Contacts of the helix formed by residues 250 - 269 (chain C) in PDB entry 3SF4
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 GLU 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212C ARG* 2.8 42.7 + - - -
245C TYR* 3.1 32.9 + - + +
248C LEU* 3.8 15.7 - - - +
249C GLY* 1.3 79.3 - - - +
251C PHE* 1.3 63.1 + - - +
252C GLU* 3.3 3.8 - - - -
253C THR* 3.2 14.5 + - - +
254C ALA* 3.0 19.1 + - - +
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Residues in contact with PHE 251 (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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246C ILE* 3.4 39.7 - - + -
249C GLY* 3.4 23.8 + - - -
250C GLU* 1.3 68.0 - - - +
252C GLU* 1.3 67.4 + - - +
254C ALA* 4.1 6.3 - - - -
255C SER* 2.9 21.3 + - - -
284C THR* 3.3 17.5 - - + +
287C LEU* 3.9 52.3 - - + -
288C LEU* 3.6 23.5 - - + +
23F MET 5.6 1.6 - - - -
32F MET* 5.4 4.0 - - + -
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Residues in contact with GLU 252 (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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250C GLU 3.3 1.0 - - - -
251C PHE* 1.3 76.6 - - - +
253C THR* 1.3 63.1 - - - +
255C SER* 2.7 29.1 + - - -
256C GLU* 3.4 30.5 + - - +
259C LYS* 5.7 2.1 + - - -
285C TYR* 5.4 2.8 + - - -
288C LEU* 3.9 27.9 - - + +
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Residues in contact with THR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C TYR* 3.7 42.4 - - + +
250C GLU* 3.2 19.7 + - - +
252C GLU* 1.3 80.2 - - - +
254C ALA* 1.3 63.3 + - - +
256C GLU* 3.3 26.4 + - - +
257C TYR* 3.3 22.0 - - + -
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Residues in contact with ALA 254 (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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242C GLY* 3.6 27.0 - - - +
245C TYR* 3.9 10.3 - - + +
246C ILE* 3.6 24.9 - - + +
250C GLU 3.0 13.1 + - - +
251C PHE 3.1 8.2 + - - +
253C THR* 1.3 78.3 - - - +
255C SER* 1.3 57.8 + - - +
257C TYR* 2.9 5.9 + - - +
258C TYR* 2.9 33.4 + - + -
284C THR* 4.5 0.2 - - + -
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C PHE 2.9 12.6 + - - -
252C GLU* 2.7 29.7 + - - -
254C ALA* 1.3 76.5 - - - +
256C GLU* 1.3 57.3 + - - +
258C TYR* 4.4 0.4 - - - -
259C LYS* 2.8 38.1 + - - +
281C LEU* 3.6 14.6 - - - +
284C THR* 3.9 15.4 - - - +
285C TYR* 3.7 33.4 + - - -
288C LEU* 4.7 0.4 - - - +
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Residues in contact with GLU 256 (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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252C GLU* 3.4 37.2 + - - +
253C THR* 3.3 20.0 + - - +
254C ALA 3.1 0.6 - - - -
255C SER* 1.3 83.6 + - - +
257C TYR* 1.3 64.5 + - + +
259C LYS* 3.5 14.3 + - + +
260C LYS* 3.3 38.3 + - - +
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Residues in contact with TYR 257 (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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219C GLU* 4.7 12.1 + - - +
222C LEU* 5.0 4.1 - - + +
238C TYR* 3.6 40.5 - + - +
241C LEU* 3.6 29.1 - - + +
242C GLY 3.9 6.7 - - - +
245C TYR* 3.5 36.8 + + - -
253C THR* 3.3 27.7 + - + -
254C ALA* 2.9 7.6 + - - +
256C GLU* 1.3 78.3 - - + +
258C TYR* 1.3 64.2 + - - +
259C LYS 3.1 1.3 - - - -
260C LYS* 3.2 23.7 + - + +
261C THR* 3.0 26.8 + - - +
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C SER* 4.0 13.0 - - - -
242C GLY* 3.7 19.1 - - - -
243C ASN* 2.7 39.0 + - - -
246C ILE* 3.4 21.0 - - + +
254C ALA* 2.9 20.5 + - + +
257C TYR* 1.3 77.2 - - - +
259C LYS* 1.3 57.1 + - - +
261C THR* 2.6 26.0 + - - +
262C LEU* 2.8 15.8 + - - +
277C SER* 4.3 5.9 - - - +
280C SER* 3.9 29.2 - - - -
281C LEU* 3.4 26.4 - - + +
284C THR* 3.2 28.0 - - - -
31F TRP* 4.0 2.3 - + - -
35F LEU* 3.8 7.1 - - - +
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Residues in contact with LYS 259 (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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252C GLU* 5.7 2.2 + - - -
255C SER* 2.8 26.1 + - - +
256C GLU* 3.6 13.6 - - + +
258C TYR* 1.3 78.3 - - - +
260C LYS* 1.3 56.9 - - + +
262C LEU* 3.2 10.7 + - + +
263C LEU* 3.0 33.8 + - + +
281C LEU* 4.1 13.7 - - + -
285C TYR* 2.6 34.6 + - - -
293C LYS* 5.4 4.2 - - - +
297C TYR* 4.2 17.3 - - - +
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Residues in contact with LYS 260 (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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238C TYR* 3.7 45.6 + - + +
256C GLU* 3.3 26.1 + - - +
257C TYR* 3.2 28.4 + - + +
259C LYS* 1.3 74.5 - - + +
261C THR* 1.3 66.1 + - - +
263C LEU* 3.5 9.0 + - + +
264C LEU* 3.1 24.8 + - - +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ARG* 3.8 15.5 - - - +
238C TYR* 3.0 32.8 - - + +
239C SER* 3.1 34.8 + - - +
257C TYR 3.0 7.7 + - - +
258C TYR* 2.6 27.3 + - + +
260C LYS* 1.3 76.2 - - - +
262C LEU* 1.3 56.7 + - - +
264C LEU* 3.8 1.3 - - - +
265C ALA* 2.8 32.7 + - - +
277C SER* 3.2 16.9 + - - -
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Residues in contact with LEU 262 (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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258C TYR 2.8 13.4 + - - +
259C LYS* 3.2 12.8 - - + +
260C LYS 3.1 0.2 - - - -
261C THR* 1.3 77.7 + - - +
263C LEU* 1.3 65.5 + - + +
265C ALA* 3.2 2.2 + - - +
266C ARG* 2.9 61.7 + - - +
274C GLU* 3.7 24.5 - - + +
277C SER* 4.0 11.0 - - - -
278C CYS* 3.9 13.5 - - - -
281C LEU* 3.9 9.6 - - + -
297C TYR* 3.8 30.7 - - + +
300C LYS* 5.5 0.4 - - + -
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Residues in contact with LEU 263 (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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259C LYS* 3.0 21.5 + - + +
260C LYS* 4.0 8.7 - - + +
261C THR 3.4 0.2 - - - -
262C LEU* 1.3 78.5 - - + +
264C LEU* 1.3 62.5 + - - +
266C ARG* 3.2 25.5 + - + +
267C GLN* 3.0 32.5 + - - +
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Residues in contact with LEU 264 (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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231C LYS* 3.6 33.0 - - + +
234C GLU* 3.7 20.9 - - + +
235C ARG* 3.3 43.7 - - + +
238C TYR* 4.1 8.1 - - + -
260C LYS 3.1 15.9 + - - +
261C THR* 3.8 3.1 - - - +
263C LEU* 1.3 72.7 - - - +
265C ALA* 1.3 60.6 + - - +
267C GLN* 3.2 25.3 + - - +
268C LEU* 2.9 42.5 + - + +
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Residues in contact with ALA 265 (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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235C ARG* 4.4 2.9 - - + +
261C THR 2.8 23.2 + - - +
262C LEU* 3.5 4.7 - - - +
264C LEU* 1.3 73.5 - - - +
266C ARG* 1.3 62.9 + - - +
268C LEU* 3.4 7.5 + - - -
269C LYS 2.9 18.0 + - - -
270C ASP* 3.0 16.9 + - - +
273C VAL* 3.8 17.5 - - + -
274C GLU* 3.8 32.1 - - - +
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Residues in contact with ARG 266 (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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262C LEU* 2.9 49.0 + - - +
263C LEU* 3.2 25.4 - - + +
265C ALA* 1.3 76.7 - - - +
267C GLN* 1.3 63.5 + - + +
269C LYS* 2.9 18.5 + - - +
271C ARG* 6.0 0.2 - - - +
274C GLU* 3.1 43.7 + - - +
278C CYS* 4.5 6.9 - - - -
297C TYR* 5.8 0.2 - - - -
300C LYS* 4.7 15.8 - - - +
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Residues in contact with GLN 267 (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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231C LYS* 4.6 13.5 - - - +
263C LEU* 3.0 19.9 + - + +
264C LEU* 3.2 29.6 + - - +
266C ARG* 1.3 73.3 - - + +
268C LEU* 1.3 63.5 + - + +
269C LYS* 2.8 21.4 + - - +
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Residues in contact with LEU 268 (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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231C LYS* 3.6 38.6 - - + +
232C ALA* 4.6 6.7 - - + +
235C ARG* 4.2 25.8 - - + +
264C LEU* 2.9 32.4 + - + +
265C ALA* 3.9 5.4 - - - +
267C GLN* 1.3 74.3 - - + +
269C LYS* 1.3 68.5 + - - +
270C ASP* 3.4 9.2 + - + +
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Residues in contact with LYS 269 (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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265C ALA 2.9 3.2 + - - -
266C ARG 3.3 12.3 - - - +
267C GLN 2.8 17.5 + - - +
268C LEU* 1.3 80.1 - - - +
270C ASP* 1.3 59.2 + - - +
271C ARG* 3.4 14.7 + - - +
274C GLU* 5.7 1.3 - - - -
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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