Contacts of the helix formed by residues 256 - 267 (chain C) in PDB entry 1FS2
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 SER 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C ASP* 2.6 31.0 + - - -
255C PHE* 1.3 77.7 - - - +
257C GLU* 1.3 58.4 + - - +
258C PHE* 2.9 28.2 - - - -
259C ALA* 3.1 3.8 + - - +
260C LEU* 2.7 35.3 + - - +
285C HIS* 3.5 5.2 - - - -
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Residues in contact with GLU 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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256C SER* 1.3 75.1 - - - +
258C PHE* 1.3 95.3 + - + +
260C LEU* 3.7 2.9 - - - +
261C GLN* 3.1 19.9 + - - +
284C LYS* 2.5 69.9 + - + +
285C HIS* 3.2 29.5 + - + +
288C VAL* 3.4 20.3 - - + +
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Residues in contact with PHE 258 (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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232C ASP* 5.8 0.9 - - - +
256C SER* 2.9 14.3 - - - -
257C GLU* 1.3 111.8 - - + +
259C ALA* 1.3 53.1 + - - +
260C LEU 3.1 0.9 - - - -
261C GLN* 2.9 15.9 + - - +
262C THR* 2.7 41.8 + - + +
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Residues in contact with ALA 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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232C ASP* 3.7 28.2 + - - +
235C VAL* 3.5 31.6 - - + +
236C ASN* 3.7 11.9 - - - +
255C PHE* 4.4 1.3 - - + -
256C SER* 3.1 10.9 + - - +
258C PHE* 1.3 77.7 - - - +
260C LEU* 1.3 64.0 + - - +
262C THR* 3.1 14.1 + - - +
263C LEU 2.9 19.6 + - - -
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Residues in contact with LEU 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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235C VAL* 4.2 5.4 - - + +
249C LEU* 5.2 5.6 - - + -
255C PHE* 3.9 19.0 - - + -
256C SER 2.7 17.2 + - - +
257C GLU* 3.7 7.0 - - - +
259C ALA* 1.3 76.7 - - - +
261C GLN* 1.3 61.6 + - - +
263C LEU* 3.1 6.2 + - + -
264C LEU* 3.0 46.8 + - + +
275C LEU* 4.1 31.4 - - + -
281C PHE* 4.2 9.0 - - + -
285C HIS* 4.0 36.8 - - + +
288C VAL* 4.2 4.9 - - + -
289C ALA 4.6 2.5 - - - +
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Residues in contact with GLN 261 (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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257C GLU 3.1 13.5 + - - +
258C PHE* 2.9 19.8 + - - +
260C LEU* 1.3 73.8 - - - +
262C THR* 1.3 66.6 + - - +
264C LEU* 4.3 1.3 - - - +
265C SER* 2.7 41.1 + - - +
288C VAL* 3.6 22.1 - - + +
292C HIS* 3.1 38.2 + - + +
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Residues in contact with THR 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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44B PRO* 4.4 22.5 - - + +
236C ASN* 3.3 29.3 + - - +
239C ALA* 4.0 16.1 - - - +
258C PHE* 2.7 29.3 + - + +
259C ALA* 3.3 7.8 + - - +
261C GLN* 1.3 75.8 - - - +
263C LEU* 1.3 59.5 + - - +
265C SER* 4.0 5.9 - - - -
266C SER* 3.5 20.4 + - - -
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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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235C VAL* 3.9 21.5 - - + +
238C LEU* 3.8 29.2 - - + +
239C ALA* 3.7 29.8 - - - +
244C LEU* 5.0 2.7 - - + -
247C LEU* 4.0 26.2 - - + -
249C LEU* 4.4 11.0 - - + -
259C ALA 2.9 15.8 + - - +
260C LEU* 3.7 7.0 - - + +
261C GLN 3.0 0.2 - - - -
262C THR* 1.3 77.7 + - - +
264C LEU* 1.3 71.4 + - + +
266C SER* 3.3 9.0 + - - -
267C CYS* 3.4 23.6 + - - -
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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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247C LEU* 4.7 10.3 - - + -
260C LEU* 3.0 43.7 + - + +
263C LEU* 1.3 78.6 - - + +
265C SER* 1.3 62.0 + - - +
267C CYS* 3.1 23.9 + - + +
268C SER* 5.1 0.3 - - - -
270C LEU* 4.4 17.0 - - + +
273C LEU* 4.1 24.9 - - + -
275C LEU* 4.6 6.5 - - + -
288C VAL* 4.7 4.0 - - + +
289C ALA* 4.1 27.1 - - - +
292C HIS* 3.6 25.0 - - + +
293C VAL* 4.4 10.3 - - + -
294C SER* 5.0 1.7 + - - -
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Residues in contact with SER 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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261C GLN* 2.7 39.1 + - - +
262C THR* 4.0 5.8 - - - -
264C LEU* 1.3 78.1 - - - +
266C SER* 1.3 58.3 + - - +
268C SER* 4.5 10.4 + - - -
292C HIS* 3.6 20.3 + - - -
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Residues in contact with SER 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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239C ALA* 2.9 31.7 + - - -
242C SER* 3.6 25.8 + - - +
262C THR 3.5 14.9 + - - -
263C LEU 3.3 5.7 + - - -
264C LEU 3.1 0.8 - - - -
265C SER* 1.3 78.1 - - - +
267C CYS* 1.3 63.4 + - - +
268C SER* 3.2 13.0 + - - -
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Residues in contact with CYS 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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238C LEU 5.4 0.2 - - - -
241C ASN 3.5 23.8 - - - -
242C SER 3.8 7.0 - - - +
244C LEU* 3.6 28.7 - - + +
247C LEU* 5.5 2.0 - - - -
263C LEU* 3.4 25.5 + - - +
264C LEU* 3.1 15.2 + - - +
266C SER* 1.3 76.3 - - - +
268C SER* 1.3 55.9 + - - +
269C ARG 3.2 5.8 - - - -
270C LEU* 3.3 29.4 - - + +
294C SER* 3.2 16.5 + - - -
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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