +
237C VAL* 4.4 1.2 - - - +
247C ALA* 3.8 9.5 - - - +
250C SER* 4.9 0.6 + - - -
401C LMR 2.7 43.8 + - - -
70D HIS* 3.3 43.2 + - + +
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASP 3.0 18.9 + - - +
174C ILE 3.5 4.3 - - - +
176C ARG* 1.3 75.0 - - - +
178C ASN* 1.3 63.6 + - - +
180C PHE* 4.1 0.6 - - - +
181C VAL* 3.0 30.8 + - - +
194C VAL* 3.8 27.4 - - + -
196C VAL* 4.1 9.2 - - + -
230C ILE* 3.7 30.2 - - + +
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Residues in contact with ASN 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 2.8 31.2 + - - +
175C VAL 3.5 7.2 - - - +
177C ALA* 1.3 77.3 - - - +
179C THR* 1.3 57.0 + - - +
182C ALA* 3.0 32.2 + - - +
189C PRO* 4.2 9.2 - - - +
192C VAL* 3.1 33.8 + - - +
193C ASN* 3.3 4.1 - - - +
194C VAL* 2.8 30.1 + - - +
257C ARG* 3.9 3.6 - - - +
72D GLU* 2.7 28.9 + - + +
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL 3.0 8.8 + - - -
176C ARG* 3.2 6.7 + - - -
178C ASN* 1.3 76.8 - - - +
180C PHE* 1.3 66.1 + - + +
182C ALA* 3.4 2.3 + - - +
183C GLU* 3.0 42.5 + - + +
189C PRO* 4.2 13.1 - - + +
45D LYS* 6.0 0.2 - - - +
69D SER 3.4 25.1 - - - +
70D HIS 2.8 23.8 + - - +
71D ILE 3.3 4.6 - - - +
72D GLU* 3.3 16.6 - - - -
73D THR 5.6 1.1 - - - +
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Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ARG* 2.9 31.1 + - + +
177C ALA 4.1 1.6 - - - +
179C THR* 1.3 84.2 - - + +
181C VAL* 1.3 65.7 + - - +
183C GLU* 3.5 12.8 + - - +
184C LEU* 3.3 28.3 + - + +
226C LEU* 3.6 18.8 - - + -
229C ARG* 3.6 59.9 - - + +
230C ILE* 3.7 18.4 - - + -
233C ALA* 4.1 4.7 - - + -
69D SER 5.2 0.7 - - - -
70D HIS* 3.6 43.1 - + - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ALA* 3.0 22.0 + - - +
178C ASN 4.0 2.2 - - - +
180C PHE* 1.3 75.2 - - - +
182C ALA* 1.3 62.6 + - - +
184C LEU* 3.3 2.9 + - - +
185C LYS* 3.1 24.6 + - + +
187C LEU* 5.2 1.3 - - + -
192C VAL* 4.1 19.5 - - + -
194C VAL* 3.9 13.9 - - + -
209C ILE* 4.0 12.6 - - + -
212C CYS* 4.2 12.8 - - - -
216C VAL* 4.3 14.4 - - + -
218C PHE* 4.2 17.9 - - + -
226C LEU* 3.9 24.7 - - + -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ASN 3.0 19.0 + - - +
179C THR 3.7 4.3 - - - +
181C VAL* 1.3 78.6 - - - +
183C GLU* 1.3 56.5 + - - +
186C GLY* 2.9 9.0 + - - -
187C LEU* 2.7 52.9 + - - +
189C PRO* 3.5 27.1 - - + -
192C VAL* 4.0 8.7 - - + +
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Residues in contact with GLU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C THR* 3.0 37.4 + - + +
180C PHE* 3.8 14.9 - - - +
181C VAL 3.3 0.2 - - - -
182C ALA* 1.3 75.7 - - + +
184C LEU* 1.3 65.8 + - + +
186C GLY* 3.5 9.9 + - - -
187C LEU 5.3 0.2 - - - -
229C ARG* 5.3 5.9 + - - -
69D SER* 4.5 8.1 - - - +
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 3.3 19.3 + - + +
181C VAL 3.8 3.6 - - - +
183C GLU* 1.3 80.4 - - + +
185C LYS* 1.3 63.3 + - - +
186C GLY 3.4 0.8 + - - -
218C PHE* 4.0 28.5 - - + -
222C GLN* 5.4 10.3 - - + +
226C LEU* 4.1 27.1 - - + -
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C VAL 3.1 15.9 + - - +
184C LEU* 1.3 79.7 - - - +
186C GLY* 1.3 63.5 + - - +
187C LEU* 3.2 27.0 + - + +
216C VAL* 3.8 29.4 - - + +
217C ASP* 2.7 32.2 + - - +
218C PHE* 3.7 27.2 - - + -
219C PRO* 6.0 0.2 - - - +
222C GLN* 5.5 1.6 + - - -
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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