Contacts of the helix formed by residues 245 - 260 (chain C) in PDB entry 5UWS
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 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C SER* 5.5 3.0 + - - -
241C LYS 4.6 1.9 + - - -
242C PHE* 3.7 2.6 + - - +
244C THR* 1.3 82.3 + - - +
246C PRO* 1.3 67.0 - - - +
247C ASP* 3.2 10.7 + - - -
248C THR* 2.6 32.7 + - - +
249C ARG* 3.0 28.0 + - - +
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Residues in contact with PRO 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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244C THR 3.8 5.6 - - - +
245C SER* 1.3 81.2 - - - +
247C ASP* 1.3 70.7 + - - +
248C THR 3.4 0.2 - - - -
249C ARG* 3.5 38.3 + - + +
250C ALA* 4.1 6.8 + - - +
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Residues in contact with ASP 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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207C SER* 4.0 25.5 + - - +
211C VAL* 3.8 22.7 - - + +
245C SER* 3.2 7.5 - - - -
246C PRO* 1.3 83.8 - - - +
248C THR* 1.3 61.7 + - + +
250C ALA* 4.4 6.1 + - - +
251C ILE* 4.5 4.0 + - - +
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Residues in contact with THR 248 (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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207C SER* 4.9 5.8 - - - +
210C ILE* 3.5 33.0 - - + -
211C VAL* 4.0 11.9 - - + -
214C LEU* 3.8 11.7 - - + -
242C PHE* 2.6 27.2 + - + -
245C SER* 2.6 26.3 + - - +
247C ASP* 1.3 80.6 - - + +
249C ARG* 1.3 56.6 + - - +
250C ALA 3.4 0.4 - - - -
251C ILE* 3.2 9.4 - - - +
252C THR* 2.5 37.7 + - - -
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Residues in contact with ARG 249 (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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242C PHE 3.7 7.0 - - - -
243C MET* 3.0 37.7 + - + +
244C THR* 2.8 28.9 + - - +
245C SER 3.0 13.5 + - - +
246C PRO* 3.9 33.7 - - + +
247C ASP 3.4 1.4 - - - -
248C THR* 1.3 77.6 - - - +
250C ALA* 1.3 65.6 + - - +
252C THR* 3.8 2.0 - - - -
253C LEU* 2.9 32.3 + - + +
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Residues in contact with ALA 250 (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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246C PRO 4.1 7.9 + - - +
247C ASP 4.4 4.0 + - - +
248C THR 3.4 0.4 - - - -
249C ARG* 1.3 80.6 - - - +
251C ILE* 1.3 62.8 + - - +
253C LEU* 3.4 7.1 + - - +
254C LYS* 3.2 29.2 + - + +
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Residues in contact with ILE 251 (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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211C VAL* 4.8 12.3 - - + +
214C LEU* 3.7 46.4 - - + +
215C GLU* 3.6 33.4 - - + +
218C LEU* 4.0 24.7 - - + -
219C ARG* 4.8 0.4 - - - +
247C ASP 4.5 3.5 + - - +
248C THR* 3.2 18.4 - - - +
250C ALA* 1.3 76.2 - - - +
252C THR* 1.3 68.9 + - - +
254C LYS* 3.2 13.3 + - + +
255C CYS* 2.9 21.6 + - - -
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Residues in contact with THR 252 (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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214C LEU* 3.5 9.7 - - - +
238C LEU* 3.0 52.0 - - + +
242C PHE* 3.2 24.4 - - + +
243C MET* 4.2 9.6 - - - -
248C THR 2.5 22.8 + - - -
249C ARG 3.8 2.7 - - - -
251C ILE* 1.3 78.2 - - - +
253C LEU* 1.3 57.4 + - - +
255C CYS* 3.1 9.1 + - - +
256C LEU* 2.9 30.1 + - + +
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Residues in contact with LEU 253 (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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243C MET* 4.1 27.1 - - + -
249C ARG* 2.9 22.2 + - + +
250C ALA* 3.7 6.7 - - - +
251C ILE 3.2 0.2 - - - -
252C THR* 1.3 76.4 - - - +
254C LYS* 1.3 58.0 + - + +
256C LEU* 3.4 11.9 + - + +
257C THR* 2.9 34.8 + - - +
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Residues in contact with LYS 254 (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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141A LYS* 3.2 22.4 + - + +
142A LYS* 5.7 1.1 - - - +
143A ASN* 3.1 29.3 + - - +
218C LEU* 3.5 30.0 - - + +
250C ALA* 3.2 16.0 + - + +
251C ILE* 3.2 20.5 + - + +
253C LEU* 1.3 77.7 - - + +
255C CYS* 1.3 63.5 + - - +
257C THR* 3.3 9.8 + - - -
258C GLU* 3.2 18.4 + - - +
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Residues in contact with CYS 255 (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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214C LEU* 3.5 28.5 - - - -
217C LEU* 4.2 12.8 - - - -
218C LEU* 3.7 26.9 - - - -
221C LEU* 3.5 13.1 - - + +
238C LEU* 4.5 13.2 - - + -
251C ILE* 2.9 19.4 + - - -
252C THR* 3.1 12.7 + - - +
254C LYS* 1.3 77.9 - - - +
256C LEU* 1.3 56.5 + - - +
258C GLU 3.0 2.9 + - - -
259C VAL* 2.8 30.8 + - - +
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Residues in contact with LEU 256 (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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235C LEU* 4.2 18.4 - - + -
238C LEU* 3.8 35.4 - - + +
239C SER* 4.2 29.4 - - - +
243C MET* 4.7 9.9 - - + -
252C THR* 2.9 22.5 + - + +
253C LEU* 3.4 11.9 + - + +
255C CYS* 1.3 75.3 - - - +
257C THR* 1.3 61.2 + - - +
259C VAL* 3.5 7.5 - - + +
260C SER* 2.9 26.9 + - - -
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Residues in contact with THR 257 (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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141A LYS* 4.5 16.2 - - + +
253C LEU* 2.9 20.3 + - - +
254C LYS* 3.4 12.5 - - - -
255C CYS 3.2 0.2 - - - -
256C LEU* 1.3 76.6 - - - +
258C GLU* 1.3 71.7 + - - +
260C SER* 3.3 20.2 + - - -
261C ASN* 3.6 12.8 + - - +
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Residues in contact with GLU 258 (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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141A LYS* 2.6 39.1 + - - +
218C LEU* 3.7 17.0 - - + +
221C LEU* 4.1 22.3 - - + +
222C HIS* 4.2 23.3 - - + +
254C LYS 3.2 12.5 + - - +
255C CYS 3.0 8.7 + - - +
257C THR* 1.3 77.7 - - - +
259C VAL* 1.3 61.2 + - - +
261C ASN* 2.8 33.0 + - - +
262C LEU* 3.3 11.0 + - - +
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Residues in contact with VAL 259 (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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221C LEU* 3.9 24.7 - - + -
229C ILE* 4.3 11.7 - - + -
230C TYR* 4.4 16.2 + - - +
235C LEU* 3.7 32.5 - - + -
238C LEU* 4.8 5.6 - - + -
255C CYS 2.8 20.7 + - - +
256C LEU* 3.3 16.6 + - + +
258C GLU* 1.3 77.2 - - - +
260C SER* 1.3 59.9 + - - +
261C ASN 2.9 5.5 + - - -
262C LEU* 3.0 27.5 + - + +
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Residues in contact with SER 260 (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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256C LEU 2.9 15.6 + - - -
257C THR* 3.4 14.2 - - - -
258C GLU 3.1 0.4 - - - -
259C VAL* 1.3 76.9 - - - +
261C ASN* 1.3 61.3 + - - +
262C LEU 3.6 1.7 - - - +
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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