Contacts of the helix formed by residues 336 - 357 (chain B) in PDB entry 3OY3
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 SER 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B ARG 3.9 11.7 - - - -
333B GLN 4.3 9.4 - - - -
334B GLU 3.2 3.6 + - - -
335B VAL* 1.3 75.4 - - - +
337B ALA* 1.3 68.3 + - - +
338B VAL* 3.3 24.3 - - - +
339B VAL* 2.8 16.6 + - - +
340B LEU* 2.9 12.2 + - - +
435B TYR* 4.1 5.6 - - - -
504B ASP* 5.2 0.9 + - - -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 1.3 73.9 - - - +
338B VAL* 1.3 63.3 + - - +
340B LEU* 3.2 13.3 + - - +
341B LEU* 2.9 27.1 + - + +
435B TYR* 4.7 1.4 + - - -
500B SER* 4.9 1.1 - - - +
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 3.3 15.9 + - - +
337B ALA* 1.3 77.4 - - - +
339B VAL* 1.3 66.9 + - + +
341B LEU* 3.3 5.2 + - - +
342B TYR* 2.9 26.2 + - - +
497B PHE* 4.0 20.6 - - + -
500B SER* 3.4 27.5 + - - +
501B SER* 4.1 17.3 - - - +
504B ASP* 4.0 29.8 - - + +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU 3.4 22.2 - - - +
335B VAL* 3.9 15.3 - - + -
336B SER* 2.8 23.8 + - - +
338B VAL* 1.3 75.9 - - + +
340B LEU* 1.3 59.5 + - - +
342B TYR* 3.1 9.3 + - + +
343B MET* 2.8 38.9 + - + +
375B HIS* 3.6 48.2 - - + +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.1 8.5 - - + -
335B VAL* 3.8 13.7 - - + -
336B SER 2.9 14.1 + - - +
337B ALA* 3.6 13.2 - - - +
339B VAL* 1.3 75.4 - - - +
341B LEU* 1.3 62.6 + - - +
343B MET* 3.2 9.6 + - - +
344B ALA* 3.2 22.0 + - - +
432B ILE* 3.7 41.7 - - + +
433B ALA* 4.4 11.4 - - - +
435B TYR* 3.8 41.5 - - + +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA* 2.9 14.2 + - + +
338B VAL* 3.4 9.9 - - - +
340B LEU* 1.3 75.2 - - - +
342B TYR* 1.3 58.2 - - - +
344B ALA* 3.4 5.4 + - - +
345B THR* 2.9 33.1 + - - -
465B PRO* 5.9 2.2 - - + -
468B VAL* 4.9 7.2 - - + -
493B PHE* 3.7 29.4 - - + +
496B MET* 3.3 37.7 - - + +
497B PHE* 4.1 9.6 - - + +
500B SER* 3.3 34.1 - - - +
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Residues in contact with TYR 342 (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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338B VAL 2.9 14.2 + - - +
339B VAL* 3.1 13.0 + - + +
341B LEU* 1.3 76.4 - - - +
343B MET* 1.3 64.1 + - + +
345B THR* 4.3 4.7 - - + -
346B GLN* 3.0 66.2 + - + +
374B ASN 3.8 15.7 + - - -
375B HIS* 3.6 24.7 - + + -
376B LEU* 4.9 4.7 - - - +
497B PHE* 3.6 39.0 - + + -
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Residues in contact with MET 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 3.8 31.2 - - + -
326B TYR* 3.9 24.0 - - + -
327B LEU* 4.3 15.0 - - - -
335B VAL* 4.7 1.3 - - - -
339B VAL* 2.8 31.0 - - + +
340B LEU* 3.2 15.0 + - - +
342B TYR* 1.3 78.3 - - + +
344B ALA* 1.3 61.5 + - - +
346B GLN* 3.2 12.3 + - - +
347B ILE* 3.0 30.4 + - + +
371B VAL* 4.6 6.7 - - + -
375B HIS* 4.7 8.3 - - + +
377B VAL* 4.0 21.0 - - + +
432B ILE* 4.4 13.0 - - + -
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Residues in contact with ALA 344 (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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340B LEU 3.2 10.2 + - - +
341B LEU* 3.7 4.7 - - - +
343B MET* 1.3 75.3 - - - +
345B THR* 1.3 61.0 + - - +
347B ILE* 3.2 5.1 + - - +
348B SER* 2.8 32.8 + - - -
425B PHE* 4.1 4.1 - - + -
429B LEU* 3.8 19.1 - - + -
432B ILE* 4.4 11.8 - - + +
493B PHE* 3.5 31.6 - - + -
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Residues in contact with THR 345 (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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341B LEU 2.9 22.0 + - - -
342B TYR* 3.8 11.0 - - + -
343B MET 3.3 0.2 - - - -
344B ALA* 1.3 75.7 - - - +
346B GLN* 1.3 62.6 + - + +
348B SER* 3.0 20.0 + - - -
349B SER* 3.0 12.6 + - - -
490B HIS* 3.9 8.1 + - + +
493B PHE* 3.3 25.1 + - - +
494B GLU* 3.4 37.9 - - - +
497B PHE* 3.5 14.1 - - + +
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Residues in contact with GLN 346 (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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297B ASN* 3.3 35.3 + - - +
342B TYR* 3.0 56.6 + - + +
343B MET* 3.2 10.5 + - - +
345B THR* 1.3 78.6 - - + +
347B ILE* 1.3 60.6 + - - +
349B SER* 3.1 7.6 + - - -
350B ALA 3.0 17.5 + - - -
375B HIS 3.0 21.4 + - - -
376B LEU* 3.4 10.6 - - - +
377B VAL* 2.8 30.4 + - + +
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Residues in contact with ILE 347 (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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297B ASN* 5.5 0.4 - - - -
323B LEU* 4.1 15.7 - - + -
343B MET* 3.0 19.1 + - + +
344B ALA* 3.8 3.8 - - - +
346B GLN* 1.3 73.6 - - - +
348B SER* 1.3 66.0 + - - +
350B ALA* 3.1 3.5 + - - +
351B MET* 3.0 27.6 + - + +
364B LEU* 4.3 1.6 - - + -
369B CYS* 4.1 4.3 - - - -
377B VAL* 4.0 17.7 - - + -
379B VAL* 3.8 25.4 - - + -
425B PHE* 3.9 21.8 - - + -
428B LEU* 4.0 24.0 - - + -
432B ILE* 3.9 25.1 - - + -
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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
----------------------------------------------------------
344B ALA 2.8 15.9 + - - -
345B THR* 3.0 23.2 + - - -
347B ILE* 1.3 76.0 - - - +
349B SER* 1.3 56.9 + - - +
351B MET* 3.8 5.1 - - - +
352B GLU* 2.9 28.1 + - - +
425B PHE* 3.9 11.8 - - - -
486B PHE* 4.1 4.2 - - - +
489B ILE* 3.7 30.1 - - - -
490B HIS* 3.4 24.0 + - - +
493B PHE* 4.1 3.6 - - - +
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Residues in contact with SER 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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295B HIS* 3.0 29.0 + - - -
297B ASN* 3.8 6.7 + - - -
345B THR* 3.0 14.1 + - - -
346B GLN* 3.2 11.0 - - - -
347B ILE 3.1 0.2 - - - -
348B SER* 1.3 74.7 + - - +
350B ALA* 1.3 65.4 + - - +
352B GLU* 3.3 4.2 + - - +
353B TYR 3.2 16.5 + - - -
490B HIS* 3.9 28.7 + - - -
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Residues in contact with ALA 350 (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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295B HIS* 3.7 12.2 - - - -
297B ASN 3.2 28.0 - - - +
298B LEU* 3.8 12.7 - - + +
346B GLN 3.0 9.5 + - - +
347B ILE 3.4 8.5 - - - +
349B SER* 1.3 76.0 - - - +
351B MET* 1.3 59.0 + - + +
353B TYR* 3.2 5.5 + - - +
354B LEU* 3.0 29.7 + - - +
379B VAL* 3.6 17.3 - - + -
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Residues in contact with MET 351 (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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347B ILE* 3.0 25.4 + - + +
348B SER 4.0 0.9 - - - +
350B ALA* 1.3 74.0 - - - +
352B GLU* 1.3 61.5 + - - +
354B LEU* 3.8 27.3 - - + +
355B GLU* 3.0 28.9 + - - +
361B HIS* 4.1 5.2 - - + -
364B LEU* 4.0 29.4 - - + -
379B VAL* 4.4 10.5 - - - -
418B ILE* 4.4 3.3 - - + +
421B ASP* 3.7 25.4 - - + +
425B PHE* 4.8 0.4 - - + -
486B PHE* 3.4 55.7 - - + -
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Residues in contact with GLU 352 (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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348B SER 2.9 17.2 + - - +
349B SER* 3.3 6.9 + - - +
351B MET* 1.3 77.3 - - - +
353B TYR* 1.3 56.8 + - - +
355B GLU* 3.4 4.8 + - - +
356B LYS* 2.9 29.5 + - + +
486B PHE* 3.6 14.7 - - - +
487B ALA* 3.8 27.8 - - + +
490B HIS* 2.9 34.4 - - - +
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Residues in contact with TYR 353 (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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292B GLU 3.4 12.2 + - - -
293B ILE* 4.1 10.5 - - + -
294B LYS* 3.0 44.2 + - - +
295B HIS* 3.5 31.2 - + + +
298B LEU* 3.4 25.6 - - + -
349B SER 3.2 6.3 + - - +
350B ALA 3.2 7.8 + - - +
352B GLU* 1.3 75.2 - - - +
354B LEU* 1.3 68.9 + - + +
356B LYS* 3.2 17.9 + - + +
357B LYS* 3.0 48.9 + - + +
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Residues in contact with LEU 354 (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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1B XY3 4.2 6.7 - - - -
293B ILE* 4.1 22.0 - - + -
298B LEU* 3.8 29.8 - - + -
350B ALA 3.0 16.9 + - - +
351B MET* 3.8 35.9 - - + +
353B TYR* 1.3 80.7 - - + +
355B GLU* 1.3 63.6 + - - +
357B LYS* 3.0 7.5 + - + -
359B PHE* 2.9 50.8 + - + +
361B HIS* 4.3 25.4 - - + +
418B ILE* 5.1 1.3 - - + -
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Residues in contact with GLU 355 (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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351B MET 3.0 19.5 + - - +
352B GLU* 3.4 6.1 - - - +
353B TYR 3.2 0.2 - - - -
354B LEU* 1.3 74.2 - - - +
356B LYS* 1.3 66.7 + - - +
358B ASN* 3.0 18.5 + - - -
359B PHE 4.7 1.6 - - - -
418B ILE* 3.9 32.6 - - + +
419B LYS* 5.4 1.0 + - - +
422B VAL* 5.2 0.3 - - - +
485B SER* 3.6 13.6 - - - -
486B PHE* 2.9 29.2 + - - +
487B ALA* 3.1 32.1 + - - +
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Residues in contact with LYS 356 (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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352B GLU* 2.9 21.0 + - + +
353B TYR* 3.2 18.0 + - + +
355B GLU* 1.3 79.7 - - - +
357B LYS* 1.3 75.2 + - + +
358B ASN* 3.2 11.3 + - - +
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLU* 3.2 27.4 + - - +
353B TYR* 3.0 48.2 + - + +
354B LEU* 3.0 6.2 + - - +
356B LYS* 1.3 95.2 - - + +
358B ASN* 1.3 73.3 + - - +
359B PHE* 3.0 40.9 - - + -
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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