Contacts of the helix formed by residues 186 - 203 (chain C) in PDB entry 5WYF
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 186 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLY 4.2 6.7 - - - +
185C GLU* 1.3 75.7 - - - +
187C GLU* 1.3 60.1 + - - +
188C HIS* 3.3 13.3 + - - +
189C ASP* 3.0 41.7 + - - +
190C VAL* 3.0 15.8 + - - +
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Residues in contact with GLU 187 (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 SER* 5.8 1.3 - - - +
186C THR* 1.3 74.2 - - - +
188C HIS* 1.3 52.9 + - - +
190C VAL* 3.7 7.7 - - - +
191C SER* 2.7 38.1 + - - +
229C PRO* 3.7 31.8 - - + +
230C GLU* 4.0 13.2 + - - +
231C GLU* 5.1 3.5 + - + +
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Residues in contact with HIS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C THR* 3.2 8.8 + - - +
187C GLU* 1.3 77.3 - - - +
189C ASP* 1.3 77.4 + - - +
191C SER* 3.8 1.3 - - - -
192C LEU* 3.0 57.1 + - + +
231C GLU* 3.6 14.7 + - - +
1004C CD 2.2 34.6 - - - -
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Residues in contact with ASP 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 5.8 1.0 - - - -
184C GLY 3.6 5.4 - - - +
185C GLU* 3.4 25.9 - - + +
186C THR* 3.0 37.4 + - - +
188C HIS* 1.3 89.1 - - - +
190C VAL* 1.3 58.2 + - - +
192C LEU* 4.1 4.8 - - - +
193C ARG* 3.0 30.5 + - - +
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C PRO* 4.4 5.2 - - + -
177C ASP 4.0 11.9 - - - +
178C SER* 4.1 17.3 - - - +
181C THR* 3.7 28.0 - - + -
185C GLU* 4.2 17.0 - - + +
186C THR 3.0 14.6 + - - +
187C GLU* 3.7 10.5 - - - +
188C HIS 3.2 0.2 - - - -
189C ASP* 1.3 73.2 - - - +
191C SER* 1.3 63.0 + - - +
193C ARG* 3.3 3.4 + - - +
194C TYR* 2.8 49.7 + - + -
229C PRO* 4.4 9.6 - - + -
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C PRO* 5.8 0.2 - - - -
187C GLU* 2.7 22.5 + - - +
188C HIS 3.8 4.3 - - - -
189C ASP 3.4 0.2 - - - -
190C VAL* 1.3 78.7 - - - +
192C LEU* 1.3 56.8 + - - +
194C TYR* 5.1 0.2 - - - -
195C PHE* 3.0 29.0 + - - +
229C PRO* 3.3 23.4 - - - +
231C GLU* 4.0 18.4 - - - +
232C TYR* 3.5 35.4 + - - -
235C LEU* 4.6 2.0 - - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C HIS* 3.0 54.6 + - + +
189C ASP* 4.1 4.3 - - - +
191C SER* 1.3 74.8 - - - +
193C ARG* 1.3 61.1 + - - +
195C PHE* 3.8 7.2 - - + +
196C ASN* 2.9 29.1 + - - +
231C GLU* 4.8 5.8 - - - +
235C LEU* 4.2 21.3 - - + -
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Residues in contact with ARG 193 (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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182A TYR* 3.3 41.2 - - + +
193A ARG* 5.5 1.8 - - - +
197A GLU* 4.8 10.1 + - - -
200A LYS* 4.9 3.2 - - - +
180C ARG 4.6 2.8 + - - -
181C THR* 4.3 15.2 - - - +
182C TYR* 3.7 29.7 - - - -
185C GLU* 2.8 40.9 + - - +
189C ASP 3.0 20.3 + - - +
190C VAL* 3.7 4.2 - - - +
192C LEU* 1.3 77.1 - - - +
194C TYR* 1.3 101.5 + - + +
196C ASN* 3.1 5.7 + - - +
197C GLU* 3.0 39.6 + - + +
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Residues in contact with TYR 194 (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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200A LYS* 3.2 28.2 + - - -
174C PRO* 3.9 22.1 - - + +
175C TYR 3.5 17.5 - - - -
176C PRO* 3.5 21.8 - - + -
177C ASP* 3.5 34.0 + - - +
180C ARG 4.9 2.3 + - - -
190C VAL* 2.8 37.1 + - + +
193C ARG* 1.3 113.1 + - - +
195C PHE* 1.3 56.9 + - - +
197C GLU* 3.2 9.4 + - + +
198C PHE* 2.9 25.8 + - - +
232C TYR* 3.5 24.6 + - + -
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Residues in contact with PHE 195 (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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191C SER 3.0 18.7 + - - +
192C LEU* 3.8 7.9 - - + +
193C ARG 3.3 0.2 - - - -
194C TYR* 1.3 73.4 - - - +
196C ASN* 1.3 60.9 + - - +
198C PHE* 3.3 28.5 + + + +
199C LYS* 3.0 69.6 + - + +
232C TYR* 3.5 7.7 - + + -
235C LEU* 3.5 67.3 - - + -
236C VAL* 4.0 7.9 - - + -
239C PHE* 4.0 14.1 - + + -
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Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 4.6 9.7 + - - +
192C LEU 2.9 18.8 + - - +
193C ARG* 3.1 8.5 + - - +
195C PHE* 1.3 75.8 - - - +
197C GLU* 1.3 64.6 + - - +
199C LYS* 3.3 20.6 + - - +
200C LYS* 3.3 42.0 + - - +
203C GLU* 5.2 6.7 + - - -
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 5.5 0.3 - - - +
174A PRO* 4.9 4.7 - - - +
182A TYR* 4.9 2.9 + - - -
193A ARG* 4.9 9.7 + - - -
197A GLU* 3.7 30.5 - - - +
173C VAL* 4.7 1.7 - - - +
174C PRO* 3.7 30.9 - - + +
193C ARG* 3.0 35.6 + - + +
194C TYR* 3.2 14.8 + - + +
196C ASN* 1.3 77.4 - - - +
198C PHE* 1.3 63.7 + - - +
200C LYS* 3.2 31.1 + - - +
201C PRO* 3.2 19.8 - - - +
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL* 4.3 8.3 - - + -
138C TYR* 3.5 25.4 - - - -
173C VAL* 4.0 20.5 - - + +
174C PRO* 5.0 1.6 + - - +
194C TYR 2.9 13.4 + - - +
195C PHE* 3.3 34.8 - + + +
197C GLU* 1.3 75.2 - - - +
199C LYS* 1.3 65.4 + - + +
201C PRO* 3.3 10.6 - - - +
202C PHE* 3.3 39.3 - + - -
214C VAL* 3.9 27.8 - - + -
232C TYR* 3.8 9.0 - - - +
236C VAL* 4.0 15.0 - - + -
239C PHE* 3.6 34.5 - + + -
240C CYS* 5.1 0.4 - - - -
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Residues in contact with LYS 199 (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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195C PHE* 3.0 62.4 + - + +
196C ASN* 3.8 20.6 - - - +
197C GLU 3.1 0.6 - - - -
198C PHE* 1.3 79.2 - - + +
200C LYS* 1.3 65.1 + - - +
201C PRO 3.3 0.2 - - - -
202C PHE* 2.9 21.9 + - + +
203C GLU* 2.9 39.8 + - + +
239C PHE* 4.3 18.4 - - + -
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Residues in contact with LYS 200 (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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139A MET* 3.7 17.0 - - + +
174A PRO* 4.2 16.3 - - + +
175A TYR 5.3 1.0 + - - -
177A ASP* 5.6 1.0 - - - +
193A ARG* 5.0 4.0 - - - +
194A TYR* 3.2 38.0 + - - -
196C ASN* 3.3 31.4 + - - +
197C GLU* 3.2 32.0 + - - +
199C LYS* 1.3 75.7 - - - +
201C PRO* 1.3 69.8 - - + +
203C GLU* 3.1 22.0 + - - +
204C SER* 3.0 16.6 + - - -
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Residues in contact with PRO 201 (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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139A MET* 3.9 13.5 - - + -
171C VAL* 4.2 10.3 - - + -
172C HIS 5.7 0.2 - - - +
173C VAL* 3.9 20.4 - - + -
197C GLU 3.2 14.8 - - - +
198C PHE 3.3 12.8 - - - +
200C LYS* 1.3 89.5 - - + +
202C PHE* 1.3 62.1 + - + +
204C SER* 3.2 13.5 + - - +
205C PHE* 3.3 25.1 + - + -
206C LEU* 2.9 35.4 + - + -
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Residues in contact with PHE 202 (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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157A LEU* 3.5 24.9 - - - +
136C VAL* 3.9 16.4 - - + -
173C VAL* 5.6 0.2 - - + -
198C PHE* 3.3 52.5 - + - -
199C LYS* 2.9 9.9 + - + +
201C PRO* 1.3 78.8 - - + +
203C GLU* 1.3 60.1 + - + +
204C SER 3.3 0.4 - - - -
206C LEU* 3.2 37.4 - - + +
208C ALA* 3.6 23.2 + - + +
211C THR* 3.4 27.6 - - + -
214C VAL* 5.2 0.9 - - + -
239C PHE* 3.8 26.2 - + + -
245C ILE* 4.2 7.2 - - + -
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Residues in contact with GLU 203 (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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155A SER 6.0 0.7 - - - -
157A LEU* 5.0 5.1 - - - +
196C ASN* 5.1 6.5 + - - +
199C LYS* 2.9 48.6 + - + +
200C LYS* 3.1 14.6 + - - +
202C PHE* 1.3 79.9 - - + +
204C SER* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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