Contacts of the helix formed by residues 237 - 253 (chain C) in PDB entry 1URP
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 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C PHE* 3.1 62.8 - - + +
18C SER* 3.7 12.3 - - - +
19C LEU* 3.4 13.3 - - + +
235C GLN 3.2 13.0 - - - +
236C LEU* 1.3 85.3 - - - +
238C ASP* 1.3 63.1 + - - +
240C ILE* 3.1 25.0 + - + +
241C GLY 3.1 10.2 + - - -
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Residues in contact with ASP 238 (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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18C SER* 3.3 31.1 + - - +
19C LEU* 4.3 0.2 - - - +
21C ASP* 5.8 1.1 - - + -
22C GLY* 3.4 19.3 - - - +
25C LYS* 5.1 8.4 + - - +
236C LEU* 3.2 11.3 - - - +
237C PRO* 1.3 80.4 - - - +
239C GLN* 1.3 73.7 + - - +
241C GLY 3.2 1.9 + - - -
242C ALA* 2.9 25.3 + - - +
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Residues in contact with GLN 239 (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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236C LEU* 2.9 30.9 + - + +
238C ASP* 1.3 91.5 - - - +
240C ILE* 1.3 56.5 + - - +
242C ALA* 3.8 10.4 - - + +
243C LYS* 2.8 37.8 + - - +
263C VAL* 3.6 20.1 - - + +
264C ASP* 5.4 6.3 - - - +
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Residues in contact with ILE 240 (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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15C PHE* 4.3 8.7 - - + -
19C LEU* 3.8 16.8 - - + -
88C LEU* 3.9 12.2 - - + +
89C ASP* 4.0 19.7 - - + +
101C ILE* 3.5 33.0 - - + +
102C ALA* 4.3 3.6 - - - -
103C SER* 3.6 28.7 - - - +
236C LEU 3.2 8.1 + - - +
237C PRO* 3.1 21.0 + - + +
239C GLN* 1.3 75.9 - - - +
241C GLY* 1.3 57.3 + - - +
244C GLY* 2.9 25.1 + - - -
263C VAL* 3.9 19.1 - - + -
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Residues in contact with GLY 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.6 32.2 - - - +
23C ALA* 3.6 11.9 - - - +
62C LEU* 4.8 1.2 - - - +
88C LEU* 4.5 5.2 - - - -
237C PRO 3.1 10.7 + - - -
238C ASP 3.2 0.4 + - - -
240C ILE* 1.3 76.4 - - - +
242C ALA* 1.3 61.3 + - - +
244C GLY* 3.3 1.6 + - - -
245C VAL* 3.1 27.7 + - - +
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Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY* 3.6 20.0 - - - +
26C GLU* 3.5 26.4 - - + +
238C ASP* 2.9 18.1 + - - +
239C GLN* 3.8 13.2 - - + +
241C GLY* 1.3 73.8 - - - +
243C LYS* 1.3 64.1 + - - +
245C VAL 3.1 3.3 + - - -
246C GLU* 3.0 20.3 + - - +
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Residues in contact with LYS 243 (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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101C ILE* 3.9 15.0 - - + -
239C GLN* 2.8 26.1 + - - +
242C ALA* 1.3 71.8 - - - +
244C GLY* 1.3 57.4 + - - +
246C GLU* 2.8 38.6 + - - +
247C THR* 2.8 39.6 + - - +
250C LYS* 4.1 8.9 - - - +
261C TYR* 3.8 46.9 - - + +
263C VAL* 4.4 6.5 - - + -
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Residues in contact with GLY 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.4 18.3 - - - +
86C ILE* 4.1 0.2 - - - +
88C LEU* 3.8 12.8 - - - -
101C ILE* 3.6 19.6 - - - +
240C ILE 2.9 17.3 + - - -
241C GLY 3.7 2.2 - - - -
242C ALA 3.2 0.2 - - - -
243C LYS* 1.3 76.5 - - - +
245C VAL* 1.3 55.4 + - - +
247C THR* 3.3 2.8 + - - -
248C ALA 2.9 24.3 + - - -
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.2 14.3 - - + +
23C ALA* 3.3 26.9 - - + +
26C GLU* 3.8 9.9 - - + -
27C ALA* 3.6 31.9 - - + +
30C LEU* 4.5 5.6 - - + -
32C TYR* 5.1 0.9 - - + -
34C LEU* 4.4 9.9 - - + -
62C LEU* 3.6 20.2 - - + +
241C GLY 3.1 15.8 + - - +
242C ALA 3.1 6.9 + - - +
244C GLY* 1.3 74.4 - - - +
246C GLU* 1.3 57.9 + - - +
248C ALA* 3.2 6.1 + - - +
249C ASP* 3.0 26.0 + - - +
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Residues in contact with GLU 246 (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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26C GLU* 3.5 23.3 - - - +
30C LEU* 3.9 16.8 - - + -
242C ALA 3.0 13.0 + - - +
243C LYS* 2.8 39.2 + - - +
245C VAL* 1.3 77.4 - - - +
247C THR* 1.3 56.9 + - - +
249C ASP* 3.2 5.5 - - - +
250C LYS* 3.0 56.7 + - + +
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Residues in contact with THR 247 (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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86C ILE* 3.9 12.8 - - + -
99C SER* 4.0 11.9 - - - -
101C ILE* 3.7 8.5 - - + +
243C LYS* 2.8 28.2 + - - +
244C GLY 3.7 4.3 - - - -
246C GLU* 1.3 76.0 + - - +
248C ALA* 1.3 66.6 + - - +
250C LYS* 3.3 6.9 + - - +
251C VAL* 3.0 22.2 + - - +
257C VAL* 3.8 17.3 - - + -
261C TYR* 3.6 39.2 - - + -
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Residues in contact with ALA 248 (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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4C ILE* 4.0 18.6 - - + -
60C ILE* 4.1 19.8 - - + +
62C LEU* 4.2 7.4 - - + -
86C ILE* 3.5 16.9 - - + +
244C GLY 2.9 13.5 + - - +
245C VAL* 3.2 9.8 + - - +
247C THR* 1.3 76.8 - - - +
249C ASP* 1.3 55.5 + - - +
251C VAL* 3.1 7.4 + - - +
252C LEU* 2.8 33.8 + - - +
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Residues in contact with ASP 249 (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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4C ILE* 4.7 0.8 - - - +
30C LEU* 3.6 33.9 - - + +
32C TYR* 2.6 41.0 + - + -
245C VAL 3.0 6.8 + - - +
246C GLU* 3.2 11.8 - - - +
248C ALA* 1.3 76.1 - - - +
250C LYS* 1.3 66.7 + - - +
252C LEU* 3.1 3.8 + - - +
253C LYS* 2.9 59.8 + - - +
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Residues in contact with LYS 250 (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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243C LYS* 4.1 8.1 - - - +
246C GLU* 3.0 49.0 + - + +
247C THR* 3.3 6.8 + - - +
249C ASP* 1.3 77.9 - - - +
251C VAL* 1.3 62.6 + - - +
253C LYS* 3.0 15.9 + - + -
255C GLU* 3.1 48.8 + - + +
257C VAL* 4.1 13.0 - - + -
261C TYR* 4.7 14.3 + - - -
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Residues in contact with VAL 251 (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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60C ILE* 3.7 22.4 - - + -
84C PRO* 4.3 15.0 - - + -
86C ILE* 4.6 9.0 - - + -
98C VAL* 4.3 12.6 - - + -
247C THR 3.0 20.4 + - - +
248C ALA 3.4 7.6 - - - +
250C LYS* 1.3 74.9 - - - +
252C LEU* 1.3 60.2 + - - +
254C GLY* 3.2 14.2 + - - -
255C GLU 3.9 11.1 + - - +
257C VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 252 (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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2C ASP* 4.9 8.1 - - + +
3C THR 5.5 0.2 - - - +
4C ILE* 4.4 9.4 - - + -
32C TYR* 3.5 37.9 - - + +
59C LYS* 3.9 27.1 - - + +
60C ILE* 3.5 33.2 - - + -
248C ALA 2.8 15.3 + - - +
249C ASP 3.1 8.0 + - - +
251C VAL* 1.3 75.7 - - + +
253C LYS* 1.3 57.9 + - - +
254C GLY 3.2 4.1 + - - -
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Residues in contact with LYS 253 (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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30C LEU* 4.9 10.3 + - - +
32C TYR* 4.8 2.2 - - - +
249C ASP* 2.9 51.9 + - - +
250C LYS* 3.0 11.3 + - + +
252C LEU* 1.3 77.1 - - - +
254C GLY* 1.3 61.6 + - - +
255C GLU* 3.3 13.2 + - + +
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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