Contacts of the helix formed by residues 234 - 247 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ASN* 5.6 0.4 + - - -
208A ALA 3.2 15.5 - - - -
209A GLN* 3.5 29.8 + - - -
210A ARG* 4.2 7.1 - - - +
234A SER* 4.6 1.3 + - - -
237A SER* 4.1 7.7 + - - -
209B GLN* 4.8 0.2 + - - -
232B ASN 4.3 0.8 + - - -
233B VAL* 1.3 74.2 - - - +
235B TYR* 1.3 64.7 + - - +
236B VAL* 4.3 0.2 - - - +
237B SER* 2.8 39.1 + - - -
238B GLN* 2.9 27.6 + - - +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA* 3.0 28.5 + - + -
209A GLN* 3.9 0.7 - - - +
44B ARG 3.7 1.4 + - - -
45B LEU* 3.4 27.4 - - + -
46B ASN* 2.9 32.8 + - - +
49B ALA* 3.6 19.1 - - + -
50B LEU* 3.9 17.7 - - + -
54B TYR* 3.4 59.4 - + + +
233B VAL 3.8 0.2 + - - -
234B SER* 1.3 71.9 - - - +
236B VAL* 1.3 61.4 + - - +
238B GLN* 3.3 3.3 + - - +
239B MET* 2.9 55.9 + - + +
242B LYS* 5.3 1.2 + - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.7 4.3 - - + -
209A GLN* 3.1 32.0 - - - +
236A VAL* 3.9 18.2 - - + -
240A PHE* 3.9 16.6 - - + -
41B VAL* 4.7 6.7 - - + -
45B LEU* 3.9 26.5 - - + -
50B LEU* 4.3 2.2 - - + -
209B GLN* 4.3 3.1 - - - +
234B SER* 4.3 0.2 - - - +
235B TYR* 1.3 74.8 - - + +
237B SER* 1.3 65.6 + - - +
239B MET* 3.2 7.2 + - - +
240B PHE* 3.0 45.3 + - + -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER* 4.0 4.3 - - - -
209B GLN* 2.7 46.2 + - - -
211B VAL* 3.9 13.4 - - - +
233B VAL* 3.8 14.4 - - - -
234B SER* 2.8 31.6 + - - -
236B VAL* 1.3 71.8 - - - +
238B GLN* 1.3 62.8 + - - +
240B PHE* 3.0 16.5 + - - +
241B ALA 3.1 9.5 + - - -
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 3.8 10.8 - - + -
55B ASP 3.0 12.5 + - - +
56B SER* 2.5 30.8 + - - +
58B ASP* 2.8 37.2 - - + +
61B LEU* 3.9 19.0 - - + +
81B VAL* 5.9 0.2 - - + -
211B VAL* 5.3 0.4 - - - -
233B VAL* 2.9 33.9 - - + +
234B SER 2.9 13.3 + - - +
235B TYR* 3.6 4.3 - - - +
237B SER* 1.3 76.2 - - - +
239B MET* 1.3 62.0 + - - +
241B ALA* 3.1 6.4 + - - +
242B LYS* 2.9 34.1 + - - +
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Residues in contact with MET 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.6 29.8 - - + +
44B ARG* 3.7 44.2 - - + +
45B LEU* 3.7 11.0 - - + -
60B GLU* 5.7 0.9 - - - +
235B TYR* 2.9 49.0 + - + +
236B VAL 3.4 10.1 - - - +
238B GLN* 1.3 75.3 - - - +
240B PHE* 1.3 58.9 + - - +
242B LYS* 3.3 25.3 + - - +
243B VAL* 2.9 35.1 + - + +
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.6 5.8 - + - -
45A LEU* 4.8 2.2 - - + -
50A LEU* 3.5 20.0 - - + -
236A VAL* 4.2 14.8 - - + -
33B PHE* 3.4 44.2 - + - -
38B VAL* 4.1 19.7 - - + -
41B VAL* 3.8 24.5 - - + -
206B LEU* 4.0 24.7 - - + +
209B GLN* 4.1 12.1 - - + -
236B VAL* 3.0 40.6 + - + -
237B SER* 3.0 9.8 + - - +
239B MET* 1.3 77.8 - - - +
241B ALA* 1.3 57.3 + - - +
243B VAL* 3.9 1.2 - - - +
244B ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.0 12.8 - - + -
200B PHE* 3.8 34.3 - - + -
206B LEU* 4.5 2.9 - - - +
211B VAL* 4.0 14.6 - - + -
237B SER 3.1 9.6 + - - +
238B GLN 3.1 9.0 + - - +
240B PHE* 1.3 76.9 - - - +
242B LYS* 1.3 57.3 + - - +
244B ALA* 3.3 7.6 - - - +
245B LEU* 3.0 33.3 + - - +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 4.8 6.3 - - - +
54B TYR* 4.0 7.3 + - - -
58B ASP* 2.7 25.3 + - - -
60B GLU* 3.2 40.4 + - + +
61B LEU* 3.8 20.0 - - + +
64B LYS* 3.4 26.8 - - + -
235B TYR* 5.3 1.0 + - - -
238B GLN* 2.9 34.1 + - - +
239B MET* 3.7 28.1 - - - +
241B ALA* 1.3 73.4 - - - +
243B VAL* 1.3 67.1 + - - +
245B LEU* 3.3 4.0 + - - +
246B ASP* 3.0 28.4 + - - +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 4.9 1.1 - - + -
37B LEU* 3.9 36.1 - - + +
40B GLU* 3.7 31.6 - - + -
41B VAL* 3.4 20.4 - - + -
44B ARG* 4.0 20.2 - - - +
239B MET* 2.9 22.5 + - + +
240B PHE 3.9 1.8 - - - +
242B LYS* 1.3 74.3 - - - +
244B ALA* 1.3 66.0 + - - +
246B ASP* 2.8 16.6 + - - -
247B HIS* 3.2 20.9 + - + +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PHE* 4.3 6.0 - - + -
37B LEU* 4.7 0.7 - - - -
200B PHE* 4.7 1.6 - - + -
204B PHE* 3.8 25.3 - - + -
206B LEU* 4.1 11.7 - - + -
240B PHE 2.9 19.7 + - - +
241B ALA* 3.3 10.8 - - - +
243B VAL* 1.3 76.6 - - - +
245B LEU* 1.3 57.6 + - - +
247B HIS* 3.0 19.6 + - - -
248B ARG* 3.2 10.6 + - - -
251B PHE* 3.6 19.5 - - + -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 4.5 2.7 - - + -
64B LYS* 3.6 39.0 - - + +
65B ILE* 3.6 28.0 - - + -
68B TYR* 3.9 30.3 - - + -
200B PHE* 3.8 20.9 - - + -
204B PHE* 3.9 15.9 - - + -
241B ALA 3.0 19.0 + - - +
242B LYS 3.9 3.8 - - - +
244B ALA* 1.3 73.8 - - - +
246B ASP* 1.3 61.9 + - - +
247B HIS 3.1 3.3 + - - -
248B ARG* 3.2 35.0 + - + +
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Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.0 28.2 + - - -
64B LYS* 3.0 30.4 + - - +
242B LYS 3.0 11.8 + - - +
243B VAL* 2.8 12.6 + - - +
245B LEU* 1.3 78.8 - - - +
247B HIS* 1.3 77.7 + - + +
248B ARG 3.7 0.7 - - - -
249B GLU* 4.4 7.3 - - - +
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Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASP* 5.7 1.1 - - - -
37B LEU* 3.8 43.0 - - + +
40B GLU* 4.9 11.2 - - + -
44B ARG* 6.3 0.4 - - - -
243B VAL* 3.2 17.2 + - + -
244B ALA 3.0 6.9 + - - +
246B ASP* 1.3 95.7 + - + +
248B ARG* 1.3 57.5 + - - +
249B GLU* 3.0 13.9 - - - -
250B ILE* 2.9 39.4 + - + +
251B PHE* 3.6 3.5 - - - -
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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