Contacts of the helix formed by residues 234 - 247 (chain D) in PDB entry 1UU1
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 234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C ASN* 5.7 0.2 + - - -
208C ALA 3.2 16.4 - - - -
209C GLN* 3.7 31.7 + - - -
210C ARG* 4.1 8.4 - - - +
234C SER* 4.4 1.7 + - - -
237C SER* 3.8 5.9 + - - -
209D GLN* 5.0 0.2 + - - -
232D ASN 4.2 0.6 + - - -
233D VAL* 1.3 74.0 - - - +
235D TYR* 1.3 66.2 + - - +
237D SER* 3.3 24.8 + - - -
238D GLN* 3.0 26.7 + - - +
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Residues in contact with TYR 235 (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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208C ALA* 3.0 26.1 + - + -
209C GLN* 3.6 7.2 - - - +
44D ARG 3.6 9.0 + - - -
45D LEU* 3.9 16.3 - - + -
46D ASN* 3.1 37.9 + - - +
49D ALA* 3.7 23.2 - - + +
50D LEU* 3.8 10.3 - - + -
54D TYR* 3.7 51.4 - + + +
233D VAL 3.9 0.4 + - - -
234D SER* 1.3 71.6 - - - +
236D VAL* 1.3 76.4 + - + +
238D GLN* 3.3 4.1 + - - +
239D MET* 3.1 38.2 + - + +
242D LYS* 5.7 0.9 - - - -
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Residues in contact with VAL 236 (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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209C GLN* 3.0 30.2 - - - +
236C VAL* 3.8 16.6 - - + -
240C PHE* 4.5 6.1 - - + -
41D VAL* 4.3 10.3 - - + -
42D PHE* 5.1 1.6 - - + -
45D LEU* 4.0 19.7 - - + -
50D LEU* 3.9 9.2 - - + -
209D GLN* 5.1 0.2 - - - +
235D TYR* 1.3 90.5 - - + +
237D SER* 1.3 56.7 + - - +
239D MET* 3.1 7.5 + - - +
240D PHE* 3.0 49.7 + - + -
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Residues in contact with SER 237 (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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234C SER* 4.0 4.2 - - - -
209D GLN* 2.6 52.2 + - - +
211D VAL* 3.9 14.7 - - - +
233D VAL* 4.1 7.2 - - - -
234D SER* 3.3 22.8 + - - -
236D VAL* 1.3 74.6 - - - +
238D GLN* 1.3 61.5 + - - +
240D PHE* 3.3 6.5 + - - +
241D ALA* 3.0 27.9 + - - +
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Residues in contact with GLN 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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54D TYR* 3.9 10.9 - - + -
55D ASP 3.2 5.1 + - - +
56D SER* 2.4 36.5 + - - +
58D ASP* 2.7 34.1 - - - +
61D LEU* 3.7 18.5 - - + +
211D VAL* 5.3 0.4 - - - -
233D VAL* 2.7 38.4 - - + +
234D SER 3.0 16.7 + - - +
235D TYR 3.6 4.0 - - - +
237D SER* 1.3 76.4 - - - +
239D MET* 1.3 56.7 + - - +
241D ALA* 3.4 4.2 + - - +
242D LYS* 2.9 40.4 + - - +
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Residues in contact with MET 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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41D VAL* 3.8 22.7 - - + +
44D ARG* 3.5 50.9 - - + +
45D LEU* 5.5 2.7 - - + -
235D TYR* 3.1 38.0 + - + +
236D VAL* 3.2 12.1 - - + +
237D SER 3.1 0.2 - - - -
238D GLN* 1.3 74.7 - - - +
240D PHE* 1.3 54.7 + - - +
242D LYS* 3.1 24.8 + - - +
243D VAL* 2.7 64.3 + - + +
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Residues in contact with PHE 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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45C LEU* 4.3 11.9 - - + -
50C LEU* 3.7 20.4 - - + -
236C VAL* 3.7 22.0 - - + -
33D PHE* 3.4 41.0 - + - -
38D VAL* 4.1 7.0 - - + -
41D VAL* 3.7 25.5 - - + +
42D PHE* 4.5 4.7 - + - -
206D LEU* 3.9 22.7 - - + +
209D GLN* 3.8 13.2 - - + -
236D VAL* 3.0 43.4 + - + -
237D SER* 3.5 8.5 - - - +
239D MET* 1.3 75.4 - - - +
241D ALA* 1.3 57.9 + - - +
243D VAL* 3.5 1.4 + - - +
244D ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 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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61D LEU* 4.2 9.2 - - + -
200D PHE* 3.9 29.6 - - + -
206D LEU* 4.1 8.9 - - + +
211D VAL* 4.1 15.9 - - + -
237D SER 3.0 15.9 + - - +
238D GLN* 3.7 5.6 - - - +
240D PHE* 1.3 79.1 - - - +
242D LYS* 1.3 57.0 + - - +
244D ALA* 3.4 3.6 + - - +
245D LEU* 3.0 34.9 + - - +
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Residues in contact with LYS 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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44D ARG* 3.9 4.4 - - - +
54D TYR* 4.2 6.3 + - - -
58D ASP* 3.1 22.5 + - - -
60D GLU* 3.2 38.6 + - + +
61D LEU* 3.6 31.4 - - + +
64D LYS* 3.5 20.8 + - + +
235D TYR* 5.7 1.8 - - - -
238D GLN* 2.9 32.9 + - - +
239D MET* 3.1 28.1 + - - +
241D ALA* 1.3 75.6 - - - +
243D VAL* 1.3 64.5 + - - +
245D LEU* 3.4 3.4 + - - +
246D ASP* 3.1 29.9 + - - +
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Residues in contact with VAL 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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33D PHE* 4.8 1.1 - - + -
37D LEU* 3.7 44.2 - - + +
40D GLU* 4.1 13.5 - - + -
41D VAL* 3.3 27.1 - - + +
44D ARG* 4.2 9.9 - - - +
239D MET* 2.7 39.6 + - + +
240D PHE 3.8 2.7 - - - +
242D LYS* 1.3 69.4 - - - +
244D ALA* 1.3 67.9 + - - +
246D ASP* 3.0 16.0 + - - -
247D HIS* 3.1 16.7 + - - +
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Residues in contact with ALA 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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33D PHE* 4.0 15.7 - - + -
37D LEU* 5.0 1.1 - - - -
200D PHE* 4.7 2.5 - - + -
204D PHE* 4.0 15.2 - - + -
206D LEU* 4.3 4.9 - - + -
240D PHE 2.9 18.8 + - - +
241D ALA* 3.6 8.3 - - - +
243D VAL* 1.3 77.8 - - - +
245D LEU* 1.3 62.4 + - - +
247D HIS 3.3 11.3 + - - -
248D ARG* 3.3 14.6 + - - +
251D PHE* 3.5 26.7 - - + -
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Residues in contact with LEU 245 (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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61D LEU* 4.5 4.7 - - + -
64D LYS* 3.5 45.8 - - + +
65D ILE* 3.8 11.2 - - + +
68D TYR* 4.0 31.6 - - + -
200D PHE* 3.5 32.5 - - + -
204D PHE* 4.5 9.4 - - + -
241D ALA 3.0 21.6 + - - +
242D LYS 3.8 4.0 - - - +
243D VAL 3.2 0.2 - - - -
244D ALA* 1.3 76.5 - - - +
246D ASP* 1.3 62.4 + - - +
247D HIS 3.5 0.3 + - - -
248D ARG* 3.3 32.5 + - - +
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Residues in contact with ASP 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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44D ARG* 3.4 13.9 + - - +
64D LYS* 2.7 41.2 + - - +
242D LYS 3.1 13.0 + - - +
243D VAL* 3.0 6.0 + - - +
245D LEU* 1.3 76.2 - - - +
247D HIS* 1.3 85.3 + - + +
248D ARG 3.8 0.9 - - - -
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Residues in contact with HIS 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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12B TYR* 6.2 2.2 - - - -
37D LEU* 3.7 32.2 - - + +
40D GLU* 4.5 19.0 - - + +
44D ARG* 6.2 0.9 - - - -
243D VAL* 3.1 16.6 + - + +
244D ALA 3.4 4.0 - - - -
246D ASP* 1.3 98.5 + - + +
248D ARG* 1.3 61.1 + - - +
249D GLU* 3.3 5.5 + - - +
250D ILE* 3.7 10.5 + - + +
251D PHE* 3.4 14.2 - - - -
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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