Contacts of the helix formed by residues 226 - 238 (chain A) in PDB entry 3ORY
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 THR 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A LEU* 3.7 8.3 - - - +
225A ILE* 1.3 76.2 - - - +
227A LEU* 1.3 65.1 + - - +
228A GLU* 3.5 10.6 + - - +
229A ASN* 3.0 35.8 + - - +
230A LEU 3.0 17.0 + - - -
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Residues in contact with LEU 227 (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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181A LEU 3.9 21.1 - - - +
182A LEU 4.0 12.1 - - - +
183A PHE 6.0 0.2 - - - -
184A GLY* 4.9 11.0 - - - +
216A LEU* 4.3 20.6 - - + -
220A LEU* 3.9 20.0 - - + +
226A THR* 1.3 73.2 - - - +
228A GLU* 1.3 57.6 + - + +
230A LEU* 3.1 9.5 + - + +
231A ILE* 2.9 37.7 + - + +
288A LEU* 4.0 22.2 - - + -
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 3.2 8.8 + - - +
227A LEU* 1.3 78.1 - - - +
229A ASN* 1.3 57.5 + - - +
231A ILE* 3.3 7.3 + - - +
232A ASP* 2.9 34.9 + - - +
284A LYS* 2.8 43.4 + - + +
285A LYS* 5.9 1.2 + - - -
288A LEU* 3.7 29.1 - - + +
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Residues in contact with ASN 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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224A GLY 4.8 1.4 + - - -
225A ILE* 3.4 24.5 - - + +
226A THR* 3.0 48.5 + - - +
228A GLU* 1.3 77.7 - - - +
230A LEU* 1.3 57.3 + - - +
232A ASP* 3.2 5.7 + - - +
233A ILE* 2.9 32.5 + - - +
258A VAL* 3.7 28.1 + - + +
259A LYS* 5.5 3.2 - - - +
262A GLY* 4.4 15.3 - - - +
263A GLY* 4.5 1.7 + - - -
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Residues in contact with LEU 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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5A LEU* 3.9 23.7 - - + +
8A ILE* 5.3 0.9 - - + -
181A LEU* 4.3 10.1 - - + +
182A LEU* 3.7 23.0 - - + +
216A LEU* 3.8 28.5 - - + -
219A LEU* 4.4 17.5 - - + -
220A LEU* 3.8 16.8 - - + -
223A LEU* 4.9 5.2 - - + -
225A ILE* 4.0 19.0 - - + +
226A THR 3.0 6.1 + - - -
227A LEU* 3.1 11.9 + - + +
229A ASN* 1.3 72.2 - - - +
231A ILE* 1.3 67.1 + - - +
233A ILE* 3.2 14.6 + - + +
234A GLY 3.2 15.8 + - - -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.5 37.3 - - + +
227A LEU* 2.9 21.5 + - + +
228A GLU* 3.6 9.2 - - - +
230A LEU* 1.3 75.1 - - - +
232A ASP* 1.3 64.1 + - - +
234A GLY* 3.0 12.3 + - - -
235A ILE* 3.0 20.0 + - + +
239A THR* 5.7 0.2 - - - +
284A LYS* 3.8 24.0 - - + +
287A PHE* 3.7 33.9 - - + -
288A LEU* 3.7 35.2 - - + +
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Residues in contact with ASP 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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228A GLU* 2.9 17.2 + - - +
229A ASN* 3.2 10.8 + - - +
231A ILE* 1.3 76.0 - - - +
233A ILE* 1.3 62.3 + - - +
235A ILE* 3.2 12.0 + - - +
236A LEU* 3.0 27.4 + - - +
258A VAL* 4.0 10.8 - - + -
263A GLY* 3.6 6.2 - - - -
264A ILE* 3.5 38.1 + - + +
280A VAL 4.9 0.3 - - - +
284A LYS* 3.6 14.1 - - - +
356A PO4 2.4 32.0 + - - -
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Residues in contact with ILE 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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5A LEU* 4.0 24.5 - - + -
8A ILE* 4.3 13.5 - - + -
225A ILE* 3.9 16.6 - - + -
229A ASN 2.9 19.5 + - - +
230A LEU* 3.2 11.9 + - + +
232A ASP* 1.3 74.7 - - - +
234A GLY* 1.3 63.3 + - - +
236A LEU* 3.2 4.7 + - - +
237A LEU* 3.1 25.2 + - + +
251A PRO 4.6 1.3 - - - +
254A ALA* 3.9 18.8 - - + +
255A LEU* 3.7 44.4 - - + +
258A VAL* 4.1 15.9 - - + -
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Residues in contact with GLY 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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3A VAL* 4.0 25.1 - - - +
5A LEU* 5.3 0.6 - - - +
182A LEU* 4.1 12.3 - - - -
230A LEU 3.2 6.7 + - - -
231A ILE 3.0 8.4 + - - -
233A ILE* 1.3 77.6 - - - +
235A ILE* 1.3 49.9 + - - +
237A LEU* 3.2 3.9 + - - +
238A GLY* 2.8 37.6 + - - +
239A THR* 3.8 6.9 - - - +
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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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231A ILE* 3.0 18.3 + - + +
232A ASP* 3.2 22.0 + - - +
234A GLY* 1.3 72.1 - - - +
236A LEU* 1.3 66.5 + - - +
238A GLY 3.3 3.8 + - - -
239A THR* 4.0 11.0 - - + -
242A ASN* 2.8 37.5 + - - +
246A PHE* 3.8 3.6 - - + -
264A ILE* 3.8 15.3 - - + -
280A VAL* 3.6 33.0 - - + +
283A ILE* 3.7 21.1 - - + -
284A LYS* 3.5 34.8 - - - +
287A PHE* 5.3 0.7 - - + -
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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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232A ASP 3.0 14.5 + - - +
233A ILE 3.2 7.6 + - - +
235A ILE* 1.3 75.7 - - - +
237A LEU* 1.3 60.8 + - - +
246A PHE* 3.0 53.3 + - + +
249A ILE* 4.4 10.0 - - + +
254A ALA* 4.0 26.5 - - + +
257A LEU* 4.6 7.4 - - + -
258A VAL* 3.8 26.5 - - + -
264A ILE* 4.0 19.1 - - + -
267A ILE* 4.1 14.1 - - + -
272A LEU* 3.8 22.9 - - + -
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Residues in contact with LEU 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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3A VAL* 4.2 10.1 - - + -
4A ASP 3.9 14.6 - - - +
5A LEU* 3.6 31.2 - - + -
93A ARG* 3.1 25.8 + - - +
97A ARG* 5.5 0.2 + - - -
233A ILE* 3.1 15.3 + - + +
234A GLY* 3.6 6.1 - - - +
236A LEU* 1.3 78.9 - - - +
238A GLY* 1.3 57.0 + - - +
244A ASP 4.3 2.3 - - - +
245A GLY* 3.7 7.4 + - - -
249A ILE 3.5 23.3 - - - +
250A GLY* 3.5 23.6 - - - +
251A PRO* 3.6 13.2 - - + -
254A ALA* 4.1 6.3 - - + -
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Residues in contact with GLY 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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3A VAL* 3.9 10.4 - - - +
93A ARG* 3.2 30.5 + - - -
234A GLY 2.8 13.7 + - - +
235A ILE 3.3 5.5 + - - -
237A LEU* 1.3 75.1 - - - +
239A THR* 1.3 64.4 + - - -
242A ASN 3.3 16.2 - - - -
245A GLY* 3.6 7.0 - - - -
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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