Contacts of the helix formed by residues 345 - 361 (chain B) 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 ALA 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B SER 3.4 3.6 + - - -
332B ILE 3.5 15.9 - - - +
334B ASN* 3.9 8.7 - - + +
341B ALA 5.1 0.2 - - - -
342B THR* 3.3 32.6 + - - +
344B GLY* 1.4 76.7 - - - +
346B PHE* 1.3 60.3 + - + +
348B SER 3.4 0.2 + - - -
349B LEU* 2.9 28.4 + - - +
381B TRP* 3.5 27.8 - - + -
382B LEU* 3.6 2.9 - - - +
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Residues in contact with PHE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP 5.8 0.2 - - - -
341B ALA* 3.9 26.7 - - + -
342B THR 4.8 1.2 + - - -
344B GLY 3.5 0.2 - - - -
345B ALA* 1.3 75.4 - - + +
347B SER* 1.4 59.8 + - - +
349B LEU* 3.6 30.1 - - + +
350B ASP* 2.9 27.7 + - - +
381B TRP* 3.7 24.7 - + - -
385B LEU* 4.5 7.9 - - + -
474B VAL* 4.4 15.6 - - + +
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Residues in contact with SER 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PRO* 3.6 29.2 + - - +
344B GLY* 3.4 7.6 + - - -
345B ALA 3.4 0.6 - - - -
346B PHE* 1.4 72.6 - - - +
348B SER* 1.4 59.6 + - - +
350B ASP* 3.2 4.5 + - - +
351B ARG* 3.0 41.1 + - - +
473B ALA* 3.4 8.3 - - - +
474B VAL* 2.9 40.3 + - - +
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PRO* 5.0 0.2 - - - +
332B ILE* 3.6 18.9 - - - +
344B GLY 3.0 17.7 + - - -
345B ALA 3.6 4.0 - - - -
347B SER* 1.4 75.6 - - - +
349B LEU* 1.4 62.1 + - - +
351B ARG* 3.0 17.7 + - - +
352B ILE* 3.2 17.6 + - - +
382B LEU* 3.9 6.1 - - - +
468B GLN* 2.9 50.8 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B ALA 2.9 18.1 + - - +
346B PHE* 3.6 36.8 - - + +
348B SER* 1.4 73.9 - - - +
350B ASP* 1.3 56.1 + - - +
352B ILE* 3.5 5.6 + - + +
353B CYS* 3.1 36.3 + - - -
381B TRP* 4.1 4.3 - - + -
382B LEU* 3.5 19.2 - - + +
385B LEU* 3.7 26.0 - - + +
386B ALA* 3.5 35.2 - - + +
389B ALA* 5.4 2.0 - - + -
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Residues in contact with ASP 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A TYR* 4.8 4.5 + - - -
346B PHE 2.9 15.1 + - - +
347B SER 3.2 11.4 + - - +
349B LEU* 1.3 74.8 - - - +
351B ARG* 1.4 77.8 + - - +
353B CYS* 3.5 5.3 + - - +
354B ARG* 2.9 36.6 + - - +
474B VAL* 3.8 20.5 - - + +
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Residues in contact with ARG 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 6.1 0.5 - - - +
386A TYR* 3.6 36.6 + - - -
194B PRO* 4.3 1.6 - - - +
347B SER* 3.0 32.4 + - - +
348B SER* 3.0 11.0 + - - +
350B ASP* 1.4 94.7 + - - +
352B ILE* 1.4 61.7 + - - +
354B ARG* 3.3 9.8 + - - +
355B ALA* 3.2 16.8 + - - +
464B LEU* 3.5 10.7 - - + +
467B VAL* 3.4 35.6 - - + +
468B GLN* 3.9 16.2 - - + -
470B GLY 2.6 31.7 + - - -
471B GLY* 3.7 3.4 + - - -
472B THR 3.5 25.3 + - - +
474B VAL* 4.0 11.5 - - - +
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER 3.2 13.4 + - - +
349B LEU* 3.6 8.3 - - - +
351B ARG* 1.4 71.7 - - - +
353B CYS* 1.3 58.5 + - - +
355B ALA* 3.1 6.1 + - - +
356B ILE* 3.0 40.2 + - + +
372B VAL* 4.6 0.7 - - + -
374B VAL* 3.6 34.1 - - + -
382B LEU* 3.9 25.1 - - + +
386B ALA* 3.7 21.1 - - + -
464B LEU* 3.8 13.9 - - + +
468B GLN* 3.4 38.1 - - + +
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Residues in contact with CYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 3.1 27.8 + - - +
350B ASP* 4.0 5.4 - - - +
352B ILE* 1.3 72.7 - - - +
354B ARG* 1.4 56.5 + - - +
356B ILE* 3.7 0.7 - - - +
357B ASP* 2.8 47.0 + - - +
386B ALA* 3.9 17.3 - - - -
389B ALA* 3.8 29.2 - - + -
390B THR* 3.9 20.4 - - + -
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Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 2.8 34.8 + - - +
383A LEU* 6.2 3.1 - - + -
386A TYR* 3.1 31.3 + - + +
350B ASP* 2.9 23.8 + - - +
351B ARG* 3.4 13.5 - - - +
353B CYS* 1.4 73.6 - - - +
355B ALA* 1.4 61.9 + - - +
357B ASP* 3.6 10.8 + - - +
358B TYR* 3.2 43.9 + - + -
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 5.8 7.9 - - + -
494A VAL* 3.6 20.7 - - + +
351B ARG 3.2 10.4 + - - +
352B ILE 3.1 9.7 + - - +
354B ARG* 1.4 73.9 - - - +
356B ILE* 1.4 67.4 + - + +
358B TYR* 3.0 9.7 + - - +
359B ILE* 2.9 27.0 + - + +
372B VAL* 5.0 1.1 - - + -
462B THR* 4.5 10.8 - - + -
464B LEU* 4.1 17.9 - - + -
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ILE* 3.0 31.8 + - + +
353B CYS 3.2 0.4 + - - +
355B ALA* 1.4 73.1 - - - +
357B ASP* 1.3 57.7 + - - +
359B ILE* 3.0 9.5 + - + -
360B ASP* 2.8 46.9 + - - +
372B VAL* 3.8 20.4 - - + -
386B ALA* 4.2 2.9 - - + -
390B THR* 3.6 45.5 - - + +
427B ILE* 4.0 18.4 - - + -
429B ILE* 3.8 26.5 - - + -
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Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B CYS* 2.8 33.2 + - - +
354B ARG* 3.7 10.1 - - - +
356B ILE* 1.3 72.9 - - - +
358B TYR* 1.4 61.9 + - + +
360B ASP* 3.2 13.0 + - - +
361B ALA* 3.0 23.2 + - - +
389B ALA 5.6 0.7 - - - +
390B THR* 4.2 13.9 - - - +
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Residues in contact with TYR 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ARG* 3.5 44.8 + - + -
382A GLU* 3.0 36.0 + - + +
383A LEU* 6.0 3.4 - - + -
493A HIS 4.6 0.2 - - - +
494A VAL* 3.9 32.1 - - + +
497A GLY* 3.4 30.0 + - - -
498A GLY* 3.9 11.4 - - - -
499A ALA 5.3 0.4 - - - -
354B ARG* 3.2 36.6 + - + -
355B ALA* 3.0 8.4 + - - +
357B ASP* 1.4 77.8 - - - +
359B ILE* 1.4 63.1 + - - +
361B ALA* 3.3 10.8 + - + +
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A HIS* 3.6 17.0 - - + -
494A VAL* 3.7 20.6 - - + +
355B ALA 2.9 23.8 + - - +
356B ILE* 3.0 12.3 + - + +
358B TYR* 1.4 75.6 - - - +
360B ASP* 1.4 53.1 + - - +
361B ALA 3.3 0.2 + - - -
362B THR* 2.7 27.9 + - - -
370B PHE* 3.7 35.4 - - + -
371B ILE 5.6 0.2 - - - +
372B VAL* 3.8 29.6 - - + -
425B LYS* 3.5 4.5 - - + +
427B ILE* 3.8 14.8 - - + -
462B THR* 4.1 18.8 - - + +
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 2.8 35.3 + - - +
357B ASP* 3.6 14.5 - - - +
359B ILE* 1.4 70.7 - - - +
361B ALA* 1.4 55.6 + - - +
362B THR 2.9 10.3 + - - +
390B THR* 4.5 12.4 - - - +
425B LYS* 3.1 26.2 + - + +
427B ILE* 3.7 26.2 - - - +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ILE 5.7 0.4 - - - +
275A GLY 3.4 17.6 - - - +
276A GLY 3.8 0.7 + - - -
497A GLY* 3.1 17.8 - - - -
498A GLY* 3.2 26.9 + - - +
357B ASP 3.0 15.9 + - - +
358B TYR* 3.5 6.7 - - + +
359B ILE 3.2 1.6 - - - -
360B ASP* 1.4 71.2 - - - +
362B THR* 1.4 58.3 + - - +
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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
------------------------------------------------------------
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