Contacts of the helix formed by residues 270 - 288 (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 ASP 270 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 3.0 13.4 + - - +
268C LEU* 3.3 12.1 - - + +
269C LYS* 1.3 73.7 - - - +
271C ARG* 1.3 57.5 + - - +
272C ALA* 3.3 11.6 + - - +
273C VAL* 2.9 43.1 + - + +
274C GLU* 2.8 28.4 + - - +
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Residues in contact with ARG 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 3.4 11.4 + - - +
270C ASP* 1.3 71.5 + - - +
272C ALA* 1.3 54.7 + - - +
274C GLU* 3.2 33.9 + - - +
275C ALA* 2.8 35.7 + - - +
303C ALA* 5.4 1.2 + - - +
304C ILE* 3.3 34.1 - - + +
307C GLU* 3.0 37.3 + - - +
308C LEU* 4.1 21.5 - - + -
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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
----------------------------------------------------------
270C ASP* 3.3 8.6 + - - +
271C ARG* 1.3 77.2 - - - +
273C VAL* 1.3 64.3 - - + +
275C ALA* 3.6 4.2 + - - +
276C GLN* 3.1 22.0 + - - +
308C LEU* 3.9 17.1 - - + +
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ARG* 3.7 48.0 - - - +
265C ALA* 3.8 13.9 - - + -
270C ASP* 2.9 40.3 + - + +
272C ALA* 1.3 74.0 - - + +
274C GLU* 1.3 57.6 + - - +
276C GLN* 2.8 17.2 + - - +
277C SER* 2.7 43.7 + - - +
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Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 3.7 15.9 - - + -
265C ALA* 3.8 16.9 - - + +
266C ARG* 3.1 44.3 + - - +
269C LYS* 5.7 0.7 - - - -
270C ASP 2.8 14.0 + - - +
271C ARG* 3.3 40.1 + - - +
273C VAL* 1.3 76.6 - - - +
275C ALA* 1.3 63.1 + - - +
277C SER* 3.1 6.1 + - - -
278C CYS* 3.0 25.8 + - - -
304C ILE* 3.4 21.2 - - + +
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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
----------------------------------------------------------
271C ARG 2.8 12.3 + - - +
272C ALA* 3.7 6.7 - - - +
274C GLU* 1.3 72.6 - - - +
276C GLN* 1.3 63.1 + - - +
278C CYS* 3.0 10.3 + - - +
279C TYR 2.9 18.7 + - - -
301C HIS* 3.3 23.5 - - + +
304C ILE* 3.4 39.2 - - + +
305C ALA* 4.8 3.4 - - - +
308C LEU* 5.4 1.3 - - + -
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Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ARG* 4.3 11.7 - - - +
239C SER* 4.7 5.5 + - - -
272C ALA 3.1 11.9 + - - +
273C VAL* 2.8 28.8 + - - +
275C ALA* 1.3 79.7 - - - +
277C SER* 1.3 64.5 + - - +
279C TYR* 3.1 9.3 + - + +
280C SER* 3.0 28.8 + - - +
301C HIS* 4.5 1.1 - - - -
38F MET* 4.1 22.8 - - - +
40F GLU* 4.8 9.1 + - - +
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C SER* 5.4 0.7 + - - -
258C TYR* 4.3 4.7 - - - +
261C THR* 3.2 29.5 + - - -
262C LEU* 3.9 24.3 + - - -
273C VAL* 2.7 27.4 + - - +
274C GLU* 3.4 9.5 - - - -
276C GLN* 1.3 75.1 + - - +
278C CYS* 1.3 57.7 + - - +
280C SER* 3.2 8.3 + - - -
281C LEU* 2.9 33.5 + - - +
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Residues in contact with CYS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 3.9 24.9 - - - -
266C ARG* 4.5 3.6 - - - -
274C GLU* 3.0 20.8 + - - -
275C ALA* 3.0 10.2 + - - +
277C SER* 1.3 78.1 - - - +
279C TYR* 1.3 56.7 + - - +
281C LEU* 3.2 6.8 + - - -
282C GLY* 2.9 24.8 + - - -
297C TYR* 3.4 31.6 - - + +
300C LYS* 3.8 26.2 - - - -
301C HIS* 3.9 8.3 - - + +
304C ILE* 4.9 2.0 - - - -
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Residues in contact with TYR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA 2.9 6.0 + - - +
276C GLN* 3.1 10.3 + - + +
278C CYS* 1.3 77.1 - - - +
280C SER* 1.3 57.4 + - - +
282C GLY* 3.4 1.4 + - - -
283C ASN* 2.6 57.8 + - - -
298C HIS* 3.8 17.5 - + - -
301C HIS* 3.5 42.1 - + + +
316C ARG* 3.5 51.1 + - + +
317C ALA* 4.2 1.3 - - - -
319C TRP* 5.3 1.4 - - - -
320C SER* 2.7 27.9 + - - -
27F SER* 4.5 8.5 + - - -
31F TRP* 3.7 22.7 - + + -
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Residues in contact with SER 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ASN* 5.3 0.2 + - - -
258C TYR* 3.9 26.1 + - - -
276C GLN* 3.0 19.1 + - - +
277C SER* 3.6 9.2 - - - -
279C TYR* 1.3 75.0 - - - +
281C LEU* 1.3 57.6 + - - +
283C ASN* 3.3 2.1 + - - +
284C THR* 2.7 37.5 + - - -
31F TRP* 3.6 32.4 + - - +
35F LEU* 4.8 4.7 - - - +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C SER* 3.6 31.2 - - - +
258C TYR* 3.4 27.8 - - + +
259C LYS* 4.1 16.2 - - + +
262C LEU* 3.9 17.5 - - + -
277C SER 2.9 19.5 + - - +
278C CYS 3.2 4.9 + - - +
280C SER* 1.3 76.5 - - - +
282C GLY* 1.3 57.3 + - - +
284C THR* 4.1 2.2 - - - -
285C TYR* 2.9 48.1 + - + -
297C TYR* 3.7 39.3 - - + -
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Residues in contact with GLY 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C CYS 2.9 15.4 + - - -
279C TYR 3.8 1.1 - - - -
280C SER 3.2 0.2 - - - -
281C LEU* 1.3 78.4 - - - +
283C ASN* 1.3 58.4 + - - +
286C THR* 2.8 27.7 + - - -
294C ALA* 3.5 22.9 - - - +
297C TYR* 3.8 4.6 - - - +
298C HIS* 3.4 21.3 - - - -
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C TYR* 2.6 54.6 + - - -
280C SER 3.8 2.9 - - - +
282C GLY* 1.3 72.4 - - - +
284C THR* 1.3 67.2 + - - +
286C THR* 3.1 9.9 + - - -
287C LEU* 3.0 28.1 + - - +
298C HIS* 3.9 6.8 + - - -
320C SER* 4.9 2.3 + - - -
27F SER* 3.9 3.5 + - - +
28F VAL* 3.5 23.2 + - + +
31F TRP* 3.3 47.4 - - + +
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Residues in contact with THR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ILE* 3.4 10.8 - - + +
251C PHE* 3.3 35.0 - - + +
255C SER* 3.9 21.1 - - - +
258C TYR* 3.2 22.0 - - - -
280C SER 2.7 24.5 + - - -
281C LEU* 3.6 7.6 - - - -
283C ASN* 1.3 75.8 - - - +
285C TYR* 1.3 58.7 + - - +
287C LEU* 3.0 16.1 + - - +
288C LEU* 3.0 27.0 + - + +
31F TRP* 4.2 0.7 - - - -
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Residues in contact with TYR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLU* 5.4 3.0 + - - -
255C SER* 3.7 13.0 + - - -
259C LYS* 2.6 35.2 + - - -
281C LEU* 2.9 37.4 + - + +
284C THR* 1.3 73.7 - - - +
286C THR* 1.3 62.7 + - - +
288C LEU* 3.2 23.8 + - + +
289C GLN 3.0 3.5 + - - -
290C ASP* 2.8 51.4 + - + +
293C LYS* 3.7 38.7 + - + +
294C ALA* 3.7 10.8 - - - +
297C TYR* 3.6 30.5 - + - -
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Residues in contact with THR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLY 2.8 20.4 + - - -
283C ASN* 3.1 10.7 + - - -
285C TYR* 1.3 75.6 - - - +
287C LEU* 1.3 58.3 + - - +
289C GLN* 2.7 27.5 + - - +
291C TYR* 4.2 24.4 + - + +
294C ALA* 3.6 13.7 - - - +
298C HIS* 4.3 6.2 + - - -
324C ALA* 5.5 3.5 - - - +
23F MET* 5.2 4.7 - - + +
25F VAL* 4.8 13.5 - - + -
28F VAL* 3.8 26.3 - - + +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ILE* 4.5 6.1 - - + -
251C PHE* 3.9 50.6 - - + -
283C ASN 3.0 18.6 + - - +
284C THR* 3.3 11.2 - - - +
286C THR* 1.3 77.4 - - - +
288C LEU* 1.3 58.8 + - - +
289C GLN* 3.1 7.3 + - - +
23F MET* 3.3 43.9 + - + +
28F VAL* 3.8 17.3 - - + -
31F TRP* 4.0 22.7 - - + -
32F MET* 4.6 9.6 - - + -
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C PHE* 3.6 31.2 - - + +
252C GLU* 3.9 43.3 - - + +
255C SER* 4.7 0.9 - - - +
284C THR* 3.0 11.7 + - + +
285C TYR* 3.6 35.4 - - + +
286C THR 3.1 0.4 - - - -
287C LEU* 1.3 74.5 - - - +
289C GLN* 1.3 70.6 + - - +
290C ASP* 3.4 6.3 + - + +
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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
------------------------------------------------------------
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