Contacts of the helix formed by residues 234 - 247 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C TYR* 6.1 0.2 - - - -
232C ASN 4.3 0.4 + - - -
233C VAL* 1.3 73.9 - - - +
235C TYR* 1.3 62.0 + - - +
237C SER* 3.1 28.1 + - - -
238C GLN* 3.0 29.3 + - - +
83D ASN* 5.5 0.4 + - - -
208D ALA 3.0 18.4 - - - -
209D GLN* 3.7 33.5 + - - -
210D ARG* 4.2 7.6 - - - +
234D SER* 4.4 1.5 + - - -
237D SER* 4.0 4.3 + - - -
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Residues in contact with TYR 235 (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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44C ARG 4.1 2.6 + - - -
45C LEU* 3.5 14.4 - - + -
46C ASN* 2.6 49.2 + - - +
49C ALA* 3.9 17.0 - - + -
50C LEU* 3.4 28.7 - - + -
54C TYR* 3.6 47.8 - + + +
234C SER* 1.3 67.7 - - - +
236C VAL* 1.3 68.8 + - + +
238C GLN* 3.1 4.8 + - - +
239C MET* 3.0 46.3 + - + +
242C LYS* 5.9 0.2 - - - -
208D ALA* 3.0 25.9 + - + -
209D GLN* 3.9 1.3 - - - +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL* 4.7 6.3 - - + -
45C LEU* 4.2 11.2 - - + -
50C LEU* 3.8 12.8 - - + -
209C GLN* 4.5 1.3 - - - +
234C SER* 4.5 0.2 - - - +
235C TYR* 1.3 79.0 - - + +
237C SER* 1.3 57.9 + - - +
239C MET* 3.0 11.3 + - - +
240C PHE* 2.9 46.5 + - + -
42D PHE* 4.9 3.4 - - + -
209D GLN* 2.9 34.9 - - - +
236D VAL* 3.8 26.7 - - + -
240D PHE* 3.7 17.3 - - + -
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Residues in contact with SER 237 (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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209C GLN* 2.8 48.3 + - - -
211C VAL* 3.9 8.9 - - - +
233C VAL* 3.9 12.1 - - - -
234C SER* 3.1 22.5 + - - -
235C TYR 3.2 0.4 - - - -
236C VAL* 1.3 79.5 - - - +
238C GLN* 1.3 61.6 + - - +
240C PHE* 3.4 7.5 + - - +
241C ALA* 3.0 23.0 + - - +
234D SER* 3.8 5.9 + - - -
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Residues in contact with GLN 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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54C TYR* 3.5 13.4 - - + -
55C ASP 3.1 11.3 - - - +
56C SER* 2.6 23.1 + - - +
58C ASP* 2.6 40.4 - - + +
61C LEU* 3.9 17.2 - - + +
211C VAL* 5.5 0.2 - - - -
233C VAL* 3.1 30.8 - - + +
234C SER 3.0 17.8 + - - +
235C TYR* 3.1 6.5 + - - +
237C SER* 1.3 74.6 - - - +
239C MET* 1.3 56.1 + - - +
241C ALA* 3.2 6.8 + - - +
242C LYS* 2.7 49.4 + - - +
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Residues in contact with MET 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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41C VAL* 4.0 20.0 - - + +
44C ARG* 3.6 50.0 - - + +
45C LEU* 5.3 3.1 - - + -
54C TYR* 5.2 0.7 - - - +
60C GLU* 4.8 2.2 - - - +
235C TYR* 3.0 45.1 + - + +
236C VAL* 3.1 13.5 - - - +
238C GLN* 1.3 76.9 - - - +
240C PHE* 1.3 57.2 + - - +
242C LYS* 3.0 31.9 + - - +
243C VAL* 2.9 37.8 + - - +
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Residues in contact with PHE 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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33C PHE* 3.4 32.3 - + - -
38C VAL* 4.2 17.5 - - + -
41C VAL* 3.7 33.0 - - + -
206C LEU* 3.9 20.8 - - + +
209C GLN* 4.5 13.0 - - + -
236C VAL* 2.9 40.4 + - + -
237C SER* 3.6 9.4 - - - +
239C MET* 1.3 77.5 - - - +
241C ALA* 1.3 56.7 + - - +
243C VAL* 3.5 3.5 + - - +
244C ALA* 2.9 30.8 + - - +
42D PHE* 4.5 4.5 - + - -
45D LEU* 4.5 7.2 - - + -
50D LEU* 3.6 28.7 - - + -
236D VAL* 4.5 10.8 - - + -
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Residues in contact with ALA 241 (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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61C LEU* 4.3 10.3 - - + -
200C PHE* 3.6 27.3 - - + -
206C LEU* 4.0 8.2 - - + +
211C VAL* 4.2 18.4 - - + -
237C SER 3.0 13.9 + - - +
238C GLN* 3.4 9.4 - - - +
240C PHE* 1.3 76.2 - - - +
242C LYS* 1.3 63.4 + - - +
244C ALA* 3.4 3.0 - - - +
245C LEU* 3.2 27.9 + - - +
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Residues in contact with LYS 242 (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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44C ARG* 4.1 10.7 - - - +
54C TYR* 4.0 4.6 + - - -
58C ASP* 2.8 25.2 + - - -
60C GLU* 2.9 39.8 + - + +
61C LEU* 3.9 21.8 - - + +
64C LYS* 3.6 26.2 - - + -
235C TYR* 5.7 0.8 - - - -
238C GLN* 2.7 29.6 + - - +
239C MET* 3.0 33.1 + - - +
241C ALA* 1.3 74.6 - - - +
243C VAL* 1.3 66.8 + - - +
245C LEU* 3.1 6.7 + - - +
246C ASP* 3.1 21.3 + - - -
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Residues in contact with VAL 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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33C PHE* 4.2 9.9 - - + -
37C LEU* 3.8 20.1 - - + +
40C GLU* 3.9 21.3 - - + +
41C VAL* 3.6 28.9 - - + -
44C ARG* 3.3 29.2 - - - +
239C MET* 2.9 18.5 + - - +
240C PHE 3.6 8.3 - - - +
242C LYS* 1.3 72.5 - - - +
244C ALA* 1.3 67.4 - - - +
246C ASP* 3.0 7.8 + - - -
247C HIS* 2.8 26.9 + - - +
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Residues in contact with ALA 244 (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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33C PHE* 4.2 8.7 - - + -
37C LEU* 4.8 0.2 - - - -
200C PHE* 4.7 2.5 - - + -
204C PHE* 4.0 23.6 - - + -
206C LEU* 4.3 4.9 - - + -
240C PHE 2.9 20.6 + - - +
241C ALA* 3.4 10.1 - - - +
242C LYS 3.1 0.2 - - - -
243C VAL* 1.3 79.2 - - - +
245C LEU* 1.3 61.7 + - - +
247C HIS 3.2 10.4 + - - -
248C ARG* 3.4 2.1 + - - -
251C PHE* 3.2 36.7 - - + -
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Residues in contact with LEU 245 (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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61C LEU* 4.5 4.0 - - + -
64C LYS* 3.6 39.7 - - + +
65C ILE* 4.0 8.5 - - + +
68C TYR* 3.7 38.8 - - + -
200C PHE* 3.8 30.7 - - + -
204C PHE* 4.3 10.5 - - + -
241C ALA 3.2 11.5 + - - +
242C LYS 3.1 8.8 + - - +
244C ALA* 1.3 80.5 - - - +
246C ASP* 1.3 61.2 + - - +
247C HIS 3.4 0.3 + - - -
248C ARG* 2.9 42.1 + - + +
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Residues in contact with ASP 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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40C GLU* 4.1 3.8 - - - +
44C ARG* 3.0 28.4 + - - -
64C LYS* 3.0 26.8 + - - +
242C LYS 3.1 10.4 + - - -
243C VAL 3.0 10.6 + - - +
245C LEU* 1.3 79.8 - - - +
247C HIS* 1.3 73.2 + - + +
248C ARG* 3.6 1.8 + - - +
249C GLU* 4.1 5.4 - - - +
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Residues in contact with HIS 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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36C ASP* 5.7 0.9 - - - -
37C LEU* 3.6 30.4 - - + +
40C GLU* 2.9 39.9 + - - -
243C VAL 2.8 15.7 + - - +
244C ALA 3.4 4.3 - - - -
245C LEU 3.2 0.2 - - - -
246C ASP* 1.3 93.5 - - + +
248C ARG* 1.3 62.7 + - - +
249C GLU* 3.2 15.5 + - - -
250C ILE* 3.3 30.0 + - + +
251C PHE* 3.1 15.2 - - - -
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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