Contacts of the helix formed by residues 289 - 303 (chain A) in PDB entry 3OPY
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 GLU 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A LYS 5.3 3.4 - - - +
286A GLU* 3.3 15.2 + - - +
288A ARG* 1.4 84.5 - - + +
290A ARG* 1.4 59.2 + - - +
291A TRP* 4.6 6.5 - - + +
292A GLY 3.1 17.8 + - - +
293A ARG* 3.2 16.3 + - - +
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Residues in contact with ARG 290 (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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289A GLU* 1.4 71.5 + - - +
291A TRP* 1.4 57.4 + - - +
292A GLY 3.1 0.2 - - - -
293A ARG* 3.1 28.7 + - - +
294A LEU* 2.9 31.2 + - - +
326A GLU* 5.0 4.7 - - - +
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Residues in contact with TRP 291 (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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289A GLU* 3.4 5.6 - - + +
290A ARG* 1.4 76.2 - - - +
292A GLY* 1.3 55.9 + - - +
294A LEU* 3.6 15.1 - - + +
295A GLN* 3.3 23.6 + - - +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A VAL* 3.4 33.1 - - - +
286A GLU* 3.6 15.3 - - - -
287A PHE* 4.8 0.7 - - - -
289A GLU* 3.1 11.9 + - - +
291A TRP* 1.3 77.2 - - - +
293A ARG* 1.3 57.7 + - - +
294A LEU 3.3 0.2 - - - -
295A GLN* 3.4 1.3 + - - -
296A ALA 3.1 21.7 + - - -
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Residues in contact with ARG 293 (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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287A PHE* 2.9 54.7 + - + +
288A ARG* 2.9 27.1 + - - +
289A GLU 3.2 3.1 + - - +
290A ARG* 3.1 35.3 + - - +
292A GLY* 1.3 72.8 - - - +
294A LEU* 1.4 59.6 + - - +
296A ALA* 3.4 5.8 + - - -
297A CYS* 3.0 24.1 + - - +
322A LEU* 3.4 24.7 - - - +
323A PHE* 3.1 31.7 - - + +
326A GLU* 2.6 36.7 + - + +
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Residues in contact with LEU 294 (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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290A ARG* 2.9 17.1 + - + +
291A TRP* 3.6 15.3 - - + +
293A ARG* 1.4 74.0 - - - +
295A GLN* 1.3 56.6 + - - +
297A CYS* 3.2 9.7 + - + +
298A TYR* 3.0 27.9 + - + +
329A GLU 5.8 4.3 - - - +
331A ILE* 3.6 41.3 - - + +
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Residues in contact with GLN 295 (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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254A VAL* 4.1 20.4 - - + +
291A TRP 3.3 15.2 + - - +
292A GLY 3.7 5.6 - - - +
293A ARG 3.4 0.2 - - - -
294A LEU* 1.3 76.7 - - - +
296A ALA* 1.3 63.6 + - - +
298A TYR* 3.2 8.2 + - - +
299A ASN* 3.0 33.2 + - - +
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Residues in contact with ALA 296 (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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253A LEU* 3.3 32.5 - - + +
254A VAL* 4.1 6.0 - - + +
287A PHE* 3.7 25.8 - - + -
292A GLY 3.1 14.1 + - - +
293A ARG 3.4 9.0 - - - +
294A LEU 3.4 0.2 - - - -
295A GLN* 1.3 74.5 - - - +
297A CYS* 1.3 61.4 + - - +
299A ASN* 3.7 2.9 + - - +
300A MET* 3.3 26.5 + - - +
323A PHE* 4.0 4.5 - - + -
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Residues in contact with CYS 297 (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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293A ARG 3.0 14.5 + - - +
294A LEU* 3.3 14.4 - - + +
295A GLN 3.2 0.2 - - - -
296A ALA* 1.3 74.9 - - - +
298A TYR* 1.3 65.5 + - - +
300A MET* 3.0 13.2 + - - +
301A VAL* 3.1 23.7 + - - +
323A PHE* 3.8 4.0 - - + -
327A TRP* 3.5 35.9 - - + -
329A GLU 5.3 0.7 - - - -
330A LEU* 3.4 33.4 - - - -
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Residues in contact with TYR 298 (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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294A LEU* 3.0 15.8 + - + +
295A GLN* 3.5 11.0 - - - +
297A CYS* 1.3 74.5 - - - +
299A ASN* 1.3 65.3 + - - +
301A VAL* 3.1 9.7 + - + +
302A SER* 2.6 62.8 + - - -
333A GLU* 4.5 9.4 - - - -
342A LYS* 4.4 20.2 - - - -
344A GLN* 5.7 2.2 - - - -
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Residues in contact with ASN 299 (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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253A LEU* 2.6 29.6 + - + +
254A VAL 2.8 23.1 + - - +
256A GLY* 3.1 31.7 - - - +
260A LEU* 5.2 6.6 - - + +
295A GLN* 3.0 12.8 + - - +
296A ALA 3.8 2.5 - - - +
298A TYR* 1.3 85.8 - - - +
300A MET* 1.3 56.8 + - + +
302A SER* 4.2 3.6 - - - -
303A ASN* 2.9 40.1 + - - +
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Residues in contact with MET 300 (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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253A LEU* 3.9 22.0 - - + -
296A ALA 3.3 8.9 + - - +
297A CYS 3.0 9.6 + - - +
299A ASN* 1.3 78.1 - - - +
301A VAL* 1.3 59.3 - - - +
304A GLY 3.1 3.8 + - - -
305A ILE* 2.7 70.5 + - + +
306A ASP 5.1 0.4 - - - -
307A ALA 4.3 4.9 - - - +
308A LEU* 3.7 28.9 - - + -
323A PHE* 3.7 30.5 - - - -
327A TRP* 3.8 12.1 - - + -
351A LEU* 3.9 16.2 - - + -
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Residues in contact with VAL 301 (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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297A CYS* 3.1 30.2 + - - +
298A TYR* 3.7 7.4 - - + +
300A MET* 1.3 74.1 - - - +
302A SER* 1.4 56.6 - - - +
304A GLY* 3.1 19.6 + - - -
305A ILE 4.4 0.2 + - - -
327A TRP* 4.2 11.4 - - + -
330A LEU* 5.5 4.0 - - + -
342A LYS* 6.1 1.6 - - - -
344A GLN* 3.7 36.2 - - + +
345A TYR* 5.5 0.7 - - - -
348A HIS* 3.4 43.3 - - + +
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Residues in contact with SER 302 (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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298A TYR* 2.6 62.2 + - - -
299A ASN* 3.9 4.5 - - - -
301A VAL* 1.4 71.6 - - - +
303A ASN* 1.3 65.4 - - - +
304A GLY 3.2 3.3 + - - -
344A GLN* 5.5 5.4 - - - -
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Residues in contact with ASN 303 (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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208A GLU* 5.7 0.7 - - - -
212A LYS* 3.4 25.9 + - - +
244A TYR* 5.7 1.4 - - + -
256A GLY 4.4 9.7 + - - +
257A GLY* 4.4 10.3 + - - -
260A LEU* 4.2 26.4 + - + +
299A ASN* 2.9 32.1 + - - +
302A SER* 1.3 79.9 - - - +
304A GLY* 1.3 61.2 + - - +
305A ILE* 3.2 19.8 + - + +
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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