Contacts of the helix formed by residues 229 - 239 (chain X) in PDB entry 1FM6
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 229 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222X TYR* 4.2 9.2 - - + -
223X ILE* 3.8 27.1 - - + +
226X PHE* 3.3 23.3 - - - +
227X PRO 3.1 7.2 + - - +
228X LEU* 1.3 77.2 - - - +
230X LYS* 1.3 65.2 + - - +
231X ALA* 3.5 5.7 + - - +
232X LYS* 3.3 29.2 + - - +
233X ALA* 3.1 22.2 + - - +
329X MET* 6.0 0.7 - - - -
332X SER* 5.0 0.7 - - - -
333X LEU* 4.8 2.0 - - - -
381X ASP* 3.6 14.6 - - - -
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Residues in contact with LYS 230 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222X TYR* 4.4 1.0 + - - -
229X THR* 1.3 70.1 - - - +
231X ALA* 1.3 59.2 + - - +
233X ALA* 3.0 2.6 + - - -
234X ARG* 2.7 60.5 + - + +
332X SER* 3.3 41.7 - - - +
374X PHE* 6.2 2.6 - - - -
375X ASN* 4.3 24.5 + - - +
378X GLU* 4.3 6.1 - - - +
379X LEU* 2.5 40.6 + - - +
380X ASP* 4.6 4.0 - - - +
381X ASP* 2.9 21.9 + - - +
384X LEU* 4.2 10.0 - - + +
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Residues in contact with ALA 231 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X THR* 3.3 5.4 - - - +
230X LYS* 1.3 77.6 - - - +
232X LYS* 1.3 65.6 + - + +
234X ARG* 3.4 4.7 + - - +
235X ALA* 3.0 20.0 + - - +
381X ASP* 2.9 19.1 + - - +
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Residues in contact with LYS 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227X PRO* 2.8 35.2 + - - +
228X LEU* 3.9 11.7 - - + -
229X THR* 3.3 20.9 + - - +
231X ALA* 1.3 78.3 - - + +
233X ALA* 1.3 64.4 + - - +
235X ALA* 3.0 11.1 + - - +
236X ILE* 2.9 29.6 + - + +
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Residues in contact with ALA 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228X LEU* 3.9 5.8 - - + +
229X THR 3.1 6.3 + - - +
230X LYS 3.0 8.2 + - - +
232X LYS* 1.3 79.2 - - - +
234X ARG* 1.3 57.5 + - - +
236X ILE* 3.1 6.2 + - - +
237X LEU* 2.8 32.1 + - - +
332X SER 3.5 12.3 - - - +
333X LEU* 3.4 33.7 - - + -
340X LEU* 3.8 15.9 - - + +
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Residues in contact with ARG 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X LYS* 2.7 46.0 + - + +
231X ALA* 4.0 4.9 - - - +
233X ALA* 1.3 69.6 - - - +
235X ALA* 1.3 65.8 + - - +
237X LEU* 4.3 9.6 - - + +
238X THR* 3.0 33.9 + - - +
332X SER 4.8 4.2 + - - +
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Residues in contact with ALA 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X ALA 3.0 12.6 + - - +
232X LYS* 3.0 16.4 + - - +
234X ARG* 1.3 75.6 - - - +
236X ILE* 1.3 63.6 + - - +
238X THR* 3.1 26.8 + - - +
239X GLY* 3.2 6.1 + - - -
240X LYS* 3.8 23.5 + - + -
241X THR* 4.1 16.5 - - + +
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Residues in contact with ILE 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228X LEU* 4.9 7.9 - - + -
232X LYS* 2.9 22.6 + - + +
233X ALA* 3.5 7.9 - - - +
235X ALA* 1.3 77.9 - - + +
237X LEU* 1.3 59.6 + - - +
238X THR 4.7 0.3 - - - -
239X GLY* 4.6 3.9 + - - -
241X THR* 4.0 20.6 - - + +
244X LYS* 4.1 13.9 - - - +
246X PRO* 3.1 42.1 - - + +
340X LEU* 3.8 18.8 - - + -
343X GLU 4.6 3.1 - - - +
344X GLY* 3.9 22.7 - - - -
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Residues in contact with LEU 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X ALA 2.8 18.2 + - - +
234X ARG* 4.1 10.5 - - + +
235X ALA 3.1 0.2 + - - -
236X ILE* 1.3 76.9 - - - +
238X THR* 1.3 66.2 + - - +
332X SER 5.1 4.0 - - - +
333X LEU 4.5 9.0 - - - +
334X MET* 3.9 15.0 - - - +
335X ASN* 3.3 35.5 + - + +
340X LEU* 3.5 35.0 - - + -
347X PHE* 3.9 20.4 - - + -
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Residues in contact with THR 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234X ARG* 3.0 23.5 + - - +
235X ALA* 3.1 15.5 - - - +
236X ILE 4.7 0.4 - - - -
237X LEU* 1.3 80.8 - - - +
239X GLY* 1.3 71.0 + - - +
240X LYS* 3.4 29.3 - - + +
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Residues in contact with GLY 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235X ALA 3.2 4.3 + - - -
236X ILE 4.6 3.1 + - - -
238X THR* 1.3 86.5 - - - +
240X LYS* 1.3 67.5 + - - +
241X THR* 4.9 0.4 - - - -
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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