Contacts of the helix formed by residues 229 - 250 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ILE* 3.5 26.8 - - + +
217I ILE* 4.1 7.7 - - + +
220I ARG* 4.5 3.8 - - + -
221I TYR* 4.1 18.6 - - + +
225I GLY 3.6 7.8 + - - +
226I LEU* 2.6 15.8 + - - +
228I ALA* 1.3 73.2 - - - +
230I MET* 1.3 66.6 + - - +
231I PRO* 3.2 3.8 - - - -
232I VAL* 2.9 10.9 + - - +
233I ALA* 2.9 20.9 + - - +
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Residues in contact with MET 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ILE* 4.6 3.3 - - + +
108H VAL* 3.4 41.3 - - + -
27I THR* 4.4 13.9 + - - +
30I LEU* 4.2 15.0 - - + -
31I GLN* 3.6 19.7 - - - +
226I LEU* 3.1 36.4 + - + +
227I SER* 4.2 12.8 - - - +
229I ALA* 1.3 74.6 - - - +
231I PRO* 1.3 72.3 - - + +
233I ALA* 2.9 10.9 + - - +
234I ALA* 2.8 24.1 + - - +
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Residues in contact with PRO 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I GLN* 3.5 23.6 - - - +
37I GLU* 4.3 23.1 - - + +
38I PHE* 4.3 6.2 - - + -
41I ALA* 3.5 23.1 - - + -
227I SER 3.6 17.5 - - - +
228I ALA* 4.1 4.7 - - - +
229I ALA 3.4 5.2 - - - +
230I MET* 1.3 95.3 - - + +
232I VAL* 1.3 63.8 + - + +
234I ALA* 3.2 2.3 + - - +
235I ILE* 2.8 29.4 + - - +
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Residues in contact with VAL 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ALA* 4.8 6.5 - - + -
47I VAL* 4.3 19.3 - - + -
216I LEU* 3.7 23.3 - - + -
217I ILE* 3.9 19.5 - - + -
220I ARG* 3.4 41.3 - - - +
228I ALA 4.6 4.0 - - - +
229I ALA* 2.9 9.5 + - - +
231I PRO* 1.3 75.9 - - + +
233I ALA* 1.3 63.8 + - - +
235I ILE* 3.3 9.2 + - + +
236I LEU* 2.9 28.8 + - + +
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Residues in contact with ALA 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H VAL* 3.7 19.0 - - + +
104H ILE* 4.0 22.7 - - + -
105H ALA* 6.3 0.2 - - + -
27I THR* 5.0 5.8 - - - +
217I ILE* 3.7 15.8 - - + +
229I ALA 2.9 11.6 + - - +
230I MET* 3.1 11.0 - - - +
232I VAL* 1.3 75.7 - - - +
234I ALA* 1.3 51.6 + - - +
236I LEU* 2.7 25.1 + - - +
237I ILE* 2.7 21.5 + - - +
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Residues in contact with ALA 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I THR* 4.3 4.1 + - - +
28I VAL* 4.2 17.7 - - + -
31I GLN* 3.3 33.4 - - + -
38I PHE* 4.1 7.2 - - + -
230I MET 2.8 10.6 + - - +
231I PRO 3.6 5.2 - - - +
233I ALA* 1.3 73.1 - - - +
235I ILE* 1.3 64.3 + - - +
237I ILE* 3.5 13.4 - - - +
238I LEU* 2.9 30.3 + - - +
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Residues in contact with ILE 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I PHE* 3.9 20.0 - - + +
41I ALA* 3.4 22.2 - - + +
42I ALA* 3.2 37.2 - - + +
47I VAL* 4.7 16.6 - - + -
48I TRP* 4.5 24.2 - - + -
231I PRO 2.8 15.6 + - - +
232I VAL* 3.5 11.9 - - - +
233I ALA 3.1 0.2 - - - -
234I ALA* 1.3 75.0 - - - +
236I LEU* 1.3 56.7 + - + +
238I LEU* 3.8 4.9 - - - +
239I LEU* 2.6 45.1 + - + +
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Residues in contact with LEU 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H PRO* 4.3 13.0 - - + +
101H VAL* 4.1 14.4 - - + -
47I VAL* 5.5 1.1 - - + -
51I VAL* 3.8 29.6 - - + -
55I TYR* 4.9 5.5 + - + +
213I ALA* 3.3 33.7 - - + +
217I ILE* 3.3 26.5 - - + -
232I VAL* 2.9 19.1 + - + +
233I ALA 2.7 13.7 + - - +
235I ILE* 1.3 70.9 - - + +
237I ILE* 1.3 68.3 + - - +
239I LEU* 3.5 11.5 - - + +
240I SER* 3.0 24.3 + - - -
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Residues in contact with ILE 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ILE* 4.7 14.4 - - + +
98H PRO* 6.1 0.2 - - - -
101H VAL* 3.6 23.8 - - + -
105H ALA* 4.9 2.2 - - + -
24I VAL* 3.6 44.2 - - + +
27I THR* 3.4 26.7 - - + +
28I VAL* 3.8 14.1 - - + -
233I ALA 2.7 18.5 + - - +
234I ALA* 3.2 10.1 + - - +
236I LEU* 1.3 70.4 - - - +
238I LEU* 1.3 55.9 + - - +
240I SER* 2.6 29.2 + - - -
241I LEU* 2.9 26.7 + - + +
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Residues in contact with LEU 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I VAL* 3.4 34.1 - - + -
38I PHE* 3.7 31.9 - - + -
234I ALA 2.9 21.7 + - - +
235I ILE* 3.8 3.1 - - - +
237I ILE* 1.3 75.1 - - - +
239I LEU* 1.3 64.1 + - - +
240I SER 2.9 1.2 + - - -
241I LEU* 3.1 19.6 + - + +
242I ALA* 3.0 25.4 + - - +
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Residues in contact with LEU 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I TRP* 3.8 22.7 - - + -
51I VAL* 3.4 43.1 - - + -
55I TYR* 3.2 29.8 - - + +
235I ILE* 2.6 25.5 + - + +
236I LEU* 3.5 15.3 - - + +
238I LEU* 1.3 73.2 - - - +
240I SER* 1.3 58.2 + - - +
242I ALA* 4.0 5.0 - - + +
243I VAL* 3.1 24.9 + - + +
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Residues in contact with SER 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H VAL* 3.1 41.1 + - - +
97H ILE* 5.6 2.2 - - - -
98H PRO* 4.8 3.3 - - - +
55I TYR* 3.7 12.8 + - - -
197I ILE* 5.0 4.9 - - - +
236I LEU 3.0 12.7 + - - -
237I ILE* 2.6 18.1 + - - -
239I LEU* 1.3 70.3 - - - +
241I LEU* 1.3 66.9 + - - -
242I ALA 3.0 2.5 + - - -
243I VAL* 3.0 2.1 + - - +
244I PHE* 2.9 34.2 + - - -
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Residues in contact with LEU 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU* 3.7 30.1 - - + -
96H VAL* 6.0 3.8 - - + -
97H ILE* 6.2 1.1 - - + -
24I VAL* 6.0 1.1 - - + -
28I VAL* 6.3 0.2 - - + -
237I ILE* 2.9 30.6 + - + +
238I LEU* 3.7 19.1 - - + +
240I SER* 1.3 75.4 - - - +
242I ALA* 1.3 58.4 + - - +
244I PHE* 5.1 2.2 - - - -
245I VAL* 2.8 43.9 + - + +
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Residues in contact with ALA 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I LEU 3.0 15.0 + - - +
239I LEU* 4.0 5.8 - - + +
240I SER 3.0 0.8 + - - -
241I LEU* 1.3 77.6 - - - +
243I VAL* 1.3 60.6 + - + +
244I PHE 3.0 0.2 + - - -
245I VAL* 5.0 1.8 - - - -
246I ALA* 2.8 36.3 + - - +
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Residues in contact with VAL 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I TYR* 3.9 21.1 - - + +
193I TRP* 3.5 34.8 - - + -
239I LEU* 3.1 24.2 + - + +
240I SER* 3.0 4.3 + - - +
242I ALA* 1.3 80.2 - - + +
244I PHE* 1.3 65.1 + - + +
246I ALA* 3.6 5.5 - - - +
247I LEU* 3.2 32.2 + - + +
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Residues in contact with PHE 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H VAL* 3.2 42.0 - - + -
55I TYR* 5.6 0.2 - - - -
190I ILE* 3.9 27.8 - - + -
193I TRP* 3.6 32.5 - + - -
194I ALA* 3.5 35.0 - - + -
197I ILE* 4.9 5.4 - - + -
240I SER* 2.9 21.6 + - - +
241I LEU* 4.3 2.0 - - - +
243I VAL* 1.3 80.1 - - + +
245I VAL* 1.3 67.2 + - + +
246I ALA 2.9 1.3 - - - -
247I LEU* 3.0 8.3 + - + +
248I ARG* 2.8 26.4 + - + +
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Residues in contact with VAL 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I LEU* 2.8 32.2 + - + +
242I ALA* 4.2 1.3 - - - +
244I PHE* 1.3 73.4 - - + +
246I ALA* 1.3 62.3 + - - +
248I ARG* 3.3 11.1 + - + +
249I ILE* 2.9 42.7 + - + +
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Residues in contact with ALA 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I ALA 2.8 21.2 + - - +
243I VAL* 3.6 8.1 - - - +
245I VAL* 1.3 78.7 - - - +
247I LEU* 1.3 63.6 + - + +
249I ILE* 3.0 14.4 + - - +
250I ILE* 2.9 30.8 + - + +
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Residues in contact with LEU 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I ILE* 3.4 48.5 - - + -
193I TRP* 5.1 6.5 - - + -
243I VAL* 3.2 24.6 + - + +
244I PHE* 3.0 17.8 + - + +
246I ALA* 1.3 81.6 - - + +
248I ARG* 1.3 61.8 + - + +
250I ILE* 3.1 22.8 + - + +
251I VAL* 3.4 22.1 - - + +
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Residues in contact with ARG 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H SER* 4.0 20.0 + - - +
88H GLU* 4.5 10.3 + - - +
89H GLY* 4.0 14.0 - - - +
92H ASP* 3.4 27.3 + - - +
244I PHE* 2.8 17.8 + - + +
245I VAL* 3.6 14.1 - - + +
247I LEU* 1.3 68.5 - - - +
249I ILE* 1.3 60.1 + - + +
250I ILE 3.0 4.9 - - - -
251I VAL* 3.1 5.3 + - - +
252I GLY* 2.8 32.1 + - - +
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Residues in contact with ILE 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I VAL* 2.9 36.8 + - + +
246I ALA* 3.0 6.9 + - - +
248I ARG* 1.3 78.6 - - + +
250I ILE* 1.3 58.6 + - + +
251I VAL 3.3 2.8 + - - -
252I GLY 4.4 9.1 + - - +
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Residues in contact with ILE 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I ALA* 2.9 28.7 - - + +
247I LEU* 3.6 19.3 - - + +
248I ARG 3.0 1.6 - - - -
249I ILE* 1.3 83.6 - - + +
251I VAL* 1.3 69.2 + - + +
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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