Contacts of the helix formed by residues 227 - 240 (chain A) in PDB entry 3FKL
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A THR* 6.0 2.0 - - + -
181A GLY* 4.4 6.3 - - - +
186A ARG* 3.3 23.6 + - - +
225A GLY 3.2 1.4 - - - -
226A THR* 1.3 90.0 + - - +
228A HIS* 1.3 61.3 + - + +
229A ILE* 2.9 33.8 + - - +
230A ASP* 3.0 13.4 + - - +
231A GLN* 2.9 23.9 + - - +
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Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A MET* 3.3 33.0 + - + +
180A THR* 4.8 8.0 + - + -
186A ARG* 3.8 24.7 - - + +
194A MET* 3.3 43.3 + - + +
195A LEU* 4.2 15.5 - - + +
227A ASP* 1.3 78.8 + - + +
229A ILE* 1.3 63.2 + - + +
232A LEU* 3.0 24.8 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 5.0 9.9 - - + -
227A ASP* 2.9 10.7 + - - +
228A HIS* 1.3 79.3 - - + +
230A ASP* 1.3 66.4 + - - +
232A LEU* 3.2 6.1 + - + +
233A LYS* 3.0 45.4 + - - +
258A TYR* 3.3 43.7 - - + +
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Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PRO 4.2 1.0 - - - +
225A GLY* 3.2 7.8 - - - -
226A THR* 2.8 49.4 + - - +
227A ASP* 3.0 13.9 + - - +
229A ILE* 1.3 77.2 - - - +
231A GLN* 1.3 61.5 + - - +
233A LYS* 3.3 12.2 + - - +
234A LEU* 3.0 34.9 + - - +
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 2.8 60.8 + - - +
187A TRP* 3.5 19.6 + - - +
189A ARG 4.1 9.7 + - - -
194A MET* 3.7 13.9 - - - -
223A PHE* 3.8 21.7 - - + +
225A GLY* 3.8 10.5 - - - -
227A ASP 2.9 17.2 + - - +
228A HIS 3.7 3.8 - - - +
230A ASP* 1.3 74.9 - - - +
232A LEU* 1.3 60.3 + - - +
234A LEU* 3.3 4.8 + - - +
235A ILE* 2.9 47.6 + - + +
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PRO* 4.5 11.7 - - + -
194A MET* 4.0 9.6 - - + +
195A LEU* 3.7 27.8 - - + -
197A TRP* 4.3 12.6 - - + -
228A HIS 3.0 15.7 + - - +
229A ILE* 3.2 9.8 + - + +
231A GLN* 1.3 75.2 - - - +
233A LYS* 1.3 59.5 + - + +
235A ILE* 3.1 8.1 + - + +
236A LEU* 2.8 58.6 + - + +
258A TYR* 3.8 23.6 - - + +
259A ILE* 3.8 19.1 - - + -
262A LEU* 4.1 8.7 - - + -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.0 38.6 + - + +
230A ASP* 3.7 13.2 - - - +
231A GLN 3.3 0.2 - - - -
232A LEU* 1.3 80.0 - - + +
234A LEU* 1.3 62.2 + - + +
236A LEU* 3.9 5.6 - - - +
237A ARG* 3.0 26.3 + - - +
258A TYR* 4.4 7.6 - - - +
262A LEU* 4.7 18.8 - - + -
265A MET* 4.6 5.2 - - + +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU 5.3 0.4 - - - +
223A PHE* 3.8 20.1 - - + -
224A PRO* 3.8 24.2 - - + +
225A GLY* 3.6 34.3 - - - +
230A ASP* 3.0 24.5 + - - +
231A GLN* 3.5 6.5 - - - +
233A LYS* 1.3 78.5 - - - +
235A ILE* 1.3 63.9 + - - +
237A ARG* 3.5 13.6 + - - +
238A LEU* 3.4 12.8 + - - +
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ARG 4.7 3.6 - - - +
191A PRO* 4.3 21.5 - - + -
194A MET* 4.7 3.8 - - + -
207A TRP* 3.6 36.3 - - + -
223A PHE* 3.6 30.5 - - + -
231A GLN* 2.9 42.5 + - + +
232A LEU* 3.4 10.1 - - + +
234A LEU* 1.3 76.4 - - - +
236A LEU* 1.3 61.1 + - + +
238A LEU* 3.0 7.4 + - - +
239A VAL* 2.9 33.0 + - + +
291A LEU* 4.3 10.5 - - + -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TRP* 5.3 2.0 - - + -
232A LEU* 2.8 46.6 + - + +
233A LYS* 4.1 3.4 - - - +
235A ILE* 1.3 70.7 - - + +
237A ARG* 1.3 61.9 + - - +
239A VAL* 4.3 0.7 - - + -
240A GLY* 2.7 52.2 + - - +
241A THR* 4.2 12.1 - - + -
242A PRO* 4.3 9.9 - - + -
259A ILE* 5.1 2.7 - - + -
262A LEU* 3.7 30.7 - - + -
265A MET* 3.5 21.1 - - + +
291A LEU* 3.7 27.8 - - + -
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Residues in contact with ARG 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LYS 3.0 18.6 + - - +
234A LEU* 3.6 15.0 - - - +
235A ILE 3.3 0.2 - - - -
236A LEU* 1.3 79.1 - - - +
238A LEU* 1.3 57.9 + - - +
265A MET* 3.6 19.9 - - - +
266A PRO 4.1 6.4 - - - +
268A MET* 3.2 53.2 - - + +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 4.4 13.0 - - + -
223A PHE* 3.6 29.8 - - + -
234A LEU 3.4 7.5 + - - +
235A ILE 3.0 8.5 + - - +
237A ARG* 1.3 79.9 - - - +
239A VAL* 1.3 64.7 + - + +
267A LYS* 3.7 3.6 - - - +
268A MET* 2.9 35.3 + - + +
270A PHE* 3.8 35.1 - - + -
273A VAL* 3.7 37.9 - - + -
274A PHE* 5.1 2.0 - - + -
289A LEU* 4.5 6.1 - - + -
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TRP* 4.1 13.5 - - + -
223A PHE* 5.1 0.2 - - + -
235A ILE* 2.9 28.1 + - + +
236A LEU* 4.3 0.2 - - - -
238A LEU* 1.3 86.1 - - + +
240A GLY* 1.3 69.6 + - - +
267A LYS* 3.6 23.5 - - + +
270A PHE* 4.4 4.7 - - + -
289A LEU* 3.2 33.7 - - + +
291A LEU* 3.8 33.5 - - + +
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 2.7 28.7 + - - +
238A LEU 3.4 2.8 + - - -
239A VAL* 1.3 80.8 - - - +
241A THR* 1.3 66.4 - - - -
265A MET 3.3 14.1 - - - -
266A PRO 3.8 2.0 - - - -
267A LYS* 3.7 11.5 - - - +
291A LEU* 3.4 16.1 - - - +
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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