Contacts of the helix formed by residues 246 - 261 (chain O) in PDB entry 1UW9
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 THR 246 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244O ALA* 3.9 2.5 - - - +
245O GLY* 1.3 82.1 - - - +
247O CYS* 1.3 64.5 + - - +
248O GLU* 3.4 9.9 + - - +
249O GLU* 3.3 27.8 + - + +
250O MET* 3.1 18.7 + - - +
111V GLY 5.6 1.1 - - - +
275V THR* 3.3 14.4 - - - +
278V THR* 3.7 20.4 - - + -
279V SER* 3.4 12.6 - - - +
282V ILE* 3.8 19.3 - - + -
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Residues in contact with CYS 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O THR* 1.3 70.5 - - - +
248O GLU* 1.3 59.9 + - - +
250O MET* 3.3 10.2 + - + +
251O MET* 2.9 37.2 + - + +
276O ALA* 4.0 4.7 - - - -
247V CYS* 2.1 50.9 - - + -
250V MET* 5.2 0.4 - - + -
251V MET* 6.0 1.1 - - + -
275V THR* 3.4 12.3 + - - +
276V ALA* 3.7 23.6 - - - -
279V SER* 2.8 16.7 + - - +
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Residues in contact with GLU 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O THR* 3.4 11.8 - - - +
247O CYS* 1.3 75.9 - - - +
249O GLU* 1.3 57.6 + - + +
251O MET* 3.6 5.6 + - - +
252O LYS* 3.1 35.0 + - + +
251V MET* 4.0 13.5 - - - +
279V SER* 2.6 37.3 + - - +
282V ILE* 5.7 4.0 - - - +
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Residues in contact with GLU 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214O TRP* 3.9 9.2 + - - -
244O ALA* 3.6 20.9 - - + -
245O GLY* 5.5 1.1 - - - +
246O THR* 3.3 19.6 + - + +
248O GLU* 1.3 75.8 - - + +
250O MET* 1.3 66.2 + - - +
252O LYS* 2.8 36.6 + - - +
253O ARG* 2.9 58.0 + - - +
109V GLU* 5.2 1.8 - - - +
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Residues in contact with MET 250 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242O ALA* 3.3 33.8 - - + +
244O ALA* 3.5 4.6 - - + +
246O THR 3.1 14.3 + - - +
247O CYS* 3.5 18.8 - - + +
249O GLU* 1.3 75.8 - - - +
251O MET* 1.3 90.0 + - + +
253O ARG* 3.3 5.9 + - - +
254O ALA* 3.1 18.4 + - - +
267O HIS* 3.9 23.6 - - + +
276O ALA* 3.5 40.2 - - + +
279O SER* 4.5 2.2 - - - -
280O LEU* 4.0 20.6 - - + -
275V THR* 4.7 4.3 - - + -
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Residues in contact with MET 251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247O CYS* 2.9 22.8 + - + +
248O GLU* 3.9 5.4 - - - +
250O MET* 1.3 96.3 - - + +
252O LYS* 1.3 65.4 + - - +
254O ALA* 3.2 3.3 + - - +
255O VAL* 2.9 33.1 + - + +
279O SER* 3.8 33.9 - - - +
280O LEU* 4.1 7.4 - - - +
283O TYR* 4.2 29.6 - - + -
247V CYS* 6.1 1.1 - - + -
248V GLU* 4.0 13.7 - - - +
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Residues in contact with LYS 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214O TRP* 3.8 17.6 - - + +
248O GLU* 3.1 20.9 + - + +
249O GLU* 2.8 39.9 + - - +
251O MET* 1.3 76.0 - - - +
253O ARG* 1.3 57.9 + - - +
255O VAL* 3.5 8.1 + - - +
256O SMC 3.1 27.0 + - - +
286R ASP* 3.4 38.4 + - - -
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Residues in contact with ARG 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207O ASN* 3.9 3.8 - - - +
208O SER* 3.8 12.3 - - - +
214O TRP* 3.5 50.4 - - + -
218O PHE* 3.3 24.9 - - + -
241O ASN 4.2 9.2 - - - -
242O ALA* 4.0 20.6 - - - -
243O THR 3.5 14.5 + - - -
244O ALA* 3.9 7.1 - - - +
249O GLU* 2.9 45.7 + - - +
250O MET 3.6 6.7 - - - +
251O MET 3.2 0.4 - - - -
252O LYS* 1.3 75.0 - - - +
254O ALA* 1.3 64.7 + - - +
256O SMC 3.4 1.0 + - - -
257O ALA* 3.2 18.4 + - - +
265O ILE* 5.1 0.6 - - - +
109V GLU* 2.6 43.2 + - - -
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Residues in contact with ALA 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242O ALA* 4.5 1.2 - - - +
250O MET 3.1 8.8 + - - +
251O MET* 3.2 8.9 + - - +
253O ARG* 1.3 75.3 - - - +
255O VAL* 1.3 57.3 + - - +
257O ALA* 3.3 6.7 + - - +
258O LYS* 3.0 24.4 + - - +
265O ILE* 4.0 17.5 - - + -
280O LEU* 3.8 28.0 - - + -
283O TYR* 3.8 22.4 - - + -
289O LEU* 3.7 7.7 - - + +
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Residues in contact with VAL 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251O MET* 2.9 24.7 + - + +
252O LYS* 3.7 7.9 - - - +
253O ARG 3.3 0.2 - - - -
254O ALA* 1.3 73.4 - - - +
256O SMC 1.3 58.8 + - - +
258O LYS* 3.1 4.8 + - + +
259O GLU* 2.9 56.9 + - + +
283O TYR* 3.4 29.8 - - + +
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Residues in contact with SMC 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M VAL* 4.1 14.4 - - + -
214O TRP* 3.5 35.9 - - + -
215O ARG* 3.8 36.8 - - + +
218O PHE* 3.8 11.4 - - - -
219O LEU* 4.5 2.2 - - + -
252O LYS 3.1 11.4 + - - +
253O ARG 3.7 1.8 - - - +
254O ALA 3.3 0.2 - - - -
255O VAL* 1.3 75.8 + - - +
257O ALA* 1.3 62.7 + - - +
259O GLU* 3.1 7.4 + - - +
260O LEU* 3.0 50.6 + - + +
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Residues in contact with ALA 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O PHE* 4.3 9.1 - - + -
240O LEU* 4.7 1.3 - - + -
253O ARG 3.2 10.8 + - - +
254O ALA 3.5 6.7 - - - +
256O SMC 1.3 76.3 + - - +
258O LYS* 1.3 61.5 + - - +
260O LEU* 3.2 14.1 + - - +
261O GLY 3.2 8.7 + - - -
262O VAL* 3.5 29.8 + - + +
265O ILE* 3.5 32.3 - - + -
289O LEU* 4.4 7.4 - - + -
65T CYS* 4.1 0.3 - - - -
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Residues in contact with LYS 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 4.6 4.4 - - - +
259A GLU* 5.2 2.8 + - - -
59M ARG 5.1 1.0 - - - +
254O ALA 3.0 9.9 + - - +
255O VAL* 3.1 10.1 + - + +
257O ALA* 1.3 73.2 - - - +
259O GLU* 1.3 63.1 + - + +
261O GLY* 3.1 15.8 + - - -
283O TYR* 3.3 25.6 - - + +
287O ASN* 2.9 33.8 + - + +
289O LEU* 4.2 9.5 - - + +
62T SER* 3.2 40.4 + - - +
63T VAL* 4.1 14.5 - - - +
64T SER 5.4 0.2 + - - -
65T CYS* 3.6 22.8 + - - -
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Residues in contact with GLU 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ARG 4.6 0.7 - - - -
60M PHE* 3.1 8.3 - - - -
61M GLY* 2.9 30.7 + - - +
62M SER 5.4 4.5 - - - -
63M VAL* 3.3 35.4 - - + +
255O VAL* 2.9 34.5 + - + +
256O SMC 3.1 9.0 + - - +
258O LYS* 1.3 81.8 - - + +
260O LEU* 1.3 57.1 + - - +
261O GLY 3.3 0.4 - - - -
258R LYS* 5.3 1.6 + - - -
62T SER* 4.6 19.3 + - - +
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Residues in contact with LEU 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ARG 4.0 0.8 - - - +
60M PHE* 3.4 41.1 - - + -
63M VAL* 3.9 17.3 - - + +
67M TYR* 5.3 0.4 - - + -
218O PHE* 4.0 18.4 - - + +
219O LEU* 4.2 19.7 - - + -
222O THR* 3.4 29.2 - - + +
226O TYR* 2.7 26.2 + - - -
240O LEU* 5.4 0.7 - - + -
256O SMC 3.0 43.8 + - + +
257O ALA* 3.2 8.2 + - - +
259O GLU* 1.3 75.7 - - - +
261O GLY* 1.3 51.7 + - - +
262O VAL* 3.2 5.9 + - + +
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Residues in contact with GLY 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ARG* 3.0 28.1 + - - -
226O TYR* 3.2 6.8 + - - -
257O ALA 3.2 0.4 + - - -
258O LYS 3.1 16.5 + - - -
259O GLU 3.3 1.4 + - - -
260O LEU* 1.3 78.0 - - - +
262O VAL* 1.3 63.4 + - - +
263O PRO* 4.1 1.4 - - - +
64T SER* 3.4 22.0 - - - -
65T CYS* 3.8 11.4 - - - -
66T LEU 4.4 0.5 + - - -
68T TYR* 4.9 0.2 + - - -
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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