Contacts of the helix formed by residues 237 - 253 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 3.2 63.3 - - + +
18D SER* 3.8 11.9 - - - +
19D LEU* 3.3 13.4 - - + +
235D GLN 3.2 13.5 - - - +
236D LEU* 1.3 85.5 - - - +
238D ASP* 1.3 63.1 + - - +
240D ILE* 3.1 17.4 + - + +
241D GLY 3.1 17.2 + - - -
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Residues in contact with ASP 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D SER* 3.3 30.9 + - - +
19D LEU* 4.2 0.2 - - - +
21D ASP* 5.8 0.7 - - + -
22D GLY* 3.4 18.3 - - - +
236D LEU* 3.2 11.5 - - - +
237D PRO* 1.3 80.0 - - - +
239D GLN* 1.3 74.1 + - - +
241D GLY 3.2 1.7 + - - -
242D ALA* 2.9 26.2 + - - +
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Residues in contact with GLN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D LEU* 3.0 31.1 + - + +
238D ASP* 1.3 91.5 - - - +
240D ILE* 1.3 56.7 + - - +
242D ALA* 3.8 10.8 - - + +
243D LYS* 2.8 38.1 + - - +
263D VAL* 3.6 20.3 - - + +
264D ASP* 5.5 6.3 - - - +
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Residues in contact with ILE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.3 7.9 - - + -
19D LEU* 3.8 16.8 - - + -
88D LEU* 3.8 13.5 - - + +
89D ASP* 4.0 19.3 - - + +
101D ILE* 3.4 33.8 - - + +
102D ALA* 4.3 3.6 - - - -
103D SER* 3.6 28.9 - - - +
236D LEU 3.2 8.1 + - - +
237D PRO* 3.1 21.8 + - + +
239D GLN* 1.3 74.0 - - - +
241D GLY* 1.3 62.9 + - - +
244D GLY* 3.0 19.6 + - - -
263D VAL* 3.9 18.8 - - + -
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Residues in contact with GLY 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.5 32.7 - - - +
23D ALA* 3.6 12.4 - - - +
62D LEU* 4.8 1.2 - - - +
88D LEU* 4.5 3.8 - - - -
237D PRO 3.1 10.7 + - - -
238D ASP 3.2 0.8 + - - -
240D ILE* 1.3 78.3 - - - +
242D ALA* 1.3 61.4 + - - +
244D GLY* 3.3 1.9 + - - -
245D VAL* 3.1 26.9 + - - +
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Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLY* 3.6 19.8 - - - +
26D GLU* 3.5 26.2 - - + +
238D ASP* 2.9 18.2 + - - +
239D GLN* 3.8 14.4 - - + +
241D GLY* 1.3 75.0 - - - +
243D LYS* 1.3 63.2 + - - +
245D VAL 3.0 3.6 + - - -
246D GLU* 3.0 20.1 + - - +
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ILE* 4.0 15.0 - - + -
239D GLN* 2.8 26.1 + - - +
242D ALA* 1.3 71.3 - - - +
244D GLY* 1.3 56.2 + - - +
246D GLU* 2.9 38.4 + - - +
247D THR* 2.8 39.9 + - - +
250D LYS* 4.6 4.2 - - - +
261D TYR* 3.8 48.1 - - + +
263D VAL* 4.4 7.0 - - + -
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU* 3.3 18.5 - - - +
88D LEU* 3.8 11.9 - - - -
101D ILE* 3.6 20.1 - - - +
240D ILE 3.0 17.6 + - - -
241D GLY 3.7 2.0 - - - -
242D ALA 3.2 0.2 - - - -
243D LYS* 1.3 77.0 - - - +
245D VAL* 1.3 55.9 + - - +
247D THR* 3.4 2.4 + - - -
248D ALA 2.9 23.6 + - - -
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Residues in contact with VAL 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.2 13.5 - - + +
23D ALA* 3.4 26.7 - - + +
26D GLU* 3.8 10.5 - - + +
27D ALA* 3.6 31.4 - - + +
30D LEU* 4.4 6.1 - - + -
32D TYR* 5.1 0.9 - - + -
34D LEU* 4.4 9.9 - - + -
62D LEU* 3.6 19.7 - - + -
241D GLY 3.1 14.6 + - - +
242D ALA 3.0 8.5 + - - +
244D GLY* 1.3 74.8 - - - +
246D GLU* 1.3 58.4 + - - +
248D ALA* 3.1 6.7 + - - +
249D ASP* 3.0 26.0 + - - +
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU* 3.6 21.5 - - - +
30D LEU* 3.9 15.9 - - + -
242D ALA 3.0 13.0 + - - +
243D LYS* 2.9 39.2 + - - +
245D VAL* 1.3 75.9 - - - +
247D THR* 1.3 57.9 + - - +
249D ASP* 3.2 5.3 + - - +
250D LYS* 2.9 57.7 + - + +
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Residues in contact with THR 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ILE* 3.9 8.1 - - + -
99D SER* 4.0 16.6 - - - +
101D ILE* 3.8 8.4 - - + +
243D LYS* 2.8 25.1 + - - +
244D GLY 3.8 4.3 - - - -
246D GLU* 1.3 74.5 + - - +
248D ALA* 1.3 65.9 + - - +
250D LYS* 3.3 6.9 + - - +
251D VAL* 2.9 22.5 + - - +
257D VAL* 3.7 17.7 - - + -
261D TYR* 3.7 39.0 - - + -
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Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.9 19.3 - - + -
60D ILE* 4.2 19.3 - - + +
62D LEU* 4.3 6.1 - - + -
86D ILE* 3.5 16.1 - - + +
244D GLY 2.9 14.4 + - - +
245D VAL* 3.1 10.3 + - - +
247D THR* 1.3 77.0 - - - +
249D ASP* 1.3 56.2 + - - +
251D VAL* 3.1 7.6 + - - +
252D LEU* 2.9 33.0 + - - +
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Residues in contact with ASP 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.8 0.6 - - - +
30D LEU* 3.6 29.8 - - + +
32D TYR* 2.8 38.4 + - + -
245D VAL 3.0 12.2 + - - +
246D GLU* 3.2 11.2 - - - +
248D ALA* 1.3 72.9 - - - +
250D LYS* 1.3 72.5 + - - +
252D LEU* 3.0 4.0 + - - +
253D LYS* 2.9 62.1 + - - +
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Residues in contact with LYS 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D LYS* 4.6 5.9 - - - +
246D GLU* 2.9 47.2 + - + +
247D THR* 3.3 6.9 + - - +
249D ASP* 1.3 81.3 - - - +
251D VAL* 1.3 60.7 + - - +
253D LYS* 3.1 16.0 + - + +
255D GLU* 3.2 48.6 + - + +
257D VAL* 4.2 12.2 - - + +
261D TYR* 4.6 14.3 + - - -
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 3.8 21.5 - - + -
84D PRO* 4.4 14.4 - - + -
86D ILE* 4.6 9.2 - - + -
98D VAL* 4.3 12.8 - - + -
247D THR 2.9 20.8 + - - +
248D ALA 3.4 7.4 - - - +
250D LYS* 1.3 73.3 - - - +
252D LEU* 1.3 61.4 + - + +
254D GLY* 3.2 14.6 + - - -
255D GLU 4.0 10.7 + - - +
257D VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 4.9 7.2 - - + +
3D THR 5.6 0.2 - - - +
4D ILE* 4.5 8.3 - - + -
32D TYR* 3.4 39.9 - - + +
59D LYS* 4.0 26.0 - - + +
60D ILE* 3.6 33.0 - - + -
248D ALA 2.9 14.7 + - - +
249D ASP 3.0 7.8 + - - +
251D VAL* 1.3 75.3 - - + +
253D LYS* 1.3 57.3 + - - +
254D GLY 3.2 3.8 + - - -
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Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.9 9.5 + - - +
32D TYR* 5.0 1.8 - - - +
249D ASP* 2.9 52.7 + - - +
250D LYS* 3.1 11.3 + - + +
252D LEU* 1.3 77.2 - - - +
254D GLY* 1.3 61.4 + - - +
255D GLU* 3.3 13.4 + - + +
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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