Contacts of the helix formed by residues 298 - 312 (chain A) in PDB entry 1OPL
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A THR 3.9 3.8 + - - +
297A MET* 1.3 79.6 - - - +
299A VAL* 1.3 67.5 + - - +
300A GLU* 4.6 5.4 - - + +
301A GLU* 3.0 29.5 + - + +
302A PHE* 3.0 19.2 + - - +
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Residues in contact with VAL 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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292A LEU* 4.0 24.9 - - + -
297A MET 3.5 2.0 + - - +
298A GLU* 1.3 72.9 - - - +
300A GLU* 1.3 77.5 + - - +
302A PHE* 3.0 1.9 + - - +
303A LEU* 2.9 48.0 + - + +
330A PHE* 4.3 10.1 - - + -
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Residues in contact with GLU 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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298A GLU* 3.4 4.3 - - + +
299A VAL* 1.3 89.5 + - - +
301A GLU* 1.3 57.7 + - - +
303A LEU* 4.0 11.6 - - - +
304A LYS* 3.0 43.8 + - + +
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Residues in contact with GLU 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 MET* 4.3 16.8 - - + +
298A GLU* 3.0 32.5 + - + +
300A GLU* 1.3 77.7 - - - +
302A PHE* 1.3 65.0 + - - +
304A LYS* 3.4 20.3 + - - +
305A GLU* 3.1 23.5 + - - +
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Residues in contact with PHE 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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290A LYS* 3.4 46.4 - - + -
291A THR 4.2 1.3 - - - -
292A LEU* 3.9 32.3 - - + -
297A MET* 3.9 23.7 - - - -
298A GLU 3.0 11.0 + - - +
299A VAL 3.0 7.2 + - - +
301A GLU* 1.3 76.3 - - - +
303A LEU* 1.3 71.2 + - + +
305A GLU* 3.2 7.3 + - - +
306A ALA* 3.1 18.9 + - + +
325A THR* 5.8 3.1 - - + -
330A PHE* 3.4 41.3 - - + -
331A TYR 4.1 2.0 - - - -
332A ILE* 3.6 27.9 - - + +
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Residues in contact with LEU 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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299A VAL* 2.9 33.0 + - + +
300A GLU* 4.0 12.8 - - - +
302A PHE* 1.3 82.6 - - + +
304A LYS* 1.3 59.2 + - - +
306A ALA* 3.2 9.6 + - + +
307A ALA* 2.9 28.6 + - - +
325A THR* 5.4 10.5 - - + -
330A PHE* 3.5 38.1 - - + -
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Residues in contact with LYS 304 (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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300A GLU* 3.0 28.4 + - + +
301A GLU* 3.7 19.1 + - - +
302A PHE 3.3 0.2 - - - -
303A LEU* 1.3 76.4 - - + +
305A GLU* 1.3 58.0 + - - +
307A ALA* 3.2 7.9 + - + +
308A VAL* 2.9 38.1 + - + +
405A ARG* 5.5 7.2 - - - +
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Residues in contact with GLU 305 (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 LYS* 2.9 32.5 + - - +
297A MET* 4.4 13.2 - - - +
301A GLU* 3.1 14.0 + - - +
302A PHE* 3.3 11.4 - - - +
303A LEU 3.1 0.2 - - - -
304A LYS* 1.3 78.0 - - - +
306A ALA* 1.3 62.4 + - - +
308A VAL* 3.4 5.4 + - - +
309A MET* 3.0 38.1 + - + +
332A ILE* 4.0 7.7 - - + +
400A ASP 4.9 0.7 - - - +
401A PHE* 3.5 22.7 - - - +
402A GLY* 3.5 18.7 + - - +
539A P16 3.1 17.5 - - - -
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Residues in contact with ALA 306 (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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302A PHE* 3.1 15.3 + - + +
303A LEU* 3.2 12.1 + - + +
305A GLU* 1.3 76.6 - - - +
307A ALA* 1.3 61.8 + - - +
309A MET* 3.3 6.9 + - - +
310A LYS* 3.2 31.0 + - - +
320A LEU* 4.2 2.8 - - - +
323A VAL* 4.3 16.8 - - + -
325A THR* 5.4 8.3 - - + -
332A ILE* 3.9 24.1 - - + +
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Residues in contact with ALA 307 (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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303A LEU 2.9 14.3 + - - +
304A LYS* 3.2 12.5 + - + +
306A ALA* 1.3 76.5 - - - +
308A VAL* 1.3 63.2 + - - +
310A LYS* 3.2 27.2 + - - +
311A GLU* 3.7 9.9 + - - +
405A ARG* 4.4 13.2 + - - +
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Residues in contact with VAL 308 (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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304A LYS* 2.9 26.2 + - + +
305A GLU* 3.7 6.1 - - - +
307A ALA* 1.3 72.2 - - - +
309A MET* 1.3 61.8 + - + +
311A GLU* 2.9 22.5 + - - +
312A ILE* 3.3 14.1 + - + +
378A PHE* 3.8 24.0 - - + -
400A ASP 5.1 1.1 - - - +
403A LEU* 4.1 38.4 - - + +
405A ARG* 3.8 34.3 - - + +
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Residues in contact with MET 309 (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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305A GLU* 3.0 25.5 + - + +
306A ALA* 3.8 4.5 - - - +
307A ALA 3.3 0.4 - - - -
308A VAL* 1.3 78.3 - - + +
310A LYS* 1.3 61.8 + - - +
311A GLU 3.3 0.3 + - - -
312A ILE* 3.5 21.8 + - + +
318A VAL* 3.8 13.0 - - + +
319A GLN* 4.9 1.6 + - - -
320A LEU* 3.8 31.7 + - + +
332A ILE* 4.3 9.9 - - - -
334A THR* 3.7 27.8 - - + -
400A ASP* 3.2 39.3 - - - +
539A P16 3.4 29.6 - - + -
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Residues in contact with LYS 310 (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 ASP* 5.4 1.8 + - - -
254A TRP* 3.6 59.0 + - + +
255A GLU* 5.3 2.4 + - - -
306A ALA* 3.2 19.2 + - - +
307A ALA* 3.2 15.5 + - - +
308A VAL 3.1 1.0 + - - -
309A MET* 1.3 76.9 - - - +
311A GLU* 1.3 68.1 + - + +
312A ILE 3.8 2.3 + - - +
313A LYS* 4.9 6.9 - - - +
319A GLN* 5.8 0.3 + - - -
320A LEU* 3.5 15.7 - - + -
323A VAL* 4.4 20.1 - - - +
325A THR* 6.2 0.6 - - - +
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Residues in contact with GLU 311 (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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307A ALA 3.9 12.6 - - - +
308A VAL 2.9 8.3 + - - +
310A LYS* 1.3 85.2 - - - +
312A ILE* 1.3 63.4 + - - +
313A LYS* 3.5 10.2 + - - +
372A TYR* 3.7 8.1 + - - -
378A PHE* 5.0 14.0 - - + -
405A ARG* 4.4 13.7 - - - +
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Residues in contact with ILE 312 (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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308A VAL* 3.3 22.2 + - + +
309A MET* 3.5 17.9 + - - +
310A LYS 4.6 0.7 - - - +
311A GLU* 1.3 75.9 - - - +
313A LYS* 1.3 68.2 + - - +
314A HIS 4.6 0.4 - - - +
317A LEU* 3.6 40.4 - - + +
318A VAL 5.3 1.6 - - - +
319A GLN* 3.3 17.4 + - - +
372A TYR* 4.0 8.5 - - + -
373A LEU* 4.1 7.0 - - + -
378A PHE* 3.8 33.4 - - + -
400A ASP* 3.9 12.8 - - + +
403A LEU* 4.0 22.2 - - + -
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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