Contacts of the helix formed by residues 246 - 261 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E GLY 5.6 1.1 - - - +
275E THR* 3.3 14.4 - - - +
278E THR* 3.8 20.6 - - + -
279E SER* 3.4 5.8 - - - +
282E ILE* 3.8 20.2 - - + -
244K ALA* 3.3 2.2 - - - +
245K GLY* 1.3 82.9 - - - +
247K CYS* 1.3 64.9 + - - +
248K GLU* 3.4 16.2 + - - +
249K GLU* 3.2 27.7 + - + +
250K MET* 3.0 19.2 + - - +
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Residues in contact with CYS 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E CYS* 2.1 50.5 - - + -
251E MET* 6.0 0.9 - - + -
275E THR* 3.3 12.3 - - - +
276E ALA* 3.8 23.1 - - - -
279E SER* 2.8 19.6 + - - +
246K THR* 1.3 70.3 - - - +
248K GLU* 1.3 58.5 + - - +
250K MET* 3.3 9.5 + - + +
251K MET* 2.9 38.1 + - + +
276K ALA* 4.0 5.2 - - - -
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Residues in contact with GLU 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E MET* 3.9 13.7 - - - +
279E SER* 2.6 36.3 + - - +
282E ILE* 5.8 3.1 - - - +
246K THR* 3.4 12.9 - - - +
247K CYS* 1.3 75.9 - - - +
249K GLU* 1.3 57.0 + - - +
251K MET* 3.6 5.8 + - - +
252K LYS* 3.1 35.3 + - + +
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Residues in contact with GLU 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E GLU* 5.1 2.0 - - - +
214K TRP* 3.9 8.7 + - - -
244K ALA* 3.6 20.4 - - + -
245K GLY 5.5 0.9 - - - +
246K THR* 3.2 20.9 + - + +
248K GLU* 1.3 75.5 - - + +
250K MET* 1.3 66.5 + - - +
252K LYS* 2.8 36.7 + - - +
253K ARG* 2.9 55.6 + - - +
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Residues in contact with MET 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E THR* 4.7 4.0 - - + -
242K ALA* 3.3 31.8 - - + +
244K ALA* 3.6 4.6 - - + +
246K THR 3.0 14.1 + - - +
247K CYS* 3.4 17.0 - - + +
249K GLU* 1.3 75.8 - - - +
251K MET* 1.3 91.6 + - + +
253K ARG* 3.3 5.5 + - - +
254K ALA* 3.1 19.9 + - - +
267K HIS* 3.9 23.6 - - + +
276K ALA* 3.5 37.2 - - + +
279K SER* 4.6 2.7 - - - -
280K LEU* 3.9 21.1 - - + -
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Residues in contact with MET 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E CYS* 6.0 1.6 - - + -
248E GLU* 3.9 13.2 - - - +
247K CYS* 2.9 23.0 + - + +
248K GLU* 3.9 6.1 - - - +
250K MET* 1.3 94.9 - - + +
252K LYS* 1.3 60.9 + - - +
254K ALA* 3.2 3.3 + - - +
255K VAL* 2.9 38.6 + - + +
279K SER* 3.8 33.4 - - - +
280K LEU* 4.1 7.6 - - - +
283K TYR* 4.3 28.3 - - + -
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Residues in contact with LYS 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASP* 3.5 38.0 + - - -
214K TRP* 3.8 17.3 - - + +
248K GLU* 3.1 20.3 + - + +
249K GLU* 2.8 39.5 + - - +
251K MET* 1.3 76.1 - - - +
253K ARG* 1.3 62.1 + - - +
255K VAL* 3.4 7.9 + - - +
256K SMC 3.1 23.0 + - - +
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Residues in contact with ARG 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E GLU* 2.6 41.6 + - - -
207K ASN* 4.0 4.0 - - - +
208K SER* 3.8 12.3 - - - +
214K TRP* 3.5 51.0 - - + -
218K PHE* 3.3 21.7 - - + -
241K ASN 4.2 11.4 - - - -
242K ALA* 4.0 21.3 - - - -
243K THR 3.5 15.4 + - - -
244K ALA* 3.8 7.5 - - - +
249K GLU* 2.9 43.0 + - - +
250K MET 3.6 7.2 - - - +
252K LYS* 1.3 75.1 - - - +
254K ALA* 1.3 65.7 + - - +
256K SMC 3.3 1.6 + - - +
257K ALA* 3.2 17.0 + - - +
265K ILE* 5.6 0.2 - - - -
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Residues in contact with ALA 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K ALA* 4.4 1.2 - - + +
250K MET 3.1 9.1 + - - +
251K MET* 3.6 9.2 - - - +
253K ARG* 1.3 75.7 - - - +
255K VAL* 1.3 62.3 + - - +
257K ALA* 3.2 7.1 + - - +
258K LYS* 3.0 19.4 + - - +
265K ILE* 4.0 16.8 - - + -
280K LEU* 3.8 28.9 - - + -
283K TYR* 3.8 20.4 - - + -
289K LEU* 3.7 7.4 - - + +
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Residues in contact with VAL 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K MET* 2.9 25.1 + - + +
252K LYS* 3.7 7.9 - - - +
254K ALA* 1.3 73.2 - - - +
256K SMC 1.3 66.2 + - - +
258K LYS* 3.2 5.8 + - + +
259K GLU* 2.9 46.7 + - - +
283K TYR* 3.4 29.8 - - + +
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Residues in contact with SMC 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I VAL* 4.1 14.1 - - + -
214K TRP* 3.5 36.8 - - + -
215K ARG* 3.8 36.3 - - - +
218K PHE* 3.8 11.0 - - - -
219K LEU* 4.5 2.5 - - + -
252K LYS 3.1 11.4 + - - +
253K ARG 3.7 1.8 - - - +
254K ALA 3.3 0.2 - - - -
255K VAL* 1.3 75.5 + - - +
257K ALA* 1.3 62.9 + - - +
259K GLU* 3.2 7.1 + - - +
260K LEU* 3.0 51.9 + - + +
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Residues in contact with ALA 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218K PHE* 4.3 7.8 - - + -
240K LEU* 4.7 1.8 - - + -
253K ARG 3.2 10.2 + - - +
254K ALA 3.5 6.5 - - - +
256K SMC 1.3 76.7 + - - +
258K LYS* 1.3 61.6 + - - +
260K LEU* 3.2 5.9 + - - -
261K GLY 3.2 17.0 + - - -
262K VAL* 3.5 29.9 + - + +
265K ILE* 3.4 33.2 - - + -
289K LEU* 4.3 5.2 - - + -
65P CYS* 4.1 1.9 - - - -
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Residues in contact with LYS 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG 5.2 0.9 - - - +
254K ALA 3.0 8.7 + - - +
255K VAL* 3.2 12.1 + - + +
257K ALA* 1.3 74.4 - - - +
259K GLU* 1.3 63.7 + - + +
261K GLY* 3.1 18.2 + - - -
283K TYR* 3.3 26.0 - - + +
287K ASN* 2.8 32.8 + - + +
289K LEU* 4.2 9.1 - - + +
62P SER* 3.1 42.6 + - - +
63P VAL* 4.1 14.1 - - - +
64P SER 5.4 0.3 + - - -
65P CYS* 3.6 19.9 + - - -
215R ARG* 4.6 4.4 - - - +
259R GLU* 5.2 2.0 + - - -
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Residues in contact with GLU 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LYS* 5.5 1.0 + - - -
59I ARG 4.0 1.0 - - - +
60I PHE* 3.2 8.8 - - - -
61I GLY* 2.9 34.1 + - - +
62I SER 4.8 2.0 - - - +
63I VAL* 3.3 32.3 - - + +
255K VAL* 2.9 38.4 + - - +
256K SMC 3.2 7.2 + - - +
258K LYS* 1.3 80.9 - - + +
260K LEU* 1.3 58.3 + - - +
261K GLY 3.3 0.2 - - - -
62P SER* 4.1 22.9 + - - +
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Residues in contact with LEU 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG 4.1 1.5 - - - +
60I PHE* 3.3 39.4 - - + -
63I VAL* 3.8 24.5 - - + +
67I TYR* 5.4 1.6 - - + -
218K PHE* 4.0 18.6 - - + +
219K LEU* 4.4 13.9 - - + -
222K THR* 3.5 28.7 - - + +
226K TYR* 2.8 24.4 + - - -
240K LEU* 5.4 0.4 - - + -
256K SMC 3.0 43.1 + - + +
257K ALA* 3.2 8.0 + - - +
259K GLU* 1.3 76.6 - - - +
261K GLY* 1.3 52.7 + - - +
262K VAL* 3.4 5.1 + - + +
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Residues in contact with GLY 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 3.0 27.0 + - - -
226K TYR* 3.1 6.1 + - - -
257K ALA 3.2 0.4 + - - -
258K LYS 3.1 16.6 + - - -
259K GLU 3.3 1.2 + - - -
260K LEU* 1.3 78.4 - - - +
262K VAL* 1.3 63.8 + - - +
263K PRO* 4.1 1.2 - - - +
64P SER* 3.4 22.0 - - - -
65P CYS* 3.8 11.7 - - - -
66P LEU 4.4 0.3 + - - -
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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
------------------------------------------------------------
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