Contacts of the helix formed by residues 246 - 261 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244E ALA* 3.3 1.8 - - - +
245E GLY* 1.3 82.0 - - - +
247E CYS* 1.3 65.0 + - - +
248E GLU* 3.4 10.5 + - - +
249E GLU* 3.2 27.1 + - + +
250E MET* 3.0 19.4 + - - +
111K GLY 5.7 0.7 - - - +
275K THR* 3.3 13.6 - - - +
278K THR* 3.8 20.6 - - + -
279K SER* 3.4 12.3 - - - +
282K ILE* 3.8 20.0 - - + -
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Residues in contact with CYS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E THR* 1.3 70.2 - - - +
248E GLU* 1.3 58.5 + - - +
250E MET* 3.3 9.5 + - + +
251E MET* 2.9 38.3 + - + +
276E ALA* 4.1 4.7 - - - -
247K CYS* 2.1 51.1 - - + -
251K MET* 6.0 0.9 - - + -
275K THR* 3.4 10.8 - - - +
276K ALA* 3.8 21.8 - - - -
279K SER* 2.8 19.2 + - - +
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Residues in contact with GLU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E THR* 3.4 11.5 - - - +
247E CYS* 1.3 77.3 - - - +
249E GLU* 1.3 57.9 + - + +
251E MET* 3.9 4.8 - - - +
252E LYS* 3.1 35.1 + - + +
251K MET* 3.9 13.5 - - - +
279K SER* 2.7 37.3 + - - +
282K ILE* 5.8 2.0 - - - +
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Residues in contact with GLU 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TRP* 3.9 9.9 + - - -
244E ALA* 3.6 20.4 - - + -
245E GLY 4.9 1.3 - - - +
246E THR* 3.2 20.6 + - + +
248E GLU* 1.3 75.5 - - - +
250E MET* 1.3 67.7 + - - +
252E LYS* 2.8 37.1 + - - +
253E ARG* 2.9 57.8 + - - +
109K GLU* 5.1 2.0 - - - +
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Residues in contact with MET 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E ALA* 3.3 33.2 - - + +
244E ALA* 3.5 4.6 - - + +
246E THR 3.0 13.9 + - - +
247E CYS* 3.5 18.6 - - + +
249E GLU* 1.3 76.8 - - - +
251E MET* 1.3 91.2 + - + +
253E ARG* 3.3 6.1 + - - +
254E ALA* 3.1 18.7 + - - +
267E HIS* 3.9 22.9 - - + +
276E ALA* 3.5 38.6 - - + +
279E SER* 4.5 2.7 - - - -
280E LEU* 3.9 22.0 - - + -
275K THR* 4.7 3.4 - - + -
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Residues in contact with MET 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E CYS* 2.9 23.2 + - + +
248E GLU* 3.9 5.8 - - - +
250E MET* 1.3 94.0 - - + +
252E LYS* 1.3 59.6 + - - +
254E ALA* 3.1 3.9 + - - +
255E VAL* 2.9 38.5 + - + +
279E SER* 3.8 33.9 - - - +
280E LEU* 4.1 7.2 - - - +
283E TYR* 4.2 30.5 - - + -
247K CYS* 6.0 0.9 - - + -
248K GLU* 3.9 13.5 - - - +
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Residues in contact with LYS 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TRP* 3.8 17.6 - - + +
248E GLU* 3.1 20.9 + - + +
249E GLU* 2.8 40.2 + - - +
251E MET* 1.3 75.9 - - - +
253E ARG* 1.3 60.9 + - - +
255E VAL* 3.5 8.6 + - - +
256E SMC 3.1 23.0 + - - +
286H ASP* 3.4 38.4 + - - -
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Residues in contact with ARG 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ASN* 3.9 3.8 - - - +
208E SER* 3.8 13.1 - - - +
214E TRP* 3.5 49.2 - - + -
218E PHE* 3.3 20.6 - - + -
241E ASN 4.2 8.9 + - - -
242E ALA* 4.0 24.9 - - - +
243E THR 3.5 14.3 + - - -
244E ALA* 3.9 6.0 - - - +
249E GLU* 2.9 44.1 + - - +
250E MET 3.6 7.2 - - - +
251E MET 3.2 0.2 - - - -
252E LYS* 1.3 73.9 - - - +
254E ALA* 1.3 64.2 + - - +
256E SMC 3.3 2.3 + - - +
257E ALA* 3.2 18.4 + - - +
265E ILE* 5.6 0.4 - - - -
109K GLU* 2.7 41.4 + - - -
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Residues in contact with ALA 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E ALA* 4.4 1.6 - - + +
250E MET 3.1 9.7 + - - +
251E MET* 3.1 9.6 + - - +
253E ARG* 1.3 76.6 - - - +
255E VAL* 1.3 60.6 + - - +
257E ALA* 3.3 7.1 + - - +
258E LYS* 3.0 19.1 + - - +
265E ILE* 4.0 17.5 - - + -
280E LEU* 3.7 28.9 - - + -
283E TYR* 3.8 21.5 - - + -
289E LEU* 3.7 7.8 - - - +
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Residues in contact with VAL 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E MET* 2.9 24.9 + - + +
252E LYS* 3.7 8.7 - - - +
254E ALA* 1.3 73.9 - - - +
256E SMC 1.3 64.7 + - - +
258E LYS* 3.1 6.2 + - + +
259E GLU* 2.9 45.8 + - + +
283E TYR* 3.4 29.4 - - + +
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Residues in contact with SMC 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TRP* 3.6 35.0 - - + -
215E ARG* 3.8 37.2 - - + +
218E PHE* 3.8 11.4 - - - -
219E LEU* 4.5 2.9 - - + -
252E LYS 3.1 10.2 + - - +
253E ARG 3.3 3.3 + - - +
255E VAL* 1.3 77.7 + - - +
257E ALA* 1.3 62.4 + - - +
259E GLU* 3.1 6.7 + - - +
260E LEU* 3.0 51.6 + - + +
63J VAL* 4.1 13.5 - - + -
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E PHE* 4.3 8.0 - - + -
240E LEU* 4.7 2.5 - - + -
253E ARG 3.2 9.8 + - - +
254E ALA 3.6 6.3 - - - +
255E VAL 3.3 0.2 - - - -
256E SMC 1.3 76.7 + - - +
258E LYS* 1.3 63.9 + - - +
260E LEU* 3.2 6.7 + - - +
261E GLY 3.2 15.9 + - - -
262E VAL* 3.5 30.0 + - + +
265E ILE* 3.5 32.1 - - + -
289E LEU* 4.4 4.9 - - + -
65F CYS* 4.1 2.3 - - - -
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Residues in contact with LYS 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG* 4.6 4.8 - - - +
259B GLU* 5.2 2.2 + - - -
254E ALA 3.0 8.8 + - - +
255E VAL* 3.1 11.2 + - + +
257E ALA* 1.3 74.9 - - - +
259E GLU* 1.3 64.1 - - + +
261E GLY* 3.1 15.9 + - - -
283E TYR* 3.3 26.0 - - + +
287E ASN* 2.9 33.3 + - + +
289E LEU* 4.3 8.9 - - + +
62F SER* 3.1 43.4 + - - +
63F VAL* 4.1 14.1 - - - +
64F SER 5.4 0.3 + - - -
65F CYS* 3.6 22.3 + - - -
59J ARG 5.1 0.9 - - - +
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Residues in contact with GLU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E VAL* 2.9 37.6 + - + +
256E SMC 3.1 6.1 + - - +
258E LYS* 1.3 84.0 - - + +
260E LEU* 1.3 55.9 + - - +
261E GLY 3.3 0.2 - - - -
62F SER* 4.3 21.9 + - - +
258H LYS* 5.3 1.7 + - - -
59J ARG 3.9 0.4 - - - +
60J PHE* 3.1 8.5 - - - -
61J GLY* 2.9 33.2 + - - +
62J SER 5.4 1.6 - - - -
63J VAL* 3.3 35.6 - - + +
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E PHE* 4.1 17.3 - - + +
219E LEU* 4.0 21.5 - - + -
222E THR* 3.4 28.0 - - + +
226E TYR* 2.7 25.3 + - - -
240E LEU* 5.4 1.8 - - + -
256E SMC 3.0 43.2 + - + +
257E ALA* 3.2 7.6 + - - +
259E GLU* 1.3 76.3 - - - +
261E GLY* 1.3 51.9 + - - +
262E VAL* 3.4 4.8 + - + +
59J ARG 4.0 1.1 - - - +
60J PHE* 3.3 39.5 - - + -
63J VAL* 3.8 20.0 - - + +
67J TYR* 5.3 0.2 - - + -
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Residues in contact with GLY 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E TYR* 3.2 10.5 + - - -
257E ALA 3.2 0.8 + - - -
258E LYS 3.1 16.5 + - - -
259E GLU 3.3 1.2 + - - -
260E LEU* 1.3 73.8 - - - +
262E VAL* 1.3 63.2 + - - +
263E PRO* 4.0 1.6 - - - +
64F SER* 3.5 22.2 - - - -
65F CYS* 3.7 11.0 - - - -
66F LEU 4.3 0.2 + - - -
68F TYR* 4.8 0.2 + - - -
59J ARG* 2.9 27.0 + - - -
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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