Contacts of the helix formed by residues 366 - 383 (chain B) in PDB entry 2OIB
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 PRO 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B HIS* 3.4 37.9 - - + +
308B ILE* 3.7 27.6 - - + -
336B SER* 4.6 11.7 - - - +
365B THR* 1.4 84.3 - - - +
367B LYS* 1.3 67.7 + - + +
368B SER 3.0 2.0 - - - -
369B ASP* 3.1 19.4 + - - +
370B ILE* 3.4 5.7 + - - +
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Residues in contact with LYS 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR* 3.0 22.7 + - + +
366B PRO* 1.3 80.9 - - + +
368B SER* 1.3 61.6 + - - +
370B ILE* 3.4 14.9 - - + +
371B TYR 3.3 12.0 + - - -
441B LYS* 3.6 30.9 - - + +
442B ASN* 3.4 29.8 + - - +
444B ARG* 2.8 34.8 + - + +
445B PRO 6.1 0.9 - - - +
446B ASP* 6.5 1.3 - - + -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 5.7 1.1 - - - -
310B ARG* 6.5 0.4 - - - -
356B ALA* 4.1 5.4 + - - +
358B GLU* 2.9 25.1 + - - +
359B ALA* 3.8 22.9 + - - +
363B GLU 4.6 1.3 + - - -
365B THR* 3.1 25.8 + - - +
366B PRO 3.0 0.2 - - - -
367B LYS* 1.3 76.1 - - - +
369B ASP* 1.3 66.5 + - - +
371B TYR* 3.2 5.0 + - - +
372B SER* 3.1 25.8 + - - -
444B ARG* 4.0 1.6 - - - +
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Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 4.6 5.9 - - + +
303B HIS* 3.0 27.3 + - + +
308B ILE* 3.6 11.7 - - - +
309B HIS* 2.9 32.1 + - - +
310B ARG* 3.1 26.9 + - - -
312B ILE* 4.1 15.6 + - + +
366B PRO 3.1 10.1 + - - +
368B SER* 1.3 75.9 - - - +
370B ILE* 1.3 61.4 + - - +
372B SER* 3.4 7.5 + - - -
373B PHE* 2.9 29.8 + - - +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 5.0 0.9 - - + -
303B HIS* 4.1 11.0 - - + -
366B PRO 3.7 11.2 - - - +
367B LYS* 3.4 14.6 + - + +
368B SER 3.2 0.4 - - - -
369B ASP* 1.3 79.1 - - - +
371B TYR* 1.3 62.1 + - - +
373B PHE* 3.3 6.5 + - + +
374B GLY 3.0 17.0 + - - -
436B CYS* 3.4 35.1 - - - +
444B ARG* 4.2 8.5 - - + -
445B PRO* 3.4 25.6 - - + +
446B ASP* 4.2 2.5 - - - -
447B ILE* 3.7 49.4 - - + +
450B VAL* 4.5 3.1 - - + -
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Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B TYR 3.7 5.6 - - - -
355B MET 3.3 21.0 + - - -
356B ALA* 3.5 28.9 - - + -
357B PRO* 4.2 13.6 - - + +
367B LYS 3.3 2.2 + - - -
368B SER 3.2 9.1 + - - +
370B ILE* 1.3 79.3 - - - +
372B SER* 1.3 62.7 + - - +
374B GLY* 3.0 12.0 + - - -
375B VAL* 3.3 15.8 + - + +
397B LEU* 3.7 31.5 - - + +
436B CYS 3.4 22.6 + - - +
437B LEU* 3.3 42.1 + - + +
438B HIS 3.8 4.0 - - - -
439B GLU* 4.9 4.5 - - + +
444B ARG* 3.8 21.3 - - - +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG 5.8 2.1 + - - -
311B ASP* 5.9 0.2 - - - -
312B ILE* 3.3 38.2 + - - -
354B TYR* 2.8 29.6 + - - +
355B MET* 4.4 4.5 - - - +
368B SER 3.1 14.0 + - - -
369B ASP* 3.7 5.9 - - - -
371B TYR* 1.3 75.1 - - - +
373B PHE* 1.3 63.8 + - - +
375B VAL* 3.0 15.9 + - - +
376B VAL* 3.1 14.4 + - - +
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.4 23.6 - - - -
295B ALA* 3.7 24.5 - - + -
296B ALA* 3.8 8.7 - - + -
299B ILE* 3.5 25.4 - - + -
312B ILE* 3.8 9.5 - - + +
317B ILE* 5.3 1.1 - - + -
369B ASP 2.9 17.8 + - - +
370B ILE* 3.5 7.6 - - - +
371B TYR 3.3 0.2 - - - -
372B SER* 1.3 75.8 - - - +
374B GLY* 1.3 56.3 + - - +
376B VAL* 3.2 18.4 + - + +
377B LEU* 2.9 53.5 + - + +
380B ILE* 5.7 0.4 - - + -
436B CYS* 4.7 4.7 - - - -
447B ILE* 4.7 5.2 - - + -
450B VAL* 3.6 31.9 - - + -
454B LEU* 3.9 7.4 - - + -
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Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE 3.0 6.9 + - - -
371B TYR 3.0 10.4 + - - -
373B PHE* 1.3 76.6 - - - +
375B VAL* 1.3 60.1 + - - +
377B LEU* 3.3 5.7 + - - +
378B LEU* 3.2 25.1 + - - +
433B ALA* 3.9 9.0 - - - +
436B CYS* 3.6 22.6 - - - +
437B LEU* 3.9 12.1 - - - -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA 4.0 16.2 - - - +
354B TYR* 3.6 32.3 - - + +
371B TYR* 3.3 15.1 + - + +
372B SER 3.0 8.1 + - - +
374B GLY* 1.3 74.5 - - - +
376B VAL* 1.3 57.9 + - - +
378B LEU* 3.1 10.6 + - + +
379B GLU* 3.0 26.1 + - + +
386B ALA* 3.7 23.6 - - + -
396B LEU* 4.2 7.8 - - + +
397B LEU* 4.6 11.0 - - + +
437B LEU* 3.8 19.3 - - + -
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.9 9.4 - - + -
312B ILE* 4.1 12.8 - - + -
313B LYS* 3.8 29.4 - - - -
314B SER* 3.9 5.6 - - - +
317B ILE* 3.8 22.0 - - + -
354B TYR* 4.4 1.1 - - + -
372B SER 3.1 13.5 + - - +
373B PHE* 3.2 17.7 + - + +
375B VAL* 1.3 76.5 - - - +
377B LEU* 1.3 58.7 + - - +
379B GLU* 3.1 15.1 + - - +
380B ILE* 2.8 44.2 + - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.9 28.3 - - + -
373B PHE* 2.9 43.4 + - + +
374B GLY* 3.6 9.6 - - - +
375B VAL 3.3 0.2 - - - -
376B VAL* 1.3 76.2 - - - +
378B LEU* 1.3 56.8 + - - +
380B ILE* 3.3 8.2 + - + +
381B ILE* 3.0 36.3 + - - +
429B MET* 3.9 20.3 - - + +
432B VAL* 3.8 20.2 - - + -
433B ALA* 3.7 33.9 - - + +
436B CYS* 4.7 1.1 - - - -
454B LEU* 4.4 4.5 - - + -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLY 3.2 12.1 + - - +
375B VAL* 3.1 11.9 + - + +
377B LEU* 1.3 72.8 - - - +
379B GLU* 1.3 56.2 + - - +
381B ILE* 4.5 6.3 - - + +
382B THR* 2.7 45.6 + - + +
396B LEU* 3.8 34.3 - - + +
397B LEU* 4.1 10.8 - - - +
399B ILE* 4.9 10.3 - - + -
400B LYS 5.2 1.8 - - - +
410B ILE* 5.5 1.8 - - + -
430B TYR* 3.8 28.5 - - + -
433B ALA* 3.7 20.2 - - + -
437B LEU* 3.5 24.0 - - + -
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.9 9.5 - - - +
274B LEU* 3.8 16.0 - - + +
314B SER* 2.8 32.3 + - - -
354B TYR* 2.9 37.2 + - - -
375B VAL 3.0 13.0 + - - +
376B VAL* 3.2 15.7 - - + +
378B LEU* 1.3 76.7 - - - +
380B ILE* 1.3 54.7 + - - +
383B GLY* 2.7 35.5 + - - -
384B LEU 3.4 21.9 - - - +
385B PRO* 4.0 2.6 - - - +
386B ALA* 3.8 12.4 + - + +
396B LEU* 3.6 7.8 - - + +
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.9 28.5 - - + -
274B LEU* 4.2 7.2 - - + -
285B TRP* 4.6 1.1 - - + -
288B ARG* 2.8 61.8 + - + +
291B ILE* 4.7 3.4 - - + -
292B ALA* 4.2 29.2 - - + +
317B ILE* 6.1 0.2 - - + -
373B PHE* 5.7 0.4 - - + -
376B VAL* 2.8 37.2 + - + +
377B LEU* 3.6 13.5 - - + +
378B LEU 3.3 0.2 - - - -
379B GLU* 1.3 72.9 - - - +
381B ILE* 1.3 57.1 + - - +
429B MET* 3.8 20.4 - - + -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TRP* 4.4 12.6 - - + -
377B LEU 3.0 25.5 + - - +
378B LEU* 3.9 13.7 - - + +
380B ILE* 1.3 77.6 - - - +
382B THR* 1.3 63.5 + - + +
410B ILE* 3.8 23.6 - - + -
414B ILE* 3.8 7.8 - - + -
415B ASP* 2.9 24.1 + - - +
418B MET* 3.9 6.2 - - - +
426B VAL* 4.0 18.4 - - + +
429B MET* 3.7 26.0 - - + +
430B TYR* 3.8 37.5 - - + +
433B ALA* 4.8 0.2 - - + -
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Residues in contact with THR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 2.7 30.5 + - + +
381B ILE* 1.3 87.7 - - + +
383B GLY* 1.3 59.8 + - - +
384B LEU* 3.1 39.5 + - - +
396B LEU* 3.8 12.2 - - + +
399B ILE* 5.5 4.3 - - + -
410B ILE* 4.9 3.6 - - + -
413B TYR* 3.3 38.8 - - + +
415B ASP* 3.4 20.0 - - - +
417B LYS* 5.4 0.2 + - - -
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 4.0 27.2 - - - +
275B SER* 5.3 1.4 - - - -
288B ARG* 4.2 3.1 - - - -
379B GLU 2.7 20.1 + - - -
380B ILE 4.1 0.6 + - - -
381B ILE 3.5 1.8 - - - -
382B THR* 1.3 72.7 - - - +
384B LEU* 1.3 62.6 + - - +
385B PRO* 4.1 3.8 - - - +
415B ASP* 3.2 20.3 + - - -
417B LYS* 4.6 5.3 + - - -
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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
------------------------------------------------------------
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