Contacts of the helix formed by residues 178 - 191 (chain C) in PDB entry 5U0A
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 SER 178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.3 31.2 - - - -
125C LEU* 5.1 0.6 - - - +
126C PHE* 3.9 11.3 - - - -
176C LEU 3.6 0.9 + - - -
177C ASP* 1.3 72.2 - - - +
179C ALA* 1.3 63.2 + - - +
181C ALA* 3.0 9.4 + - - +
182C VAL* 2.9 27.9 + - - +
288C GLY 2.4 26.1 + - - -
289C SER* 2.8 23.9 + - - -
290C HIS* 3.1 5.0 + - - +
291C VAL* 5.0 0.9 - - - -
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Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.9 9.2 - - + -
26C PRO 4.0 11.0 - - - +
27C TRP* 3.6 25.4 - - + +
41C MET* 5.6 3.6 - - - -
177C ASP* 3.2 5.1 - - + +
178C SER* 1.3 78.7 - - - +
180C GLU* 1.3 61.3 + - - +
182C VAL* 3.2 22.9 + - - +
183C TRP* 3.4 26.0 + - + -
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Residues in contact with GLU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ARG* 4.3 6.5 + - - -
176C LEU* 2.7 33.4 - - + +
177C ASP* 3.0 41.4 + - + +
179C ALA* 1.3 77.1 - - - +
181C ALA* 1.3 64.4 + - - +
183C TRP* 2.9 45.3 + - + +
184C HIS* 3.3 27.4 + - - -
211N SER* 5.1 9.2 - - - -
213N ARG* 4.6 15.7 - - - +
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Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 5.9 1.1 - - + -
151C LEU* 5.0 5.8 - - + +
176C LEU* 4.3 9.6 - - + -
177C ASP 2.6 15.8 + - - +
178C SER* 3.0 10.1 + - - +
180C GLU* 1.3 73.2 - - - +
182C VAL* 1.3 64.6 + - + +
184C HIS* 3.3 7.1 + - - +
185C LEU* 3.0 24.5 + - - +
282C LEU* 4.5 9.6 - - + +
291C VAL* 3.3 37.0 - - + -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.1 12.8 - - + -
22C VAL* 5.4 4.9 - - + -
27C TRP* 4.4 31.6 - - + -
125C LEU* 3.9 24.5 - - + -
132C TRP* 5.2 14.1 - - + +
178C SER 2.9 19.1 - - - +
179C ALA* 3.4 12.1 - - - +
180C GLU 3.1 0.2 - - - -
181C ALA* 1.3 78.1 - - - +
183C TRP* 1.3 61.9 + - - +
185C LEU* 3.4 11.7 + - + +
186C LEU* 3.2 29.1 + - + +
282C LEU* 5.6 0.2 - - - -
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Residues in contact with TRP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TRP* 3.5 43.4 + + - -
29C ILE* 4.4 12.7 - - + +
41C MET* 4.8 12.8 - - + -
59C ILE* 3.5 40.9 - - + +
60C PRO* 4.5 17.9 - - + +
61C LEU* 4.5 25.1 - - + +
64C GLY* 4.2 5.5 - - - -
177C ASP* 5.9 0.2 - - - -
179C ALA* 3.4 16.6 - - + -
180C GLU* 2.9 52.8 + - + +
182C VAL* 1.3 78.0 - - - +
184C HIS* 1.3 66.1 + - + +
186C LEU* 3.3 6.3 + - - +
187C ALA* 3.1 21.0 + - - +
213N ARG* 6.0 5.4 - - - -
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Residues in contact with HIS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 3.4 33.7 - - + +
151C LEU* 4.4 11.4 - - + +
152C ALA* 3.6 21.9 - - + +
153C TRP* 3.7 28.5 + - + -
155C ARG* 5.1 2.0 + - - -
176C LEU* 2.9 38.0 - - + +
180C GLU* 3.3 23.7 + - - +
181C ALA* 3.3 6.0 + - - +
183C TRP* 1.3 76.1 - + + +
185C LEU* 1.3 65.4 + - - +
187C ALA* 3.1 5.5 + - - +
188C THR* 2.9 28.9 + - - +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 5.3 5.6 - - + -
132C TRP* 3.7 19.1 - - + +
133C LEU* 4.1 9.4 - - + +
134C GLN* 3.4 28.9 - - + +
151C LEU* 4.3 7.4 - - + +
181C ALA 3.0 16.6 + - - +
182C VAL* 3.8 11.2 - - + +
183C TRP 3.3 0.2 - - - -
184C HIS* 1.3 76.9 - - - +
186C LEU* 1.3 59.7 + - + +
188C THR* 3.0 17.0 + - - -
189C LEU* 2.8 41.9 + - + +
280C VAL* 4.2 17.3 - - + -
282C LEU* 3.9 14.4 - - + -
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TRP* 4.7 11.0 - - + -
59C ILE* 5.5 1.3 - - + -
64C GLY* 3.0 31.0 - - - +
67C VAL* 3.3 41.4 - - + +
68C LEU* 3.3 26.5 - - + +
71C ILE* 4.9 8.5 - - + -
132C TRP* 5.7 5.8 - - + +
133C LEU* 5.1 12.6 - - + -
182C VAL* 3.2 20.7 + - + +
183C TRP* 3.6 5.2 - - - +
184C HIS 3.1 0.2 - - - -
185C LEU* 1.3 82.1 - - + +
187C ALA* 1.3 63.7 + - - +
189C LEU* 3.3 10.5 + - - +
190C GLY 3.0 16.5 + - - -
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.5 3.8 - - + -
63C PRO* 3.8 31.2 - - + -
64C GLY* 4.0 8.7 - - - +
153C TRP* 3.9 19.5 - - + +
183C TRP 3.1 13.4 + - - +
184C HIS* 3.1 8.3 + - - +
186C LEU* 1.3 77.6 - - - +
188C THR* 1.3 51.2 + - - +
190C GLY* 2.8 4.9 + - - -
191C TYR* 2.6 40.2 + - + +
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Residues in contact with THR 188 (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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150C LYS 5.4 1.1 - - - +
151C LEU* 3.2 48.8 - - + +
153C TRP* 3.2 20.0 - - + +
184C HIS 2.9 17.5 + - - +
185C LEU 3.0 11.8 + - - -
187C ALA* 1.3 75.1 - - - +
189C LEU* 1.3 61.1 + - - +
190C GLY 3.8 0.7 - - - +
191C TYR 2.8 19.4 - - - +
192C GLY* 3.9 5.4 - - - -
193C PRO* 5.5 3.1 - - + -
278C HIS* 3.8 17.1 - - - +
280C VAL* 4.0 8.9 - - - +
296C VAL* 5.3 8.3 - - + -
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 5.5 1.6 - - + -
133C LEU* 3.6 40.4 - - + +
185C LEU* 2.8 41.9 + - + +
186C LEU* 3.5 6.7 - - - +
187C ALA 3.1 0.2 - - - -
188C THR* 1.3 79.5 - - - +
190C GLY* 1.3 62.5 + - - +
213C GLY* 5.1 0.3 - - - -
214C PRO* 3.9 5.9 - - - +
276C PHE* 3.3 47.3 - - + +
277C ARG 5.6 0.2 + - - -
278C HIS* 3.4 28.7 + - - +
279C ALA* 4.9 0.2 - - - -
280C VAL* 4.1 16.6 - - + +
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 3.6 21.7 - - - +
186C LEU 3.0 8.1 + - - -
187C ALA 2.8 6.3 + - - -
188C THR 3.8 0.7 - - - +
189C LEU* 1.3 82.0 - - - +
191C TYR* 1.3 63.7 + - - -
213C GLY* 3.2 21.4 - - - -
214C PRO* 3.3 8.2 - - - +
215C LEU* 4.2 13.9 - - - -
276C PHE* 5.3 1.1 - - - -
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Residues in contact with TYR 191 (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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62C PRO 4.5 0.5 + - - -
63C PRO* 3.0 49.6 - - + +
66C ALA* 3.1 23.0 - - + +
67C VAL* 4.7 1.8 - - + -
153C TRP* 3.9 9.6 - - + -
187C ALA 2.6 27.6 + - - +
188C THR* 2.8 14.1 - - - +
190C GLY* 1.3 71.4 - - - -
192C GLY* 1.3 58.4 + - - +
213C GLY* 4.7 2.7 - - - -
215C LEU* 2.7 38.5 - - + +
216C ARG* 3.8 12.3 - - - +
217C GLY 4.4 0.9 - - - -
218C THR* 4.1 13.9 + - - -
220C SER* 4.6 2.6 + - - -
377C PHE 4.4 5.7 + - - -
379C PHE* 3.9 26.9 - + + +
381C GLN* 3.8 26.9 - - - +
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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