Contacts of the helix formed by residues 229 - 250 (chain H) in PDB entry 2ONK
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 229 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H ILE* 4.2 7.7 - - + +
220H ARG* 4.5 4.7 - - + -
221H TYR* 4.1 19.3 - - + +
225H GLY 4.0 7.9 - - - +
226H LEU* 2.6 16.1 + - - +
228H ALA* 1.3 74.2 - - - +
230H MET* 1.3 65.4 + - - +
231H PRO* 3.2 2.9 - - - -
232H VAL* 2.9 10.6 + - - +
233H ALA* 2.9 21.4 + - - +
104I ILE* 3.6 25.4 - - + +
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Residues in contact with MET 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H THR* 4.3 15.6 + - - +
30H LEU* 4.1 16.4 - - + -
31H GLN* 3.6 18.4 - - - +
226H LEU* 3.1 36.4 + - + +
227H SER* 4.2 13.0 - - - +
229H ALA* 1.3 74.5 - - - +
231H PRO* 1.3 72.3 - - + +
233H ALA* 2.9 9.9 + - - +
234H ALA* 2.8 24.1 + - - +
104I ILE* 4.6 3.7 - - + +
108I VAL* 3.3 41.3 - - + -
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Residues in contact with PRO 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H GLN* 3.4 26.9 - - - +
37H GLU* 4.3 23.1 - - + +
38H PHE* 4.3 6.4 - - + +
41H ALA* 3.7 21.1 - - + -
227H SER 3.6 17.3 - - - +
228H ALA* 4.1 4.3 - - - +
229H ALA 3.4 5.8 - - - +
230H MET* 1.3 93.9 - - + +
232H VAL* 1.3 60.0 + - + +
234H ALA* 3.2 2.8 + - - +
235H ILE* 2.9 34.4 + - - +
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Residues in contact with VAL 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ALA* 4.5 6.5 - - + +
47H VAL* 4.4 18.4 - - + -
216H LEU* 3.7 23.3 - - + +
217H ILE* 3.9 19.1 - - + -
220H ARG* 3.4 41.1 - - - +
228H ALA 4.6 3.4 - - - +
229H ALA* 2.9 12.2 + - - +
231H PRO* 1.3 72.9 - - + +
233H ALA* 1.3 64.3 + - - +
235H ILE* 3.3 9.3 + - + +
236H LEU* 2.9 30.3 + - + +
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Residues in contact with ALA 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H THR* 5.0 5.4 - - + +
217H ILE* 3.7 16.3 - - + +
229H ALA 2.9 11.6 + - - +
230H MET* 3.1 9.4 - - - +
232H VAL* 1.3 75.9 - - - +
234H ALA* 1.3 52.4 + - - +
236H LEU* 2.7 26.0 + - - +
237H ILE* 2.7 21.5 + - - +
101I VAL* 3.8 18.5 - - + +
104I ILE* 3.9 25.1 - - + -
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Residues in contact with ALA 234 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H THR* 4.2 7.5 + - - +
28H VAL* 4.1 18.2 - - + -
31H GLN* 3.4 33.9 - - + -
38H PHE* 4.2 5.8 - - + -
230H MET 2.8 10.4 + - - +
231H PRO 3.6 4.9 - - - +
233H ALA* 1.3 71.8 - - - +
235H ILE* 1.3 63.6 + - - +
237H ILE* 3.5 10.2 - - - +
238H LEU* 2.9 31.8 + - - +
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Residues in contact with ILE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 3.7 22.2 - - + +
41H ALA* 3.4 22.0 - - + +
42H ALA* 3.2 36.6 - - + +
47H VAL* 4.8 14.8 - - + -
48H TRP* 4.6 24.0 - - + -
231H PRO 2.9 16.5 + - - +
232H VAL* 3.5 11.9 - - + +
234H ALA* 1.3 75.5 - - - +
236H LEU* 1.3 56.4 + - + +
238H LEU* 3.8 3.6 - - - +
239H LEU* 2.6 45.9 + - + +
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Residues in contact with LEU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 5.4 0.7 - - + -
51H VAL* 3.8 29.6 - - + -
55H TYR* 4.9 5.3 + - + +
213H ALA* 3.3 32.8 - - + +
217H ILE* 3.4 28.5 - - + -
232H VAL* 2.9 19.0 + - + +
233H ALA 2.7 14.4 + - - +
235H ILE* 1.3 71.9 - - + +
237H ILE* 1.3 67.0 + - - +
239H LEU* 3.5 12.2 - - + +
240H SER* 3.0 23.9 + - - -
98I PRO* 4.5 12.2 - - + +
101I VAL* 4.1 14.6 - - + -
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Residues in contact with ILE 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 3.5 44.0 - - + +
27H THR* 3.4 26.0 - - - +
28H VAL* 3.9 13.2 - - + -
233H ALA 2.7 13.5 + - - +
234H ALA* 3.5 8.7 - - - +
236H LEU* 1.3 70.9 - - - +
238H LEU* 1.3 58.0 + - - +
240H SER* 2.6 28.8 + - - -
241H LEU* 2.9 26.2 + - + +
97I ILE* 4.6 14.3 - - + +
98I PRO* 6.0 0.2 - - - -
101I VAL* 3.4 30.5 - - + +
105I ALA* 4.8 3.8 - - + -
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Residues in contact with LEU 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 3.3 36.6 - - + -
38H PHE* 3.8 28.7 - - + -
234H ALA 2.9 21.9 + - - +
235H ILE* 3.8 2.9 - - - +
237H ILE* 1.3 74.3 - - + +
239H LEU* 1.3 64.8 + - - +
240H SER 2.9 1.2 + - - -
241H LEU* 3.1 20.1 + - + +
242H ALA* 3.0 24.4 + - - +
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Residues in contact with LEU 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H TRP* 3.8 24.5 - - + -
51H VAL* 3.5 41.3 - - + -
55H TYR* 3.2 27.6 - - + +
235H ILE* 2.6 27.0 + - + +
236H LEU* 3.5 16.8 - - + +
238H LEU* 1.3 74.1 - - - +
240H SER* 1.3 56.8 + - - +
242H ALA* 4.0 4.1 - - - +
243H VAL* 3.1 25.1 + - + +
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Residues in contact with SER 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H TYR* 3.7 12.5 + - - -
197H ILE* 4.7 4.9 - - - +
236H LEU 3.0 11.7 + - - -
237H ILE* 2.6 17.2 + - - -
239H LEU* 1.3 69.8 - - - +
241H LEU* 1.3 67.9 + - - -
242H ALA 3.0 2.1 + - - -
243H VAL* 3.0 2.5 + - - -
244H PHE* 2.9 33.6 + - - -
96I VAL* 3.1 40.4 + - - +
97I ILE* 5.5 2.2 - - - -
98I PRO* 4.6 4.3 - - - +
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Residues in contact with LEU 241 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 5.8 1.3 - - + -
28H VAL* 6.3 0.2 - - + -
237H ILE* 2.9 29.9 + - + +
238H LEU* 3.1 19.0 + - + +
240H SER* 1.3 76.6 - - - +
242H ALA* 1.3 58.9 + - - +
244H PHE* 5.1 2.2 - - - -
245H VAL* 2.8 44.3 + - + +
93I LEU* 3.6 31.2 - - + -
96I VAL* 5.3 5.4 - - + -
97I ILE* 5.9 2.0 - - + -
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Residues in contact with ALA 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H LEU 3.0 15.4 + - - +
239H LEU* 4.0 6.1 - - - +
240H SER 3.0 0.4 + - - -
241H LEU* 1.3 76.1 - - - +
243H VAL* 1.3 58.9 + - + +
244H PHE 3.0 0.2 + - - -
245H VAL* 4.2 2.2 - - - +
246H ALA* 2.8 36.4 + - - +
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Residues in contact with VAL 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H TYR* 3.8 20.9 - - + +
193H TRP* 3.3 36.3 - - + -
239H LEU* 3.1 24.0 + - + +
240H SER* 3.0 4.1 + - - +
242H ALA* 1.3 80.8 - - + +
244H PHE* 1.3 62.3 + - + +
246H ALA* 3.6 5.7 - - - +
247H LEU* 3.2 31.4 + - + +
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Residues in contact with PHE 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H TYR* 5.5 0.2 - - - -
190H ILE* 4.0 25.4 - - + -
193H TRP* 3.1 44.2 - + - -
194H ALA* 3.6 32.8 - - + -
197H ILE* 4.4 7.9 - - + -
240H SER* 2.9 20.1 + - - +
241H LEU* 4.3 1.8 - - - +
243H VAL* 1.3 78.5 - - + +
245H VAL* 1.3 67.0 + - + +
246H ALA 2.9 1.1 - - - -
247H LEU* 3.0 8.7 + - + +
248H ARG* 2.8 26.4 + - + +
96I VAL* 3.1 42.6 - - + -
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Residues in contact with VAL 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H LEU* 2.8 32.0 + - + +
242H ALA* 4.2 2.0 - - - +
244H PHE* 1.3 72.1 - - + +
246H ALA* 1.3 63.7 + - - +
248H ARG* 3.3 10.8 + - + +
249H ILE* 2.9 42.6 + - + +
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Residues in contact with ALA 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ALA 2.8 21.0 + - - +
243H VAL* 3.6 8.3 - - - +
245H VAL* 1.3 78.1 - - - +
247H LEU* 1.3 61.8 - - + +
249H ILE* 3.1 14.5 + - - +
250H ILE* 2.9 31.9 - - + +
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Residues in contact with LEU 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H ILE* 3.7 45.1 - - + -
193H TRP* 4.9 7.0 - - + -
243H VAL* 3.2 25.7 + - + +
244H PHE* 3.0 18.7 + - + +
246H ALA* 1.3 81.1 - - + +
248H ARG* 1.3 60.3 + - - +
250H ILE* 3.1 23.4 + - + +
251H VAL* 3.4 22.9 - - + +
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Residues in contact with ARG 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H ILE* 6.0 0.4 - - + -
244H PHE 2.8 17.6 + - - +
245H VAL* 3.6 14.4 - - + +
246H ALA 3.2 0.2 - - - -
247H LEU* 1.3 68.6 - - - +
249H ILE* 1.3 60.1 + - + +
250H ILE 3.0 4.9 - - - -
251H VAL* 3.1 5.0 + - - +
252H GLY* 2.8 31.9 + - - -
85I SER 4.4 7.3 + - - -
88I GLU* 4.7 7.7 + - - +
89I GLY* 4.1 21.9 - - - +
92I ASP* 3.2 30.1 + - - +
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Residues in contact with ILE 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H VAL* 2.9 36.6 + - + +
246H ALA* 3.1 7.2 + - - +
248H ARG* 1.3 75.9 - - + +
250H ILE* 1.3 60.5 + - + +
251H VAL 3.3 2.5 + - - -
252H GLY 4.4 9.4 + - - +
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Residues in contact with ILE 250 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H ALA* 2.9 30.5 + - + +
247H LEU* 3.1 18.4 + - + +
248H ARG 3.0 1.0 - - - -
249H ILE* 1.3 83.8 - - + +
251H VAL* 1.3 68.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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