Contacts of the helix formed by residues 268 - 288 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN* 4.3 5.4 + - - -
87E ASP* 2.7 14.5 + - - -
55F GLY* 3.5 38.5 + - - -
56F ILE* 3.8 15.0 - - + +
261F LYS* 4.1 10.1 + - - +
266F SER* 3.5 10.5 + - - +
267F ALA* 1.3 82.9 - - - +
269F LEU* 1.3 66.5 + - - +
270F SER 3.5 0.4 - - - -
271F MET* 3.3 3.1 + - - +
272F ALA* 2.7 34.9 + - - +
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN* 3.7 57.7 - - + +
59E PRO* 4.3 2.5 - - + -
62E MET* 3.5 26.3 - - + +
84E VAL* 3.8 20.9 - - + -
87E ASP* 2.9 16.6 + - + +
88E ILE* 3.9 17.5 - - + -
91E MET* 4.9 0.4 - - - -
59F PRO* 3.9 26.2 - - + -
268F THR* 1.3 75.9 - - - +
270F SER* 1.3 59.6 + - - +
272F ALA* 3.0 4.5 + - - +
273F TYR* 2.8 26.9 + - - +
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Residues in contact with SER 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ASP* 2.7 44.7 + - - -
90E HIS* 4.3 10.1 + - - +
91E MET* 3.9 23.7 - - - -
192F LEU* 3.7 17.8 - - - +
195F VAL* 5.7 0.2 - - - -
196F ARG* 4.8 1.0 + - - -
267F ALA* 3.6 13.3 - - - +
269F LEU* 1.3 72.4 - - - +
271F MET* 1.3 57.8 + - - +
273F TYR* 3.3 4.7 + - - +
274F ALA* 2.8 29.8 + - - +
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Residues in contact with MET 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ILE* 3.4 30.7 - - + -
160F ILE* 4.0 22.4 - - + -
189F VAL* 4.2 16.8 - - + +
192F LEU* 4.0 31.0 - - + -
220F HIS* 5.4 7.2 - - - -
267F ALA 3.9 16.4 - - - +
268F THR 3.3 9.1 + - - +
269F LEU 3.1 0.4 - - - -
270F SER* 1.3 80.4 + - - +
272F ALA* 1.3 59.9 + - - +
274F ALA* 3.3 6.2 + - + -
275F ALA* 2.9 48.1 + - + +
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Residues in contact with ALA 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E MET* 4.1 4.3 - - - -
56F ILE* 4.0 12.3 - - - +
59F PRO* 3.6 29.4 - - + -
60F LEU* 3.6 17.9 - - - +
63F LEU* 4.2 0.4 - - + -
268F THR 2.7 18.7 + - - +
269F LEU 3.3 7.4 - - - +
271F MET* 1.3 71.1 - - - +
273F TYR* 1.3 65.8 - - - +
275F ALA* 3.1 3.1 + - - +
276F VAL* 2.9 29.9 + - - +
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Residues in contact with TYR 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E MET* 4.6 3.6 - - - -
66E MET* 3.9 24.9 - - + -
91E MET* 3.6 34.5 - - + -
92E ASP* 2.8 39.4 + - - -
93E THR* 3.5 28.2 - - + +
63F LEU* 4.0 12.2 - - - +
195F VAL* 4.0 15.0 - - + -
269F LEU 2.8 12.8 + - - +
270F SER 3.4 9.6 - - - +
272F ALA* 1.3 75.7 - - - +
274F ALA* 1.3 60.3 + - - +
276F VAL* 3.4 2.3 + - - +
277F LYS* 3.0 66.0 + - + +
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Residues in contact with ALA 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F MET* 3.4 16.4 - - + +
192F LEU* 3.8 38.6 - - + +
195F VAL* 4.1 12.8 - - + -
270F SER 2.8 17.9 + - - +
271F MET* 3.7 6.1 - - + +
273F TYR* 1.3 77.8 - - - +
275F ALA* 1.3 65.5 + - - +
277F LYS* 3.4 2.5 + - - +
278F PHE* 3.0 19.6 + - - +
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Residues in contact with ALA 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LEU* 3.5 30.5 - - + -
117F ILE* 4.8 2.3 - - + +
158F ASN* 5.0 0.5 - - - +
160F ILE* 3.6 20.6 - - + -
189F VAL* 4.4 9.0 - - - +
271F MET* 2.9 23.2 + - + +
272F ALA 3.1 1.5 + - - +
274F ALA* 1.3 76.6 - - - +
276F VAL* 1.3 52.5 + - - +
278F PHE* 3.3 2.8 + - - +
279F ALA* 2.7 37.3 + - - +
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Residues in contact with VAL 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LEU* 3.5 21.1 - - + +
63F LEU* 3.4 47.6 - - + +
64F MET* 4.1 14.1 - - - -
67F ASN* 5.3 4.3 - - + +
272F ALA 2.9 16.8 + - - +
273F TYR* 3.7 4.3 - - + +
275F ALA* 1.3 73.2 - - - +
277F LYS* 1.3 58.5 + - - +
279F ALA* 3.0 7.2 + - - +
280F ASP* 2.7 38.8 + - + +
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Residues in contact with LYS 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ASP* 4.8 9.4 + - - +
93E THR* 5.6 0.6 - - - +
191F MET* 4.7 13.5 - - + -
195F VAL* 5.3 4.5 - - + -
210F ARG* 6.3 0.4 - - - +
273F TYR* 3.0 58.3 + - + +
274F ALA* 3.8 6.3 - - - +
276F VAL* 1.3 76.3 - - - +
278F PHE* 1.3 63.4 + - - +
280F ASP* 3.5 9.0 + - - +
281F ALA* 3.2 19.4 + - - +
284F ARG* 4.7 4.5 + - - +
294F GLU* 4.7 7.2 - - - +
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Residues in contact with PHE 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F ASN* 3.5 35.9 - - - -
187F LEU* 3.5 30.7 - - + -
188F GLY 5.1 0.2 - - - -
189F VAL* 3.9 22.9 - - + -
190F THR 6.2 0.2 - - - -
191F MET* 4.0 28.4 - - + -
274F ALA 3.0 18.0 + - - +
275F ALA 3.6 3.6 - - - +
277F LYS* 1.3 75.2 - - - +
279F ALA* 1.3 65.5 + - - +
281F ALA* 2.9 16.1 + - - +
282F CYS* 3.0 18.8 + - - -
294F GLU* 3.9 23.6 - - + -
295F CYS 4.0 4.9 - - - -
296F ALA* 3.7 23.3 - - + -
312F VAL* 5.7 0.2 - - + -
314F LEU* 4.4 7.4 - - + -
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Residues in contact with ALA 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F MET* 4.0 13.0 - - + -
115F LEU* 3.9 5.8 - - + +
117F ILE* 3.6 31.0 - - + -
158F ASN* 3.6 17.0 - - - +
275F ALA 2.7 20.7 + - - +
276F VAL* 3.4 3.6 - - - +
278F PHE* 1.3 73.0 - - - +
280F ASP* 1.3 63.1 - - - +
282F CYS* 3.1 6.4 + - - +
283F LEU* 3.0 25.9 + - - +
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Residues in contact with ASP 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ASN* 3.0 35.1 + - - +
69F LEU* 4.4 8.7 - - - +
276F VAL* 2.7 22.6 + - + +
277F LYS* 3.6 7.5 - - - +
279F ALA* 1.3 73.5 - - - +
281F ALA* 1.3 62.4 + - - +
283F LEU* 3.2 4.1 + - - +
284F ARG* 2.6 59.9 + - - -
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Residues in contact with ALA 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F LYS 3.2 12.4 + - - +
278F PHE* 2.9 12.2 + - + +
280F ASP* 1.3 77.6 + - - +
282F CYS* 1.3 64.2 + - - +
284F ARG* 3.4 16.3 + - - +
285F GLY 3.1 16.5 + - - -
292F VAL* 3.2 18.0 - - + +
294F GLU* 3.7 34.5 - - + +
314F LEU* 3.8 9.2 - - + +
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Residues in contact with CYS 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F LEU* 4.4 14.8 - - + -
156F ILE* 4.4 11.4 - - + -
158F ASN* 3.7 15.9 - - - -
187F LEU* 4.4 6.7 - - - -
278F PHE* 3.0 40.4 + - - -
279F ALA 3.4 8.5 - - - +
281F ALA* 1.3 78.7 - - - +
283F LEU* 1.3 57.1 + - + +
285F GLY* 3.1 3.1 + - - -
286F LEU* 2.8 34.0 + - + +
314F LEU* 3.8 20.5 - - - +
315F GLY 4.9 0.9 - - - +
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Residues in contact with LEU 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F PHE* 4.0 27.3 - - + -
47F VAL* 4.3 2.9 - - + -
64F MET* 4.2 9.0 - - + -
67F ASN* 3.8 14.1 - - - +
69F LEU* 3.6 29.8 - - + -
70F VAL* 3.7 28.3 - - + -
115F LEU* 3.8 22.9 - - + -
279F ALA 3.0 16.3 + - - +
280F ASP* 3.2 6.7 + - - +
282F CYS* 1.3 74.2 - - - +
284F ARG* 1.3 54.9 + - - +
286F LEU* 2.9 16.8 + - + +
287F ARG* 2.7 35.5 + - - +
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Residues in contact with ARG 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU* 3.8 12.1 - - + +
277F LYS* 4.7 4.9 + - - +
280F ASP* 2.6 54.2 + - - +
281F ALA* 3.7 21.3 - - - +
282F CYS 3.3 0.2 - - - -
283F LEU* 1.3 76.6 - - - +
285F GLY* 1.3 60.6 + - - +
287F ARG* 3.3 28.0 + - - +
288F GLY 3.2 4.3 + - - -
289F ASP* 2.9 42.7 + - + +
292F VAL* 4.0 26.4 - - + +
293F ILE 5.7 0.4 - - - +
294F GLU* 4.7 8.5 + - - -
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Residues in contact with GLY 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F ALA 3.1 13.3 + - - -
282F CYS 3.5 4.3 - - - -
283F LEU 3.1 0.8 - - - -
284F ARG* 1.3 79.1 - - - +
286F LEU* 1.3 60.2 + - - +
288F GLY* 3.2 11.6 + - - -
289F ASP 4.3 2.5 - - - -
292F VAL* 4.1 5.6 - - - +
314F LEU* 3.3 25.6 - - - -
315F GLY* 3.1 25.2 - - - -
316F ARG* 3.2 3.3 + - - -
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Residues in contact with LEU 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F PHE* 3.4 35.8 - - + -
114F ASP* 4.1 17.9 - - + +
115F LEU* 4.8 2.5 - - + -
156F ILE* 3.9 30.7 - - + -
185F ARG* 5.8 1.6 - - - +
282F CYS* 2.8 19.4 + - + +
283F LEU* 3.4 22.9 - - + +
285F GLY* 1.3 73.5 - - - +
287F ARG* 1.3 65.8 + - - +
288F GLY 3.0 1.3 + - - -
315F GLY 4.1 5.2 - - - +
316F ARG* 3.3 44.0 + - - +
318F GLY 4.6 0.2 - - - +
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Residues in contact with ARG 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F PHE* 3.4 18.3 - - + -
69F LEU* 3.7 34.6 - - + +
283F LEU 2.7 12.8 + - - +
284F ARG* 3.5 20.4 - - - +
286F LEU* 1.3 76.9 - - - +
288F GLY* 1.3 58.0 + - - +
289F ASP* 2.7 37.3 + - - +
316F ARG* 3.2 15.4 + - - -
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Residues in contact with GLY 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F ARG 3.2 1.2 + - - -
285F GLY 3.2 7.6 + - - -
286F LEU 3.0 4.0 - - - -
287F ARG* 1.3 81.3 - - - +
289F ASP* 1.3 67.3 + - - +
290F ALA* 3.6 2.6 + - - +
316F ARG* 3.5 29.2 + - - -
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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