Contacts of the helix formed by residues 268 - 278 (chain A) in PDB entry 1OZN
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 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A VAL 3.6 17.7 - - - +
264A CYS* 3.8 12.6 - - + -
265A ASP 3.0 12.2 + - - +
267A ARG* 1.3 78.2 - - - +
269A ARG* 1.3 58.9 + - - +
270A PRO 3.4 1.8 - - - -
271A LEU* 3.4 8.7 + - + +
272A TRP* 2.8 30.5 + - - +
298A LEU* 4.1 22.2 - - + +
306A LEU* 4.2 3.6 - - + -
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Residues in contact with ARG 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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3A ACY 3.8 13.3 + - - -
266A CYS 3.0 16.4 + - - +
268A ALA* 1.3 77.9 - - - +
270A PRO* 1.3 69.4 - - + +
272A TRP* 3.3 7.0 + - + +
273A ALA* 3.0 22.3 + - - +
303A ALA* 3.2 31.5 + - + +
304A ASN* 5.1 1.8 - - - +
306A LEU* 2.8 45.2 + - + +
307A GLN 2.8 20.5 + - - -
308A GLY* 3.6 5.7 - - - -
309A CYS* 4.0 16.2 - - - +
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Residues in contact with PRO 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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241A LEU 5.9 0.7 - - - +
243A THR* 3.4 27.0 - - + +
266A CYS 3.8 5.2 - - - +
267A ARG* 3.5 17.0 - - - +
269A ARG* 1.3 93.8 - - + +
271A LEU* 1.3 62.5 + - - +
273A ALA* 3.1 8.2 + - + +
274A TRP* 2.9 18.7 + - - +
309A CYS* 6.0 0.7 - - - -
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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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240A ALA* 6.1 0.2 - - - -
241A LEU* 4.5 22.2 + - + +
243A THR* 3.5 12.7 - - + +
246A LEU* 4.1 26.5 - - + -
257A LEU* 4.6 7.4 - - + -
262A TRP* 4.0 34.3 - - + -
267A ARG 4.9 2.2 + - - +
268A ALA* 3.4 11.3 + - - +
269A ARG 3.4 0.4 - - - -
270A PRO* 1.3 80.6 - - - +
272A TRP* 1.3 63.2 + - - +
274A TRP* 3.2 4.6 + - + +
275A LEU* 2.9 39.4 + - + +
285A VAL* 4.4 9.4 - - + -
298A LEU* 4.1 14.8 - - + -
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Residues in contact with TRP 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 ALA 2.8 19.6 + - - +
269A ARG* 3.5 7.6 - - + +
270A PRO 3.2 0.2 - - - -
271A LEU* 1.3 78.7 - - - +
273A ALA* 1.3 90.4 + - + +
275A LEU* 3.3 3.7 + - - +
276A GLN* 3.0 62.2 + - + +
298A LEU* 3.3 40.1 + - + +
301A LEU* 2.8 28.2 + - + -
302A ALA* 4.3 1.6 - - - -
303A ALA* 3.4 40.6 - - + +
306A LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 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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269A ARG 3.0 13.7 + - - +
270A PRO* 3.1 10.5 + - + +
272A TRP* 1.3 92.5 - - + +
274A TRP* 1.3 65.5 + - - +
276A GLN* 3.2 15.6 + - - +
277A LYS* 3.2 12.3 + - - +
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Residues in contact with TRP 274 (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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243A THR* 3.8 23.1 - - + -
246A LEU* 3.8 50.5 + - + +
247A ALA* 4.8 4.7 - - + +
249A LEU 6.1 0.9 - - - -
252A LEU* 4.1 10.8 - - + -
255A LEU* 3.7 31.2 - - + -
270A PRO 2.9 16.1 + - - +
271A LEU* 3.7 5.6 - - + +
273A ALA* 1.3 76.5 - - - +
275A LEU* 1.3 77.1 + - + +
277A LYS* 3.1 17.8 + - + +
278A PHE* 3.0 66.6 + + + -
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Residues in contact with LEU 275 (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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255A LEU* 4.9 0.2 - - + -
257A LEU* 4.8 8.1 - - + -
271A LEU* 2.9 35.3 + - + +
272A TRP* 3.6 5.4 - - - +
274A TRP* 1.3 99.0 - - + +
276A GLN* 1.3 67.4 + - - +
277A LYS 3.5 0.2 + - - -
278A PHE* 3.7 15.0 + - + +
282A SER* 4.4 12.6 - - - +
285A VAL* 3.9 21.3 - - + -
298A LEU* 4.0 17.5 - - + -
299A LYS* 3.7 42.2 - - + +
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Residues in contact with GLN 276 (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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272A TRP* 3.0 67.4 + - + +
273A ALA* 3.4 9.9 - - - +
274A TRP 3.1 0.2 - - - -
275A LEU* 1.3 83.1 - - - +
277A LYS* 1.3 58.3 + - - +
278A PHE 4.6 2.4 - - - +
299A LYS* 3.4 26.0 + - - +
301A LEU 5.2 0.9 - - - +
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Residues in contact with LYS 277 (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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273A ALA 3.2 7.8 + - - +
274A TRP* 3.1 20.3 + - + +
276A GLN* 1.3 80.4 - - - +
278A PHE* 1.3 62.8 + - - +
279A ARG* 3.3 16.9 + - - +
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Residues in contact with PHE 278 (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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252A LEU* 3.3 50.9 - - + -
253A GLN 4.2 3.4 - - - -
255A LEU* 4.3 6.3 - - + -
274A TRP* 3.0 45.9 + + + +
275A LEU* 4.0 13.0 - - + +
276A GLN 3.5 2.9 - - - +
277A LYS* 1.3 75.3 - - - +
279A ARG* 1.3 63.0 + - - +
280A GLY* 3.4 39.4 + - - +
281A SER 3.5 18.6 - - - -
282A SER* 3.9 17.5 - - - -
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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