Contacts of the helix formed by residues 268 - 288 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E GLY* 3.5 35.9 - - - +
56E ILE* 3.7 14.4 - - + +
59E PRO* 5.3 0.2 - - - -
261E LYS* 3.6 10.3 + - - +
266E SER* 3.5 12.3 - - - +
267E ALA* 1.3 82.7 - - - +
269E LEU* 1.3 76.1 + - - +
270E SER 3.6 0.4 - - - -
271E MET* 3.2 3.5 - - - +
272E ALA* 2.8 30.4 + - - +
58F GLN* 4.4 5.7 + - - -
87F ASP* 2.7 15.5 + - - -
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Residues in contact with LEU 269 (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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59E PRO* 3.9 25.6 - - + -
261E LYS* 6.2 0.2 - - - +
268E THR* 1.3 84.5 + - - +
270E SER* 1.3 66.8 + - - +
271E MET 3.0 1.6 + - - -
272E ALA* 3.0 3.4 + - - -
273E TYR 2.9 19.8 + - - -
58F GLN* 3.8 55.0 - - + +
59F PRO* 4.3 2.7 - - + -
62F MET* 3.4 26.9 - - + +
84F VAL* 4.0 9.9 - - + -
87F ASP* 3.0 10.7 + - + +
88F ILE* 3.8 30.1 - - + -
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Residues in contact with SER 270 (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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192E LEU* 3.7 19.6 - - - +
196E ARG* 5.0 0.9 + - - -
257E VAL* 5.8 0.2 - - - +
267E ALA* 3.9 10.2 - - - +
269E LEU* 1.3 74.1 - - - +
271E MET* 1.3 62.3 + - - +
273E TYR* 3.3 5.4 - - - +
274E ALA* 3.0 22.5 + - - +
87F ASP* 2.5 46.7 + - - -
90F HIS* 4.4 7.9 + - - +
91F MET* 3.6 26.3 - - - -
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Residues in contact with MET 271 (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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56E ILE* 3.5 31.6 - - + -
160E ILE* 4.1 24.5 - - + -
189E VAL* 4.8 10.8 - - + +
192E LEU* 3.7 30.3 - - + -
220E HIS* 5.7 6.1 - - - -
267E ALA* 4.2 5.6 - - + +
268E THR* 3.2 19.2 - - - +
269E LEU 3.0 0.4 - - - -
270E SER* 1.3 79.2 + - - +
272E ALA* 1.3 56.1 + - - +
274E ALA* 2.9 11.6 + - + -
275E ALA* 2.8 51.3 + - + +
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Residues in contact with ALA 272 (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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56E ILE* 3.8 10.3 - - - +
59E PRO* 3.7 13.7 - - + -
60E LEU* 3.5 39.2 - - - +
63E LEU* 4.1 2.5 - - + -
268E THR 2.8 15.9 + - - +
269E LEU 3.0 6.9 + - - +
271E MET* 1.3 73.4 - - - +
273E TYR* 1.3 63.8 + - - +
275E ALA* 4.2 1.8 - - - -
276E VAL* 2.9 29.8 + - - +
62F MET* 4.3 3.1 - - - -
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Residues in contact with TYR 273 (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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63E LEU* 4.1 11.1 - - - +
195E VAL* 3.7 19.1 - - + -
269E LEU 2.9 12.3 + - - +
270E SER 3.3 10.8 - - - +
272E ALA* 1.3 77.1 - - - +
274E ALA* 1.3 57.7 + - - +
276E VAL* 4.0 1.6 - - - +
277E LYS* 2.9 56.1 + - + +
62F MET* 4.5 3.8 - - - -
66F MET* 3.8 28.5 - - + -
91F MET* 3.3 47.1 - - + -
92F ASP* 2.6 31.2 + - - -
93F THR* 3.5 19.6 - - + +
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Residues in contact with ALA 274 (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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191E MET* 3.4 17.1 - - + +
192E LEU* 3.6 32.1 - - + +
195E VAL* 3.8 16.6 - - + -
270E SER 3.0 12.9 + - - +
271E MET* 2.9 13.5 + - + +
273E TYR* 1.3 73.2 - - - +
275E ALA* 1.3 67.7 + - - +
277E LYS* 3.3 3.1 + - - -
278E PHE* 2.9 21.5 + - - +
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Residues in contact with ALA 275 (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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56E ILE* 5.5 0.4 - - + -
60E LEU* 3.4 23.3 - - + -
117E ILE* 4.6 3.1 - - + +
158E ASN* 4.7 2.3 - - - +
160E ILE* 3.3 33.2 - - + -
189E VAL* 4.4 7.1 - - - +
271E MET* 2.8 24.9 + - + +
272E ALA* 3.6 1.6 - - - +
274E ALA* 1.3 73.0 - - - +
276E VAL* 1.3 57.8 + - - +
278E PHE* 3.3 3.3 + - - +
279E ALA* 2.7 29.4 + - - +
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Residues in contact with VAL 276 (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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60E LEU* 3.1 28.5 - - + +
63E LEU* 3.3 44.2 - - + +
64E MET* 3.9 17.7 - - - -
67E ASN* 5.1 9.4 - - - +
272E ALA 2.9 13.4 + - - +
273E TYR 4.0 2.9 - - - +
275E ALA* 1.3 74.3 - - - +
277E LYS* 1.3 59.4 + - - +
279E ALA* 2.7 8.9 + - - +
280E ASP* 2.7 35.2 + - + +
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Residues in contact with LYS 277 (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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191E MET* 3.4 32.1 - - + -
195E VAL* 4.9 4.7 - - + -
273E TYR* 2.9 56.5 + - + +
274E ALA* 3.3 6.3 + - - +
276E VAL* 1.3 79.2 - - - +
278E PHE* 1.3 62.5 + - - +
280E ASP* 3.3 7.9 + - - +
281E ALA* 3.2 17.8 + - - +
284E ARG* 4.9 2.3 + - - -
294E GLU* 5.3 3.0 - - - +
92F ASP* 3.7 15.9 + - - +
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Residues in contact with PHE 278 (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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158E ASN* 3.3 42.0 - - - -
187E LEU* 3.7 30.7 - - + -
188E GLY 5.2 0.2 - - - -
189E VAL* 3.8 32.1 - - + -
191E MET* 4.0 17.7 - - + -
274E ALA 2.9 16.8 + - - +
275E ALA 3.6 2.7 - - - +
277E LYS* 1.3 77.1 - - - +
279E ALA* 1.3 63.7 + - - +
281E ALA* 3.1 8.9 + - - +
282E CYS* 3.0 24.4 + - - -
294E GLU* 3.9 28.3 - - + -
295E CYS 4.0 3.8 - - - -
296E ALA* 3.7 23.1 - - + -
312E VAL* 5.3 0.2 - - + -
314E LEU* 4.4 6.7 - - + -
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Residues in contact with ALA 279 (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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64E MET* 3.8 24.7 - - + -
115E LEU* 3.9 4.6 - - + +
117E ILE* 4.0 13.2 - - + -
158E ASN* 3.7 14.4 - - - +
275E ALA 2.7 14.4 + - - +
276E VAL* 2.7 21.7 + - - +
278E PHE* 1.3 69.2 - - - +
280E ASP* 1.3 63.6 + - - +
282E CYS* 3.0 5.3 + - - +
283E LEU* 2.9 28.7 + - - +
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Residues in contact with ASP 280 (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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64E MET* 5.4 0.2 - - - +
67E ASN* 3.1 32.1 + - - +
68E PRO* 5.9 0.7 - - - +
69E LEU* 4.2 12.8 - - - +
276E VAL* 2.7 16.1 + - + +
277E LYS* 3.6 11.8 - - - +
279E ALA* 1.3 73.2 - - - +
281E ALA* 1.3 57.3 + - - +
283E LEU* 3.2 7.3 + - - +
284E ARG* 2.8 57.5 + - - +
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Residues in contact with ALA 281 (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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277E LYS 3.2 8.2 + - - +
278E PHE 3.1 12.0 + - - +
280E ASP* 1.3 79.5 - - - +
282E CYS* 1.3 63.5 + - - +
284E ARG* 3.2 25.1 + - - +
285E GLY* 2.9 19.4 + - - -
292E VAL* 3.5 10.9 - - + +
294E GLU* 3.6 21.1 - - + -
314E LEU* 3.5 20.1 - - + +
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Residues in contact with CYS 282 (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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115E LEU* 4.0 17.5 - - + -
156E ILE* 4.3 14.4 - - + -
158E ASN* 3.4 31.0 - - - -
187E LEU* 4.6 5.8 - - - -
278E PHE* 3.0 28.7 + - - -
279E ALA 3.4 8.5 - - - +
281E ALA* 1.3 75.4 - - - +
283E LEU* 1.3 57.7 + - - +
285E GLY* 3.3 1.6 + - - -
286E LEU* 2.9 33.4 + - + +
314E LEU* 3.7 15.0 - - - +
315E GLY 4.8 1.0 - - - +
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Residues in contact with LEU 283 (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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45E PHE* 3.9 31.3 - - + -
47E VAL* 4.3 2.9 - - + -
64E MET* 4.2 13.0 - - + -
67E ASN* 4.1 11.7 - - - +
69E LEU* 4.2 20.2 - - + +
70E VAL* 4.0 26.9 - - + -
115E LEU* 3.9 26.2 - - + -
279E ALA 2.9 17.5 + - - +
280E ASP* 3.5 12.3 - - - +
282E CYS* 1.3 72.8 - - - +
284E ARG* 1.3 56.0 + - - +
285E GLY 3.0 1.8 - - - -
286E LEU* 2.9 10.9 + - + +
287E ARG* 2.6 36.5 + - - +
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Residues in contact with ARG 284 (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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69E LEU* 4.1 10.1 - - + -
277E LYS 4.9 2.4 + - - -
280E ASP* 2.8 41.2 + - - +
281E ALA* 3.5 31.4 - - - +
283E LEU* 1.3 73.0 - - - +
285E GLY* 1.3 58.9 + - - +
287E ARG* 3.7 25.4 - - - +
288E GLY 3.3 2.6 + - - -
289E ASP* 2.9 48.5 + - + +
292E VAL* 3.7 27.2 - - + +
294E GLU* 4.2 11.1 + - - -
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Residues in contact with GLY 285 (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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281E ALA 2.9 13.7 + - - -
282E CYS 3.6 3.6 - - - -
283E LEU 3.0 0.2 - - - -
284E ARG* 1.3 75.7 - - - +
286E LEU* 1.3 59.8 + - - +
288E GLY* 2.9 21.5 + - - -
289E ASP 4.0 3.3 + - - +
292E VAL* 4.4 4.4 - - - +
314E LEU* 3.6 25.4 - - - -
315E GLY* 3.4 20.9 - - - -
316E ARG 3.5 1.7 + - - -
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Residues in contact with LEU 286 (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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45E PHE* 3.6 33.4 - - + -
114E ASP* 4.3 19.3 - - + +
115E LEU* 5.1 1.6 - - + -
156E ILE* 3.9 32.8 - - + -
282E CYS 2.9 18.0 + - - +
283E LEU* 2.9 18.9 + - + +
285E GLY* 1.3 74.2 - - - +
287E ARG* 1.3 62.3 + - - +
288E GLY 3.3 0.2 + - - -
315E GLY 3.5 6.4 + - - +
316E ARG* 3.2 47.4 + - - +
317E ASN 4.4 0.4 - - - +
318E GLY 4.4 0.9 - - - +
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Residues in contact with ARG 287 (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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45E PHE* 3.4 18.5 - - + -
69E LEU* 3.0 43.3 - - - +
283E LEU 2.6 19.4 + - - +
284E ARG* 3.5 15.0 - - - +
285E GLY 3.1 0.2 - - - -
286E LEU* 1.3 74.9 - - - +
288E GLY* 1.3 57.7 + - - +
289E ASP* 3.0 37.5 + - - +
316E ARG* 3.7 13.0 + - - -
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Residues in contact with GLY 288 (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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285E GLY 2.9 11.7 + - - -
287E ARG* 1.3 80.7 - - - +
289E ASP* 1.3 69.3 + - - +
290E ALA* 3.7 1.7 + - - +
316E ARG* 3.8 27.7 + - - -
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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