Contacts of the helix formed by residues 227 - 240 (chain X) in PDB entry 2FSL
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 227 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186X ARG* 3.3 16.6 + - - +
225X GLY 4.3 0.2 - - - -
226X THR* 1.3 83.8 + - - +
228X HIS* 1.3 66.7 + - - +
229X ILE* 3.5 5.7 + - - +
230X ASP* 2.9 27.7 + - - +
231X GLN* 3.0 21.8 + - - +
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Residues in contact with HIS 228 (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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186X ARG* 3.8 33.9 - - - +
194X MET* 2.7 53.6 + - + +
227X ASP* 1.3 78.6 - - - +
229X ILE* 1.3 66.3 + - + +
231X GLN* 3.3 14.6 + - - +
232X LEU* 3.5 18.2 + - + +
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Residues in contact with ILE 229 (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 ASP* 3.4 5.7 + - - +
228X HIS* 1.3 79.0 - - + +
230X ASP* 1.3 67.3 + - - +
232X LEU* 3.2 23.4 + - + +
233X LYS* 2.9 33.7 + - + +
258X TYR* 6.2 0.7 - - + +
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Residues in contact with ASP 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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224X PRO 4.2 0.3 - - - +
225X GLY* 3.4 7.1 - - - -
226X THR* 3.0 40.9 + - - +
227X ASP* 2.9 23.5 + - - +
229X ILE* 1.3 79.2 - - - +
231X GLN* 1.3 61.1 + - - +
233X LYS* 3.2 26.5 + - - +
234X LEU* 3.0 36.4 + - - +
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Residues in contact with GLN 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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186X ARG* 3.5 27.3 + - + +
187X TRP* 3.4 15.9 + - - -
189X ARG 5.2 1.2 + - - -
194X MET* 3.5 30.0 - - + +
223X PHE* 3.0 36.3 + - - +
225X GLY* 3.0 29.9 + - - -
227X ASP 3.0 11.6 + - - +
228X HIS* 3.4 12.3 - - - +
229X ILE 3.2 0.2 - - - -
230X ASP* 1.3 75.3 - - - +
232X LEU* 1.3 62.7 + - - +
234X LEU* 3.2 5.5 + - - +
235X ILE* 3.1 33.2 + - + +
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Residues in contact with LEU 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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191X PRO* 4.1 32.8 - - + +
194X MET* 4.2 16.6 - - + -
195X LEU* 3.7 30.3 - - + -
228X HIS* 3.5 28.0 + - + +
229X ILE* 3.2 26.7 + - + +
231X GLN* 1.3 76.1 - - - +
233X LYS* 1.3 64.1 + - - +
235X ILE* 3.2 6.0 + - + +
236X LEU* 3.0 35.6 + - + +
1000X BOG 4.9 7.9 - - + -
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Residues in contact with LYS 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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229X ILE* 2.9 24.2 + - + +
230X ASP* 3.2 26.0 + - - +
232X LEU* 1.3 77.4 - - - +
234X LEU* 1.3 63.2 + - + +
236X LEU* 3.4 9.0 + - - +
237X ARG* 3.1 38.8 + - + +
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Residues in contact with LEU 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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222X LEU 5.6 0.2 - - - +
223X PHE* 3.5 23.1 - - + -
224X PRO* 3.6 49.1 - - + +
225X GLY* 3.6 9.4 - - - +
230X ASP* 3.0 28.3 + - - +
231X GLN 3.2 6.7 + - - +
233X LYS* 1.3 75.9 - - + +
235X ILE* 1.3 66.7 + - - +
237X ARG* 3.4 32.9 + - - +
238X LEU* 3.5 2.3 + - - +
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Residues in contact with ILE 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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189X ARG 4.5 4.9 - - - +
191X PRO* 4.4 14.1 - - + -
194X MET* 4.2 24.2 - - + -
207X TRP* 3.7 34.5 - - + +
223X PHE* 3.6 28.3 - - + -
231X GLN* 3.1 24.6 + - + +
232X LEU* 3.2 9.6 + - + +
234X LEU* 1.3 74.7 - - - +
236X LEU* 1.3 66.0 + - + +
238X LEU* 3.1 14.0 + - - +
239X VAL* 3.2 13.3 + - + +
291X LEU* 3.9 20.6 - - + -
1000X BOG 6.5 0.2 - - + -
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Residues in contact with LEU 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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232X LEU* 3.0 26.7 + - + +
233X LYS* 3.8 6.7 - - - +
235X ILE* 1.3 76.7 - - + +
237X ARG* 1.3 62.9 + - - +
239X VAL* 4.6 0.2 - - - -
240X GLY* 3.0 46.1 + - - +
241X THR* 4.4 12.4 - - + +
242X PRO* 4.4 1.8 - - + -
258X TYR* 6.1 1.3 - - + -
262X LEU* 4.4 19.7 - - + -
265X MET* 5.4 3.6 - - - +
291X LEU* 3.9 23.8 - - + -
1000X BOG 3.9 31.0 - - + -
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Residues in contact with ARG 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 LYS* 3.1 29.6 + - + +
234X LEU* 3.5 29.1 - - - +
235X ILE 3.2 0.2 - - - -
236X LEU* 1.3 78.0 - - - +
238X LEU* 1.3 59.5 + - - +
240X GLY* 4.5 1.2 + - - -
265X MET* 6.0 2.2 - - - +
266X PRO 4.9 3.1 - - - +
268X MET* 3.4 29.3 - - - +
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Residues in contact with LEU 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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222X LEU* 4.2 19.3 - - + -
223X PHE* 3.5 34.3 - - + -
234X LEU 3.5 2.2 + - - +
235X ILE 3.1 7.8 + - - +
237X ARG* 1.3 78.9 - - - +
239X VAL* 1.3 64.4 + - + +
240X GLY 3.4 0.2 - - - -
267X LYS* 3.8 0.3 - - - -
268X MET* 3.0 54.3 + - + +
270X PHE* 3.8 38.4 - - + -
273X VAL* 4.0 21.3 - - + -
274X PHE* 5.1 2.0 - - + -
289X LEU* 4.4 3.6 - - + -
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Residues in contact with VAL 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X TRP* 4.4 8.7 - - + -
223X PHE* 5.0 0.7 - - + -
235X ILE* 3.2 17.5 + - + +
238X LEU* 1.3 98.8 - - + +
240X GLY* 1.3 66.6 + - - +
241X THR 4.9 0.9 - - - +
267X LYS* 3.4 23.5 - - + +
270X PHE* 4.3 4.9 - - + -
289X LEU* 3.3 29.2 - - + +
290X VAL* 5.4 0.2 - - - -
291X LEU* 3.6 38.3 - - + +
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Residues in contact with GLY 240 (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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236X LEU* 3.0 33.9 + - - +
237X ARG 4.5 0.6 + - - -
238X LEU 3.4 2.4 + - - -
239X VAL* 1.3 87.5 - - - +
241X THR* 1.3 67.2 + - - -
265X MET* 3.6 16.4 - - - -
266X PRO 4.0 11.2 - - - -
267X LYS* 4.1 0.2 - - - +
291X LEU* 4.0 3.3 - - - +
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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