Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 2O7R
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 PRO 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.6 23.1 - - + +
217A ALA 3.3 16.6 - - - +
218A ASN* 4.5 4.0 - - - +
219A ASP 3.3 21.2 - - - +
221A ARG 3.2 10.5 - - - +
222A LEU* 1.4 96.7 - - - +
224A THR* 1.3 68.9 + - - +
225A PHE* 3.7 27.8 - - + -
226A VAL* 3.0 17.8 + - + -
227A LEU* 3.2 7.4 + - - +
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Residues in contact with THR 224 (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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209A ARG* 3.3 45.5 - - - +
213A GLU* 4.2 5.8 + - + +
217A ALA* 3.1 37.2 + - - +
223A PRO* 1.3 72.1 - - - +
225A PHE* 1.4 58.6 + - - +
226A VAL 3.2 0.3 + - - -
227A LEU* 3.3 9.7 + - + +
228A ASP* 2.9 30.0 + - - +
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Residues in contact with PHE 225 (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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18A LEU* 4.3 24.2 - - + -
21A TYR* 3.6 33.2 - + - -
223A PRO* 3.1 26.3 + - + -
224A THR* 1.4 78.9 - - - +
226A VAL* 1.3 69.2 + - + +
228A ASP* 3.7 8.3 - - - +
229A LEU* 2.9 30.2 + - + +
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Residues in contact with VAL 226 (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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18A LEU* 4.5 7.2 - - + -
21A TYR* 3.6 27.8 - - + -
22A LEU* 3.9 23.1 - - + -
221A ARG 4.3 3.8 - - - +
222A LEU* 4.1 17.3 - - + -
223A PRO* 3.0 17.1 + - + +
225A PHE* 1.3 100.5 - - + +
227A LEU* 1.3 61.6 + - - +
229A LEU* 3.1 6.6 + - - +
230A ILE* 2.8 40.5 + - + +
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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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213A GLU* 5.1 9.4 - - + +
222A LEU* 3.6 46.2 - - + +
223A PRO 3.2 9.7 + - - +
224A THR* 3.7 9.4 - - + +
226A VAL* 1.3 78.7 - - - +
228A ASP* 1.3 65.1 + - - +
230A ILE* 3.3 12.6 + - + +
231A TRP* 3.0 39.0 + - + +
277A PRO* 4.0 22.2 - - + -
278A MET* 4.3 25.4 - - + -
369A 4PA 4.9 6.1 - - + -
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Residues in contact with ASP 228 (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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209A ARG* 2.9 43.5 + - - -
224A THR* 2.9 25.9 + - - +
225A PHE* 3.7 7.8 - - - +
227A LEU* 1.3 74.4 - - - +
229A LEU* 1.3 57.7 + - - +
231A TRP* 3.3 6.3 + - - +
232A GLU* 2.9 29.3 + - - +
241A ARG* 3.3 27.5 + - - +
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Residues in contact with LEU 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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18A LEU* 3.8 38.8 - - + -
22A LEU* 4.0 13.5 - - + -
24A ILE* 4.3 2.5 - - + -
26A LEU* 4.0 26.5 - - + -
225A PHE* 2.9 21.6 + - + +
226A VAL* 3.1 5.8 + - - +
228A ASP* 1.3 74.0 - - - +
230A ILE* 1.3 67.7 + - - +
232A GLU* 3.1 14.7 + - + +
233A LEU* 2.9 45.9 + - + +
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Residues in contact with ILE 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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22A LEU* 4.5 20.6 - - + -
93A GLY* 3.4 39.5 - - - +
94A PHE* 4.2 4.5 - - + -
95A ILE* 4.8 6.7 - - + -
222A LEU* 4.5 10.8 - - + -
226A VAL* 2.8 34.8 + - + +
227A LEU* 3.6 14.8 - - + +
229A LEU* 1.3 77.6 - - - +
231A TRP* 1.3 65.5 + - + +
233A LEU* 3.3 6.4 + - - +
234A SER* 2.7 31.5 + - - +
369A 4PA 4.1 29.4 - - + +
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Residues in contact with TRP 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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94A PHE* 3.5 32.5 - + - -
132A LEU* 4.7 1.6 - - + -
173A ASN* 3.8 7.6 - - - -
203A GLY 3.5 17.5 - - - -
204A PHE* 3.5 26.5 + - - -
205A GLY* 3.7 10.2 - - - -
227A LEU* 3.0 37.6 + - + +
228A ASP 3.9 4.0 - - - +
230A ILE* 1.3 74.2 - - + +
232A GLU* 1.3 67.1 + - - +
234A SER* 4.4 2.7 - - - +
235A LEU* 2.9 50.8 + - + +
241A ARG* 3.9 32.3 - - + -
245A TYR 4.3 1.8 - - - -
246A CYS* 3.6 35.0 - - + -
278A MET* 5.6 0.6 - - - -
369A 4PA 3.6 21.4 - - + +
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Residues in contact with GLU 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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131A ARG* 2.9 26.4 + - - +
228A ASP 2.9 14.3 + - - +
229A LEU* 3.1 21.0 + - + +
231A TRP* 1.3 79.3 - - - +
233A LEU* 1.3 61.7 + - + +
235A LEU* 4.1 1.6 - - - +
236A PRO 5.6 0.2 - - - +
237A MET* 6.0 1.6 - - - -
238A GLY 5.7 3.1 + - - -
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Residues in contact with LEU 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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24A ILE* 4.2 13.7 - - + -
26A LEU* 4.5 2.5 - - + -
30A ARG 4.8 8.7 - - - +
32A ILE* 3.9 31.2 - - + -
95A ILE* 4.0 26.5 - - + -
127A ALA* 3.5 1.7 - - - +
128A PRO* 3.4 36.0 - - + +
131A ARG* 3.4 17.9 + - - +
229A LEU* 2.9 45.1 + - + +
230A ILE* 3.9 3.8 - - - +
232A GLU* 1.3 80.7 - - + +
234A SER* 1.3 59.7 + - - +
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Residues in contact with SER 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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93A GLY 3.3 19.6 + - - -
94A PHE* 3.3 30.4 - - - +
95A ILE* 4.0 4.3 - - - +
127A ALA* 3.8 5.6 - - - -
131A ARG* 3.5 1.4 - - - +
132A LEU* 2.8 39.1 + - - +
230A ILE 2.7 21.8 + - - -
231A TRP* 3.2 4.7 + - - -
233A LEU* 1.3 79.0 - - - +
235A LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 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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131A ARG* 2.8 29.1 + - - -
132A LEU* 4.3 6.1 - - + -
231A TRP* 2.9 42.9 + - + +
232A GLU* 4.1 1.7 - - - +
234A SER* 1.3 78.5 - - - +
236A PRO* 1.3 78.0 - - + +
239A ALA* 4.2 7.2 - - + +
240A ASP* 3.5 30.7 - - - +
241A ARG* 4.1 1.6 - - + -
243A HIS* 4.4 5.4 - - + -
245A TYR* 3.8 30.1 - - + -
246A CYS* 3.9 24.5 - - + +
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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