Contacts of the helix formed by residues 268 - 288 (chain A) in PDB entry 1SMK
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 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLY* 3.7 34.7 + - - -
56A ILE* 3.7 15.4 - - + +
59A PRO* 4.8 0.4 - - - -
261A LYS* 4.3 7.3 + - - +
266A SER* 3.2 20.4 + - - +
267A ALA* 1.3 76.7 - - - +
269A LEU* 1.3 78.0 + - - +
270A SER 3.5 0.7 - - - -
271A MET* 3.3 3.5 + - - +
272A ALA* 2.8 30.4 + - - +
58B GLN* 4.3 5.7 + - - -
87B ASP* 2.9 8.0 + - - -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 5.6 0.2 - - - +
59A PRO* 4.1 23.1 - - + -
268A THR* 1.3 85.5 + - - +
270A SER* 1.3 60.9 + - - +
272A ALA* 3.0 5.0 + - - +
273A TYR* 2.7 29.7 + - - +
58B GLN* 3.7 54.3 - - + +
59B PRO* 4.4 2.7 - - + -
62B MET* 3.5 22.1 - - + +
84B VAL* 4.0 14.1 - - + -
87B ASP* 3.0 15.0 + - + +
88B ILE* 3.9 23.6 - - + -
91B MET* 4.8 0.4 - - - -
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.7 19.5 - - - +
196A ARG* 4.9 0.9 + - - -
267A ALA* 3.5 15.2 - - - +
269A LEU* 1.3 72.9 - - - +
271A MET* 1.3 59.3 + - - +
273A TYR* 3.5 3.4 - - - +
274A ALA* 2.8 30.7 + - - +
87B ASP* 2.7 44.5 + - - -
90B HIS* 4.4 8.5 + - - +
91B MET* 3.9 23.9 - - - -
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Residues in contact with MET 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 3.5 31.6 - - + -
160A ILE* 4.0 21.5 - - + -
162A ASN* 5.8 2.0 - - - -
189A VAL* 4.2 13.5 - - + +
192A LEU* 4.1 28.7 - - + +
220A HIS* 5.3 9.4 - - - -
267A ALA 4.0 15.9 - - - +
268A THR 3.4 9.6 - - - +
269A LEU 3.1 0.6 - - - -
270A SER* 1.3 82.1 + - - +
272A ALA* 1.3 58.1 + - - +
274A ALA* 3.1 9.9 + - + -
275A ALA* 2.8 50.8 + - + +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 3.8 7.4 - - - +
59A PRO* 3.6 19.1 - - + +
60A LEU* 3.6 34.1 - - - +
63A LEU* 4.2 0.9 - - - -
268A THR 2.8 14.7 + - - +
269A LEU 3.0 7.4 + - - +
271A MET* 1.3 77.1 - - - +
273A TYR* 1.3 63.5 + - - +
275A ALA* 3.4 2.5 + - - +
276A VAL* 3.0 30.8 + - - +
62B MET* 4.3 3.4 - - - -
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Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.0 10.5 - - - +
195A VAL* 3.8 19.1 - - + -
269A LEU 2.7 20.5 + - - +
270A SER* 3.5 6.3 - - - +
272A ALA* 1.3 73.6 - - - +
274A ALA* 1.3 60.0 + - - +
276A VAL* 3.4 2.6 + - - +
277A LYS* 3.0 47.9 + - + +
62B MET* 4.5 4.0 - - - -
66B MET* 3.8 33.0 - - + -
91B MET* 3.7 33.4 - - + -
92B ASP* 2.6 37.1 + - - -
93B THR* 3.7 18.5 - - + +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A MET* 3.4 20.6 - - + +
192A LEU* 3.7 37.2 - - + +
195A VAL* 4.1 7.6 - - + -
270A SER 2.8 20.5 + - - +
271A MET* 3.5 6.1 - - + +
273A TYR* 1.3 76.5 - - - +
275A ALA* 1.3 65.2 + - - +
277A LYS* 3.1 3.5 + - - +
278A PHE* 2.9 19.8 + - - +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.6 19.7 - - + -
117A ILE* 4.7 3.6 - - + +
158A ASN* 5.0 0.3 - - - +
160A ILE* 3.4 32.8 - - + -
189A VAL* 4.3 10.7 - - + +
271A MET* 2.8 25.8 + - + +
272A ALA 3.9 0.2 - - - +
274A ALA* 1.3 71.8 - - - +
276A VAL* 1.3 51.4 + - - +
278A PHE* 3.2 3.1 + - - +
279A ALA* 2.6 37.3 + - - +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.4 26.2 - - + +
63A LEU* 3.5 42.4 - - + +
64A MET* 4.0 15.9 - - - -
67A ASN* 4.7 9.2 - - - +
272A ALA 3.0 17.8 + - - +
273A TYR 3.8 3.6 - - - +
275A ALA* 1.3 75.0 - - - +
277A LYS* 1.3 60.6 + - - +
279A ALA* 4.2 5.6 - - - -
280A ASP* 2.7 30.0 + - + +
66B MET* 6.4 1.3 - - + -
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A MET* 4.1 25.2 - - - +
194A VAL* 5.3 1.6 - - - +
195A VAL* 4.5 6.4 - - - +
198A ASN* 4.4 8.7 - - - +
273A TYR* 3.0 43.4 + - + +
274A ALA* 3.1 10.1 + - - +
276A VAL* 1.3 76.7 - - - +
278A PHE* 1.3 63.1 + - - +
280A ASP* 3.5 7.3 + - + +
281A ALA* 3.2 19.6 + - - +
284A ARG* 4.8 2.3 + - - -
294A GLU* 4.4 14.9 + - - +
92B ASP* 3.3 23.2 + - - -
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 3.4 39.3 - - - -
187A LEU* 3.6 30.3 - - + -
188A GLY 5.3 0.2 - - - -
189A VAL* 4.1 23.6 - - + -
191A MET* 4.0 21.0 - - + -
274A ALA 2.9 12.5 + - - +
275A ALA 3.5 7.4 - - - +
277A LYS* 1.3 76.0 - - - +
279A ALA* 1.3 64.2 + - - +
281A ALA* 2.9 15.8 + - - +
282A CYS* 3.0 19.6 + - - -
294A GLU* 3.9 26.2 - - + -
295A CYS 3.9 18.8 - - - -
296A ALA* 3.6 13.0 - - + -
312A VAL* 5.2 0.7 - - + -
314A LEU* 4.4 7.4 - - + -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 4.0 11.4 - - + -
115A LEU* 4.0 10.3 - - + +
117A ILE* 3.6 30.1 - - + -
158A ASN* 3.7 13.9 - - - +
275A ALA 2.6 21.7 + - - +
276A VAL* 3.8 2.9 - - - +
278A PHE* 1.3 73.4 - - - +
280A ASP* 1.3 65.3 + - - +
282A CYS* 3.0 4.4 + - - +
283A LEU* 2.9 27.8 + - - +
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASN* 2.9 37.0 + - - +
69A LEU* 4.0 10.7 - - - +
276A VAL* 2.7 20.3 + - + +
277A LYS* 3.6 7.4 - - - +
279A ALA* 1.3 78.0 - - - +
281A ALA* 1.3 55.6 + - - +
283A LEU* 3.3 4.4 + - - +
284A ARG* 2.9 54.1 + - - +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LYS 3.2 12.1 + - - +
278A PHE* 2.9 11.7 + - + +
280A ASP* 1.3 74.3 - - - +
282A CYS* 1.3 65.7 + - - +
284A ARG* 3.3 22.9 + - - +
285A GLY* 3.0 17.8 + - - -
292A VAL* 3.4 15.2 - - + +
294A GLU* 3.8 21.5 - - + +
314A LEU* 3.8 16.4 - - + +
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Residues in contact with CYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.3 15.7 - - + -
156A ILE* 4.3 14.4 - - + -
158A ASN* 3.7 31.9 - - - -
187A LEU* 4.6 1.3 - - - -
278A PHE* 3.0 26.1 + - - -
279A ALA 3.0 7.4 + - - +
281A ALA* 1.3 76.2 - - - +
283A LEU* 1.3 58.6 + - + +
285A GLY* 2.9 2.9 + - - -
286A LEU* 2.9 33.1 + - + +
314A LEU* 3.8 24.2 - - - +
315A GLY 4.8 0.9 - - - +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.5 41.0 - - + -
47A VAL* 4.2 4.5 - - + -
64A MET* 4.0 13.9 - - + -
67A ASN* 4.3 9.2 - - - +
69A LEU* 3.9 25.6 - - + -
70A VAL* 3.7 30.5 - - + -
115A LEU* 3.9 18.2 - - + -
279A ALA 2.9 15.7 + - - +
280A ASP* 3.6 7.6 - - - +
282A CYS* 1.3 77.0 - - - +
284A ARG* 1.3 56.7 + - - +
286A LEU* 3.1 12.3 + - + +
287A ARG* 2.9 24.1 + - - +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.7 14.8 - - + -
277A LYS 4.8 2.4 + - - -
280A ASP* 2.9 36.1 + - - +
281A ALA* 3.5 29.6 - - - +
283A LEU* 1.3 76.3 - - - +
285A GLY* 1.3 59.1 + - - +
287A ARG* 3.7 20.9 - - - +
288A GLY 3.4 2.1 + - - -
289A ASP* 3.1 51.4 + - + +
292A VAL* 3.9 23.1 - - + +
294A GLU* 4.4 8.3 + - - -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA 3.0 9.8 + - - -
282A CYS 2.9 9.1 + - - -
284A ARG* 1.3 77.0 - - - +
286A LEU* 1.3 63.3 + - - +
288A GLY* 3.0 14.0 + - - -
289A ASP 4.7 1.3 - - - -
292A VAL* 4.3 4.7 - - - +
314A LEU* 3.7 24.2 - - - -
315A GLY* 3.0 24.8 - - - -
316A ARG 3.3 2.4 + - - -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.6 26.3 - - + -
114A ASP* 4.1 35.2 - - + +
115A LEU* 5.0 2.0 - - + -
156A ILE* 3.9 25.6 - - + -
185A ARG* 5.7 0.9 - - - +
282A CYS* 2.9 18.5 + - + +
283A LEU* 3.1 19.7 + - + +
285A GLY* 1.3 76.3 - - - +
287A ARG* 1.3 62.3 + - - +
288A GLY 3.3 0.5 + - - -
315A GLY 3.5 9.8 + - - +
316A ARG* 3.4 41.3 + - - +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.5 17.0 - - + -
69A LEU* 3.1 38.6 - - + +
283A LEU 2.9 15.1 + - - +
284A ARG* 3.7 15.4 - - - +
285A GLY 3.1 0.4 - - - -
286A LEU* 1.3 76.9 - - - +
288A GLY* 1.3 58.6 + - - +
289A ASP* 2.6 41.8 + - - +
316A ARG* 3.4 14.6 + - - -
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLY 3.0 12.4 + - - -
286A LEU 3.1 0.6 - - - -
287A ARG* 1.3 80.9 - - - +
289A ASP* 1.3 69.5 + - - +
290A ALA* 3.5 2.3 + - - +
316A ARG* 3.6 28.4 + - - -
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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