Contacts of the helix formed by residues 268 - 288 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY* 2.8 42.2 - - - +
56C ILE* 3.9 9.7 + - - +
59C PRO* 4.0 1.1 - - + -
261C LYS* 3.7 12.1 + - - -
266C SER 3.2 9.7 + - - -
267C ALA* 1.3 72.8 + - - +
269C LEU* 1.3 78.8 - - + +
270C SER 3.6 0.4 - - - -
271C MET* 3.6 2.7 - - - +
272C ALA* 2.8 28.6 + - - +
58D GLN* 4.9 6.7 - - - +
87D ASP* 2.7 8.9 + - - -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PRO* 4.1 17.3 - - + -
268C THR* 1.3 86.8 - - + +
270C SER* 1.3 61.9 + - - +
271C MET 3.1 1.1 - - - -
272C ALA* 3.1 1.1 + - - -
273C TYR* 2.8 30.5 + - - +
58D GLN* 3.4 53.6 - - + +
59D PRO* 4.3 2.7 - - + -
62D MET* 3.3 26.3 - - + +
84D VAL* 4.1 9.6 - - + +
87D ASP* 3.1 11.7 + - + +
88D ILE* 3.6 29.6 - - + -
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Residues in contact with SER 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU* 3.9 17.9 - - - +
196C ARG* 4.7 1.6 + - - -
267C ALA* 3.8 12.1 - - - +
269C LEU* 1.3 72.8 - - - +
271C MET* 1.3 59.2 + - - +
273C TYR* 3.3 4.7 + - - +
274C ALA* 2.8 30.8 + - - +
87D ASP* 2.6 44.9 + - - -
90D HIS* 4.4 8.5 + - - +
91D MET* 3.7 25.2 - - - -
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Residues in contact with MET 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 3.7 28.9 - - + -
160C ILE* 3.7 21.1 - - + -
189C VAL* 4.1 17.3 - - + +
192C LEU* 3.8 30.5 - - + -
267C ALA* 3.7 17.0 - - + +
268C THR 3.6 9.1 + - - +
269C LEU 3.1 0.8 - - - -
270C SER* 1.3 78.3 + - - +
272C ALA* 1.3 60.7 + - - +
274C ALA* 3.1 4.6 + - + +
275C ALA* 2.8 49.0 + - + +
1313C CIT 3.9 18.6 - - - +
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 3.9 11.2 - - - +
59C PRO* 3.7 17.0 - - + -
60C LEU* 3.6 30.7 - - - +
63C LEU* 4.0 0.7 - - + -
268C THR 2.8 21.9 + - - +
269C LEU 3.5 4.3 - - - +
271C MET* 1.3 73.5 - - - +
273C TYR* 1.3 58.2 + - - +
275C ALA* 3.3 2.3 + - - +
276C VAL* 2.9 36.3 + - - +
62D MET* 4.1 4.0 - - - -
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Residues in contact with TYR 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 3.8 10.7 - - + +
195C VAL* 3.8 17.7 - - + -
269C LEU 2.8 15.6 + - - +
270C SER 3.4 7.6 - - - +
272C ALA* 1.3 77.8 - - - +
274C ALA* 1.3 64.8 + - - +
276C VAL* 3.4 2.1 + - - +
277C LYS* 2.9 60.3 + - + +
62D MET* 4.5 3.8 - - - -
66D MET* 3.8 29.2 - - + -
91D MET* 3.3 37.2 - - + -
92D ASP* 2.9 32.5 + - - -
93D THR* 3.6 21.7 - - + +
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C MET* 3.4 21.0 - - + +
192C LEU* 3.7 38.4 - - + +
195C VAL* 4.2 7.6 - - + -
270C SER 2.8 19.8 + - - +
271C MET* 3.6 6.1 - - + +
273C TYR* 1.3 76.8 - - - +
275C ALA* 1.3 61.2 + - - +
277C LYS* 3.1 3.6 + - - +
278C PHE* 2.9 25.8 + - - +
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ILE* 5.4 0.2 - - + -
60C LEU* 4.1 16.8 - - + -
117C ILE* 4.9 3.9 - - + +
158C ASN* 5.0 1.0 + - - -
160C ILE* 3.8 19.3 - - + -
189C VAL* 4.6 5.8 - - + +
271C MET* 2.8 34.0 + - + +
272C ALA 3.6 4.7 - - - +
274C ALA* 1.3 76.4 - - - +
276C VAL* 1.3 53.4 + - - +
278C PHE* 3.3 6.6 + - - +
279C ALA* 2.7 35.6 + - - +
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Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 3.2 24.0 - - + +
63C LEU* 3.4 42.0 - - + +
64C MET* 4.0 15.7 - - - -
67C ASN* 5.0 9.2 - - + +
272C ALA 2.9 18.5 + - - +
273C TYR 3.8 4.3 - - - +
275C ALA* 1.3 72.5 - - - +
277C LYS* 1.3 58.8 + - + +
279C ALA* 3.5 5.6 - - - +
280C ASP* 2.7 36.0 + - + +
66D MET* 6.5 0.7 - - + -
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Residues in contact with LYS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C MET* 4.5 13.9 - - + -
195C VAL* 5.0 6.3 - - + -
273C TYR* 2.9 57.7 + - + +
274C ALA* 3.1 10.1 + - - +
276C VAL* 1.3 77.4 - - - +
278C PHE* 1.3 62.4 + - - +
280C ASP* 3.3 6.7 + - - +
281C ALA* 3.1 22.2 + - - +
284C ARG* 4.9 1.9 + - - -
294C GLU* 5.8 0.4 - - - -
92D ASP* 3.9 16.7 + - - +
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Residues in contact with PHE 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ASN* 3.4 36.8 - - - -
187C LEU* 3.4 34.1 - - + -
189C VAL* 3.7 27.1 - - + -
191C MET* 4.1 22.4 - - + +
274C ALA 2.9 16.0 + - - +
275C ALA 3.7 4.3 - - - +
277C LYS* 1.3 78.1 - - - +
279C ALA* 1.3 61.1 + - - +
281C ALA* 3.2 5.7 + - + +
282C CYS* 3.1 29.9 + - - -
294C GLU* 4.1 25.4 - - + -
295C CYS 3.9 17.7 - - - -
296C ALA* 3.7 13.2 - - + -
312C VAL* 5.6 0.7 - - + -
314C LEU* 4.3 9.0 - - + -
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 4.0 14.4 - - + -
115C LEU* 4.0 7.1 - - + +
117C ILE* 3.7 29.4 - - + -
158C ASN* 3.6 13.4 - - - +
275C ALA 2.7 21.9 + - - +
276C VAL 3.1 4.2 + - - +
278C PHE* 1.3 73.2 - - - +
280C ASP* 1.3 64.1 + - - +
282C CYS* 3.1 5.4 + - - +
283C LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 5.5 0.4 - - - -
67C ASN* 3.1 30.2 + - - +
69C LEU* 3.9 14.4 - - - +
276C VAL* 2.7 21.9 + - + +
277C LYS* 3.6 7.0 - - - +
279C ALA* 1.3 73.6 - - - +
281C ALA* 1.3 56.2 + - - +
283C LEU* 3.1 7.6 + - - +
284C ARG* 2.8 57.7 + - - +
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C LYS 3.1 12.2 + - - +
278C PHE* 3.5 10.1 - - + +
280C ASP* 1.3 77.6 + - - +
282C CYS* 1.3 56.0 + - - +
284C ARG* 3.2 25.7 + - - +
285C GLY* 2.8 24.1 + - - -
292C VAL* 3.3 23.6 - - + +
294C GLU* 3.9 24.0 - - + +
314C LEU* 4.0 5.3 - - + +
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Residues in contact with CYS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU* 4.4 15.3 - - + -
156C ILE* 4.3 15.0 - - + -
158C ASN* 3.5 26.0 - - - -
187C LEU* 4.6 4.3 - - - -
278C PHE* 3.1 30.1 + - - -
279C ALA 3.5 8.5 - - - +
281C ALA* 1.3 76.1 - - - +
283C LEU* 1.3 58.5 + - - +
285C GLY* 3.1 2.1 + - - +
286C LEU* 2.8 33.7 + - + +
314C LEU* 3.9 21.7 - - - +
315C GLY 4.7 0.9 - - - +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 3.5 35.5 - - + -
47C VAL* 4.5 3.1 - - + -
64C MET* 4.3 11.9 - - + -
67C ASN* 4.3 9.9 - - - +
69C LEU* 3.7 25.1 - - + -
70C VAL* 4.0 27.4 - - + -
115C LEU* 3.9 22.4 - - + -
279C ALA 3.0 14.5 + - - +
280C ASP* 3.1 7.2 + - - +
282C CYS* 1.3 72.8 - - - +
284C ARG* 1.3 60.0 + - - +
285C GLY 3.0 1.8 - - - -
286C LEU* 3.0 17.0 + - + +
287C ARG* 2.7 25.5 + - - +
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Residues in contact with ARG 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 3.9 11.9 - - + -
277C LYS 4.9 2.0 + - - -
280C ASP* 2.8 36.6 + - - +
281C ALA* 3.5 30.6 - - - +
283C LEU* 1.3 76.2 - - - +
285C GLY* 1.3 59.4 + - - +
287C ARG* 3.4 25.3 + - - +
288C GLY 3.4 2.6 + - - -
289C ASP* 3.0 48.2 + - - +
292C VAL* 4.1 21.2 - - + +
294C GLU* 4.7 7.1 + - - -
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Residues in contact with GLY 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ALA 2.8 14.5 + - - -
282C CYS 3.5 4.5 - - - -
283C LEU 3.0 0.2 - - - -
284C ARG* 1.3 78.6 - - - +
286C LEU* 1.3 60.6 + - - +
288C GLY* 3.0 12.8 + - - -
289C ASP 4.2 1.7 + - - -
292C VAL* 4.3 4.2 - - - +
314C LEU* 3.5 25.6 - - - -
315C GLY* 2.9 24.6 - - - -
316C ARG 3.1 2.3 + - - -
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 3.7 26.4 - - + -
114C ASP* 4.4 16.6 - - + +
115C LEU* 5.1 1.1 - - + -
156C ILE* 3.9 33.9 - - + -
282C CYS* 2.8 19.8 + - + +
283C LEU* 3.0 28.2 + - + +
285C GLY* 1.3 75.9 - - - +
287C ARG* 1.3 62.6 + - - +
288C GLY 3.3 0.3 + - - -
315C GLY 3.8 4.5 - - - +
316C ARG* 3.1 48.1 + - - +
317C ASN* 4.8 0.2 - - - -
318C GLY* 4.5 0.7 - - - +
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 3.5 16.1 - - + -
69C LEU* 3.4 31.5 - - + +
283C LEU 2.7 15.4 + - - +
284C ARG* 3.6 24.5 - - - +
285C GLY 3.1 0.2 - - - -
286C LEU* 1.3 78.6 - - - +
288C GLY* 1.3 57.9 + - - +
289C ASP* 2.9 36.7 + - - +
316C ARG* 3.5 15.9 + - - -
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Residues in contact with GLY 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C GLY 3.0 12.5 + - - -
286C LEU 3.1 0.4 - - - -
287C ARG* 1.3 79.6 - - - +
289C ASP* 1.3 69.2 + - - +
290C ALA* 3.6 1.6 + - - +
315C GLY* 5.9 0.4 - - - -
316C ARG* 3.7 29.6 + - - -
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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