Contacts of the helix formed by residues 223 - 235 (chain B) in PDB entry 5U03
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 ASP 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B GLN* 3.8 7.7 + - - +
221B PRO 4.0 0.6 + - - -
222B LEU* 1.3 78.1 - - - +
224B THR* 1.3 64.7 + - - +
225B SER* 2.7 16.7 + - - -
226B VAL* 2.7 34.0 + - - +
227B LYS* 3.3 19.1 + - - +
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Residues in contact with THR 224 (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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223B ASP* 1.3 75.0 + - - +
225B SER* 1.3 66.4 + - - +
227B LYS* 2.9 13.7 + - + +
228B GLU* 2.8 42.9 + - + +
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Residues in contact with SER 225 (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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223B ASP* 2.7 28.0 + - - -
224B THR* 1.3 76.3 - - - +
226B VAL* 1.3 59.5 + - - +
228B GLU* 3.3 8.9 + - - +
229B LYS* 2.9 45.4 + - - +
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Residues in contact with VAL 226 (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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192B GLN* 3.4 31.2 - - + +
194B THR* 3.6 26.0 - - + -
222B LEU* 3.9 19.7 - - + -
223B ASP* 2.7 29.4 + - - +
225B SER* 1.3 80.2 + - - +
227B LYS* 1.3 57.0 + - - +
229B LYS* 3.1 15.0 + - + +
230B ILE* 2.9 36.8 + - + +
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Residues in contact with LYS 227 (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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221B PRO* 6.1 1.4 - - - +
222B LEU* 3.7 41.1 + - + +
223B ASP 3.3 12.5 + - - +
224B THR* 2.9 11.5 + - + +
226B VAL* 1.3 77.7 - - - +
228B GLU* 1.3 60.0 + - - +
230B ILE* 3.3 3.9 + - - +
231B SER* 2.8 28.6 + - - -
238B PRO* 4.9 13.8 - - + +
241B VAL* 3.9 30.6 + - + +
243B CYS* 4.3 16.5 - - - +
260B GLN* 5.3 10.3 + - - +
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Residues in contact with GLU 228 (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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224B THR* 2.8 38.0 + - + +
225B SER* 3.6 8.3 - - - +
227B LYS* 1.3 76.8 - - - +
229B LYS* 1.3 64.1 + - + +
231B SER* 3.3 9.1 + - - -
232B MET* 3.0 22.2 + - - +
238B PRO* 4.0 23.8 - - - +
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Residues in contact with LYS 229 (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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54A GLU* 5.2 7.7 + - - -
602A UTP 5.1 18.1 + - - +
194B THR* 5.3 6.7 - - + +
225B SER* 2.9 31.4 + - - +
226B VAL* 3.4 13.7 - - + +
228B GLU* 1.3 73.4 - - + +
230B ILE* 1.3 60.8 + - + +
232B MET* 3.1 9.2 + - + +
233B PHE* 2.8 53.3 + - + -
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Residues in contact with ILE 230 (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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183B VAL* 5.1 4.3 - - + -
194B THR* 3.7 23.6 - - + -
197B THR* 5.3 10.5 - - + -
198B GLN* 6.2 0.7 - - + -
214B VAL* 5.9 3.6 - - + -
216B CYS* 4.6 12.6 - - - -
222B LEU* 3.7 28.5 - - + -
226B VAL* 2.9 26.1 + - + +
227B LYS 3.6 5.8 - - - +
229B LYS* 1.3 73.7 - - - +
231B SER* 1.3 65.4 + - - +
233B PHE* 3.0 7.4 + - - +
234B CYS* 2.8 42.3 + - + +
236B VAL* 5.0 0.4 - - + -
241B VAL* 3.7 27.8 - - + -
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Residues in contact with SER 231 (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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227B LYS 2.8 14.8 + - - -
228B GLU* 3.3 17.3 + - - -
230B ILE* 1.3 75.7 - - - +
232B MET* 1.3 52.6 + - - -
235B HIS* 2.6 32.1 + - - -
236B VAL* 2.6 38.1 + - - +
238B PRO* 3.9 21.7 - - - +
241B VAL* 4.0 1.1 - - - +
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Residues in contact with MET 232 (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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228B GLU 3.0 14.1 + - - +
229B LYS* 3.1 9.2 + - + +
231B SER* 1.3 76.9 - - - +
233B PHE* 1.3 104.2 + - + +
235B HIS* 3.1 27.9 + - + +
114C VAL* 5.4 3.4 - - - -
115C PRO* 4.2 36.6 - - + -
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Residues in contact with PHE 233 (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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602A UTP 3.3 24.2 - - - -
194B THR* 4.4 5.2 - - - -
198B GLN* 3.4 49.1 - - + -
205B ARG* 3.1 16.2 + - - -
229B LYS* 2.8 52.0 + - + +
230B ILE* 3.6 7.0 - - - +
232B MET* 1.3 99.2 - - + +
234B CYS* 1.3 59.8 + - - +
235B HIS* 3.3 11.7 - - - -
112C GLN* 5.0 11.2 - - - -
114C VAL* 5.2 15.2 - - + +
115C PRO* 5.3 1.3 - - + -
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Residues in contact with CYS 234 (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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197B THR* 4.8 6.7 - - - -
198B GLN* 5.3 6.1 - - - -
201B VAL* 4.1 35.4 - - + +
205B ARG* 2.9 24.7 + - - +
214B VAL* 5.3 6.7 - - + -
230B ILE* 2.8 33.5 + - - +
233B PHE* 1.3 76.1 - - - +
235B HIS* 1.3 71.7 + - - +
236B VAL* 3.4 26.1 - - + +
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Residues in contact with HIS 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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205B ARG* 3.0 23.7 + - - +
231B SER 2.6 18.1 + - - -
232B MET* 3.1 15.6 + - + +
233B PHE* 3.3 16.8 - - - -
234B CYS* 1.3 73.2 - - - +
236B VAL* 1.3 58.2 + - - +
114C VAL* 5.1 13.4 - - + +
115C PRO* 6.3 1.0 - - - +
161C GLU* 4.1 8.3 + - - -
164C ARG* 3.7 15.9 - - - -
165C GLN* 3.3 39.6 + - + +
169C LYS* 6.2 0.7 - - - -
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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