Contacts of the helix formed by residues 230 - 241 (chain F) in PDB entry 1K9A
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 ALA 230 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79F LEU* 3.6 21.8 - - + -
80F MET* 5.2 1.6 - - - -
148F ASN* 5.1 2.7 - - + -
150F MET* 4.9 2.9 - - + -
227F ASP* 3.0 27.6 + - - +
229F THR* 1.3 79.7 - - - +
231F GLN* 1.3 58.9 + - - +
232F ALA 3.2 2.5 - - - -
233F PHE* 2.8 3.3 + - + +
234F LEU* 2.8 30.8 + - + +
262F LEU* 3.4 28.5 - - + -
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Residues in contact with GLN 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PHE* 5.2 6.0 - - - -
116F TYR* 5.3 0.8 + - - -
227F ASP* 3.4 0.8 + - - +
229F THR* 2.6 39.0 + - - +
230F ALA* 1.3 76.4 - - - +
232F ALA* 1.3 58.6 + - - +
234F LEU* 3.0 9.5 + - + +
235F ALA* 2.7 37.5 + - + +
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Residues in contact with ALA 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F ILE* 3.9 17.3 - - + +
226F ASN 5.4 2.2 - - - +
227F ASP* 3.3 21.5 + - + +
231F GLN* 1.3 78.7 - - - +
233F PHE* 1.3 61.1 + - - +
235F ALA* 4.1 4.8 - - - +
236F GLU* 3.2 28.1 + - - +
334F GLY* 5.2 1.2 - - - -
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Residues in contact with PHE 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F LEU* 3.8 24.9 - - + -
183F PHE* 5.4 1.1 - + - -
224F ILE* 3.6 17.0 - - + -
227F ASP* 2.8 17.1 + - - +
230F ALA* 2.8 12.3 + - - +
232F ALA* 1.3 78.3 - - - +
234F LEU* 1.3 66.5 + - + -
236F GLU* 4.1 0.9 - - - +
237F ALA* 2.9 34.7 + - + +
254F VAL* 3.3 28.3 - - + -
255F ILE 4.2 5.4 - - - -
256F VAL* 4.5 7.4 - - + -
262F LEU* 3.7 44.9 - - + -
263F TYR 3.7 7.9 - - - -
264F ILE* 3.6 31.7 - - + +
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Residues in contact with LEU 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F ALA* 5.4 1.1 - - + -
77F LEU* 3.7 41.7 - - + +
78F SER* 4.2 0.9 - - - -
79F LEU* 3.7 37.9 - - + +
179F ALA* 3.7 12.1 - - + -
183F PHE* 3.7 28.3 - - + -
229F THR 5.5 1.6 - - - +
230F ALA* 2.8 21.0 + - + +
231F GLN* 3.7 8.3 - - + +
233F PHE* 1.3 77.0 - - + +
235F ALA* 1.3 61.8 + - - +
237F ALA* 2.8 3.0 + - - -
238F SER* 2.6 37.6 + - - -
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Residues in contact with ALA 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F ALA* 5.0 5.8 - - - +
231F GLN* 2.7 21.9 + - + +
232F ALA* 4.1 4.9 - - - +
234F LEU* 1.3 71.9 - - - +
236F GLU* 1.3 60.0 + - - +
238F SER* 2.9 19.8 + - - -
239F VAL* 3.2 20.0 + - - +
334F GLY 4.3 6.7 - - - +
337F LYS* 4.2 25.8 - - - +
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Residues in contact with GLU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F LYS* 3.4 31.0 + - - +
224F ILE* 3.7 16.8 - - + +
232F ALA 3.2 15.8 + - - +
233F PHE 4.2 1.6 - - - +
234F LEU 3.1 0.8 - - - -
235F ALA* 1.3 80.5 - - - +
237F ALA* 1.3 61.2 + - - +
239F VAL* 4.0 2.0 - - - +
240F MET* 3.0 54.1 + - + +
264F ILE* 4.3 6.4 - - + +
332F ASP* 4.6 3.8 - - - -
333F PHE 3.9 7.9 + - - -
334F GLY* 3.4 36.1 + - - +
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Residues in contact with ALA 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F PHE* 3.8 21.8 - - + -
233F PHE* 2.9 30.7 + - + +
234F LEU* 2.8 8.5 + - - +
236F GLU* 1.3 71.5 - - - +
238F SER* 1.3 65.4 + - - +
240F MET* 3.2 14.8 + - - +
241F THR* 3.2 16.6 + - - +
251F LEU* 4.2 5.2 - - + +
254F VAL* 4.7 6.1 - - + -
264F ILE* 4.4 16.1 - - + +
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Residues in contact with SER 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL* 3.0 28.1 - - - +
73F ALA* 3.1 29.7 - - - +
77F LEU* 4.9 2.2 - - - -
183F PHE* 4.0 11.3 - - - -
234F LEU 2.6 26.3 + - - -
235F ALA 2.9 12.3 + - - -
237F ALA* 1.3 73.1 - - - +
239F VAL* 1.3 63.4 + - - +
241F THR* 2.5 26.4 + - - -
242F GLN* 3.5 8.1 - - - +
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F ALA* 6.2 0.4 - - + -
235F ALA* 3.2 19.6 + - - +
236F GLU 4.0 3.6 - - - +
238F SER* 1.3 84.8 + - - +
240F MET* 1.3 58.8 + - - +
241F THR 3.0 0.2 - - - -
242F GLN* 2.8 35.6 + - - +
243F LEU* 3.4 29.0 + - + +
310F PHE* 5.5 8.1 - - + -
333F PHE* 4.3 7.4 - - + +
336F THR* 3.2 39.3 - - + +
337F LYS* 4.6 10.1 - - + -
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Residues in contact with MET 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F TRP* 5.0 0.9 - - - -
236F GLU* 3.0 61.6 + - + +
237F ALA* 3.2 7.2 + - - +
239F VAL* 1.3 81.5 - - - +
241F THR* 1.3 56.4 + - - +
242F GLN 3.0 3.9 + - - -
243F LEU* 3.6 22.2 - - + +
249F VAL* 4.5 10.1 - - - +
250F GLN* 4.5 1.4 + - - -
251F LEU* 3.8 42.3 - - + +
264F ILE* 4.6 13.9 - - + -
266F THR* 5.1 6.3 - - - -
333F PHE* 3.7 37.2 - - + -
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Residues in contact with THR 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F GLU 4.4 0.3 - - - -
70F GLY* 3.4 14.0 + - - -
71F VAL* 2.8 23.1 + - + -
183F PHE* 4.2 15.7 - - + -
188F TRP* 3.2 50.4 + - + +
237F ALA 3.2 14.8 - - - +
238F SER 2.5 17.5 + - - +
239F VAL 3.0 0.2 + - - -
240F MET* 1.3 76.4 - - - +
242F GLN* 1.3 57.3 + - - +
243F LEU 4.9 0.9 - - - -
244F ARG* 5.5 2.8 + - - -
251F LEU* 3.6 15.3 - - + -
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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