Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 1OE5
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 GLY 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ALA 4.6 0.2 + - - -
259A ASN 4.1 0.6 - - - -
260A LYS* 1.3 87.6 - - - +
262A TRP* 1.3 66.4 + - - +
263A GLU 3.2 2.9 + - - -
264A GLY* 3.2 6.8 + - - -
265A ILE* 2.8 27.4 + - - +
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Residues in contact with TRP 262 (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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151A ARG* 3.4 41.1 - - + +
152A PHE* 3.8 21.3 - + + -
155A LEU* 3.7 31.6 - - + -
248A ILE* 4.7 6.1 - - + -
249A MET* 2.9 39.1 + - - -
250A HIS 3.6 15.3 - - - -
251A PRO* 3.3 28.1 - - + -
258A ALA* 3.2 26.2 + - + +
260A LYS 3.4 3.8 - - - -
261A GLY* 1.3 74.8 - - - +
263A GLU* 1.3 72.9 + - + +
265A ILE* 3.3 6.6 + - - +
266A VAL* 2.8 57.2 + - + +
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Residues in contact with GLU 263 (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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151A ARG 4.5 2.3 - - - +
154A SER* 3.9 8.1 + - - +
155A LEU* 3.2 44.2 + - + +
158A SER* 4.1 10.5 + - - -
261A GLY* 3.2 1.3 - - - -
262A TRP* 1.3 93.6 - - + +
264A GLY* 1.4 53.0 + - - +
266A VAL* 3.1 1.9 + - - +
267A ARG* 2.7 67.2 + - - +
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Residues in contact with GLY 264 (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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261A GLY* 3.2 8.9 + - - -
263A GLU* 1.4 76.8 - - - +
265A ILE* 1.3 65.4 + - - +
267A ARG* 3.5 9.4 + - - +
268A GLY* 3.2 17.5 + - - -
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Residues in contact with ILE 265 (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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249A MET* 4.1 33.0 - - + -
257A GLN* 4.0 13.2 - - + +
260A LYS 3.9 15.3 - - - +
261A GLY 2.8 25.5 + - - +
262A TRP* 3.7 3.6 - - - +
264A GLY* 1.3 71.5 - - - -
266A VAL* 1.3 60.1 + - - +
268A GLY* 3.3 2.8 + - - -
269A GLN* 2.9 48.2 + - + +
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Residues in contact with VAL 266 (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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155A LEU* 3.7 26.2 - - + -
248A ILE* 3.8 24.5 - - + -
249A MET* 3.9 11.4 - - + +
262A TRP* 2.8 56.8 + - + +
263A GLU 4.0 2.5 - - - +
265A ILE* 1.3 71.7 - - + +
267A ARG* 1.3 61.6 + - - +
269A GLN* 3.8 17.0 - - - +
270A LEU* 2.8 35.2 + - + +
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Residues in contact with ARG 267 (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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155A LEU* 3.8 15.8 - - + +
158A SER* 3.9 21.6 + - - -
159A LEU* 3.2 34.8 - - + +
263A GLU* 2.7 49.7 + - - +
264A GLY* 3.8 8.3 - - - +
266A VAL* 1.3 76.9 - - - +
268A GLY* 1.3 56.2 + - - +
270A LEU* 3.9 8.0 - - - +
271A LEU* 3.1 30.0 + - - +
276A LEU* 4.1 12.0 - - + +
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Residues in contact with GLY 268 (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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264A GLY 3.2 11.2 + - - -
265A ILE* 3.7 3.6 - - - -
267A ARG* 1.3 75.6 - - - +
269A GLN* 1.3 64.7 + - - +
271A LEU* 3.3 14.5 + - - +
272A GLU* 3.1 34.5 + - - +
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Residues in contact with GLN 269 (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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247A GLY 4.8 4.9 + - - +
248A ILE* 3.1 22.1 - - + +
249A MET* 2.9 36.9 + - - +
265A ILE* 2.9 38.0 + - + +
266A VAL* 3.4 9.8 + - - +
268A GLY* 1.3 72.0 - - - +
270A LEU* 1.3 62.5 + - - +
272A GLU* 3.2 17.3 + - - +
273A LEU* 3.1 27.4 + - + +
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Residues in contact with LEU 270 (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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92A PHE* 3.8 26.5 - - + -
155A LEU* 4.1 3.8 - - + -
156A PHE* 3.8 24.0 - - + -
159A LEU* 3.9 18.8 - - + -
222A ILE* 4.4 4.0 - - + -
248A ILE* 4.0 13.9 - - + -
266A VAL* 2.8 38.6 + - + +
267A ARG* 3.9 4.7 - - - +
269A GLN* 1.3 73.3 - - - +
271A LEU* 1.3 56.9 + - - +
273A LEU* 3.3 2.9 + - + +
274A GLY 2.9 21.7 + - - -
275A VAL* 3.0 36.4 + - + +
276A LEU* 3.8 15.9 + - + -
279A LEU* 4.7 1.1 - - + -
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Residues in contact with LEU 271 (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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267A ARG 3.1 14.8 + - - +
268A GLY* 3.4 15.9 - - - +
270A LEU* 1.3 73.8 - - - +
272A GLU* 1.3 59.8 + - + +
274A GLY* 2.8 22.3 + - - -
276A LEU* 3.8 27.5 - - + +
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Residues in contact with GLU 272 (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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268A GLY* 3.1 22.4 + - - +
269A GLN* 3.2 20.6 + - - +
271A LEU* 1.3 77.4 - - + +
273A LEU* 1.3 63.2 + - + +
274A GLY* 3.3 0.7 + - - -
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Residues in contact with LEU 273 (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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220A LEU* 4.9 8.2 - - + +
222A ILE* 4.1 22.0 - - + -
246A LYS* 3.7 43.5 - - + +
247A GLY 3.9 20.2 - - - +
248A ILE* 4.2 10.3 - - + -
269A GLN* 3.1 16.7 + - + +
270A LEU* 3.8 8.7 - - - +
271A LEU 3.3 0.2 - - - -
272A GLU* 1.3 78.8 - - + +
274A GLY* 1.3 62.5 + - - +
275A VAL* 3.5 16.2 + - + +
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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
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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