Contacts of the helix formed by residues 382 - 395 (chain B) in PDB entry 4OIV
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 THR 382 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LYS 3.4 5.8 + - - +
381B MET* 1.3 77.4 - - - +
383B GLN* 1.3 64.6 + - - +
384B GLU* 3.6 18.3 - - + +
385B GLU* 3.0 35.6 + - - +
386B TYR* 3.0 20.8 + - - +
426B HIS* 5.6 15.3 + - + +
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Residues in contact with GLN 383 (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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261B MET* 3.7 16.7 - - + +
264B TYR* 3.7 20.5 - - + -
265B ASN* 3.0 34.0 + - - +
267B GLN* 4.3 5.0 - - - +
338B GLU* 4.4 7.6 - - - +
381B MET 3.9 1.0 + - - -
382B THR* 1.3 69.7 - - - +
384B GLU* 1.3 66.4 + - + +
386B TYR* 3.4 9.2 + - + +
387B ALA* 3.0 24.1 + - - +
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Residues in contact with GLU 384 (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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257B LEU* 3.6 24.9 - - + +
261B MET* 3.8 30.0 - - + +
382B THR* 3.2 12.6 - - + +
383B GLN* 1.3 78.4 - - + +
385B GLU* 1.3 56.9 + - + +
387B ALA* 3.3 2.9 + - - +
388B LEU* 3.0 35.2 + - - +
422B LEU* 4.0 27.9 - - + +
426B HIS* 4.2 13.5 - - - -
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LYS 4.3 1.7 - - - +
381B MET* 3.5 22.4 - - + +
382B THR* 3.0 35.7 + - - +
384B GLU* 1.3 76.9 - - + +
386B TYR* 1.3 64.1 + - - +
388B LEU* 4.0 0.9 - - - +
389B LEU* 3.1 26.9 + - - +
419B LEU* 3.8 26.1 - - + +
422B LEU* 4.4 17.9 - - + +
423B CYS* 4.1 4.9 - - - -
426B HIS* 4.7 9.9 + - - +
433B HIS* 3.0 36.9 + - - -
437B LEU* 4.1 6.5 - - + +
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Residues in contact with TYR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 3.6 18.6 - - + +
334B LEU* 3.6 44.6 - - + -
335B ARG* 5.9 0.4 - - - -
337B ALA* 3.5 3.9 + - + +
338B GLU* 3.2 46.7 + - + +
341B ASN* 4.3 5.9 + - + +
376B ILE* 3.2 27.9 - - + +
381B MET* 3.6 30.2 - - + +
382B THR 3.0 18.2 + - - -
383B GLN* 3.8 10.1 - - + +
385B GLU* 1.3 75.6 - - - +
387B ALA* 1.3 63.4 + - - +
389B LEU* 3.9 1.8 - - - +
390B THR* 2.8 32.4 + - - -
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Residues in contact with ALA 387 (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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260B ILE* 4.0 8.9 - - + +
261B MET* 3.5 30.1 - - - -
264B TYR* 3.4 38.8 - - + -
305B PHE* 3.8 5.9 - - - -
383B GLN 3.0 8.2 + - - +
384B GLU 3.7 0.2 - - - +
386B TYR* 1.3 79.5 - - - +
388B LEU* 1.3 63.8 + - - +
390B THR* 3.4 2.9 + - - -
391B ALA* 3.1 21.8 + - - +
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Residues in contact with LEU 388 (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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257B LEU* 4.0 20.9 - - + -
260B ILE* 4.1 25.4 - - + -
384B GLU 3.0 22.6 + - - +
385B GLU 4.0 0.4 - - - +
386B TYR 3.2 0.2 - - - -
387B ALA* 1.3 74.7 - - - +
389B LEU* 1.3 60.2 + - - +
391B ALA* 3.2 6.0 + - - +
392B ILE* 2.8 35.8 + - + +
415B LEU* 4.2 18.1 - - + +
418B VAL* 4.2 9.4 - - + -
419B LEU* 3.8 35.4 - - + -
422B LEU* 3.4 33.2 - - + -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.1 14.8 - - + +
381B MET* 3.6 30.3 - - + -
385B GLU 3.1 13.8 + - - +
386B TYR 3.9 3.1 - - - +
388B LEU* 1.3 78.7 - - - +
390B THR* 1.3 56.7 + - - +
392B ILE* 3.6 5.3 - - + +
393B VAL* 2.8 32.1 + - - +
419B LEU* 3.8 24.0 - - + +
437B LEU* 4.1 26.7 - - + +
438B LEU* 4.3 7.9 - - + -
440B ARG* 5.3 3.8 - - + -
441B LEU* 3.7 40.0 - - + +
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Residues in contact with THR 390 (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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264B TYR* 4.1 15.5 + - + -
302B LEU* 5.0 3.6 - - + -
305B PHE* 3.7 20.9 - - + -
331B ALA* 4.7 14.1 - - + +
334B LEU* 3.4 21.1 - - + +
335B ARG* 5.2 6.0 + - - +
386B TYR* 2.8 25.7 + - - -
387B ALA 3.6 5.4 - - - -
389B LEU* 1.3 74.5 - - - +
391B ALA* 1.3 65.4 + - - +
393B VAL* 3.3 3.0 - - - +
394B ILE* 3.0 40.6 + - + +
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Residues in contact with ALA 391 (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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260B ILE* 4.3 9.4 - - + -
305B PHE* 3.9 8.7 - - + -
309B LEU* 3.7 27.6 - - + -
387B ALA 3.1 13.7 + - - +
388B LEU* 3.5 8.1 - - - +
390B THR* 1.3 77.4 - - - +
392B ILE* 1.3 57.3 + - - +
394B ILE* 3.4 1.6 + - - +
395B LEU* 3.0 33.8 + - - +
415B LEU* 3.7 21.3 - - + -
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Residues in contact with ILE 392 (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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388B LEU 2.8 27.9 + - - +
389B LEU* 3.6 6.5 - - + +
391B ALA* 1.3 71.1 - - - +
393B VAL* 1.3 66.1 + - - +
394B ILE 3.4 0.3 + - - -
395B LEU 3.4 8.0 + - - -
396B SER* 3.6 0.7 + - - -
412B GLN* 3.0 44.4 + - + +
415B LEU* 3.8 37.0 - - + +
416B LEU* 4.0 29.4 - - + +
419B LEU* 3.9 22.4 - - + -
438B LEU* 4.6 4.7 - - + -
441B LEU* 4.0 16.8 - - + -
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Residues in contact with VAL 393 (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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327B SER* 3.2 1.9 + - - +
330B GLU* 3.9 21.1 - - + +
331B ALA* 4.2 24.9 - - + +
334B LEU* 4.5 7.4 - - + -
389B LEU 2.8 20.1 + - - +
390B THR* 3.3 17.0 - - - +
392B ILE* 1.3 74.1 - - - +
394B ILE* 1.3 62.0 + - - +
396B SER* 2.7 22.2 + - - +
399B ARG* 3.0 31.0 + - - +
441B LEU* 4.0 28.9 - - + -
444B LEU* 5.8 1.6 - - + -
445B ARG* 6.1 0.7 - - - +
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Residues in contact with ILE 394 (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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302B LEU* 3.6 17.7 - - + -
305B PHE* 3.7 23.3 - - + -
306B THR* 3.5 34.3 - - + +
309B LEU* 3.7 18.8 - - + -
312B PHE* 5.2 2.9 - - + -
323B LEU* 3.5 15.0 - - + +
324B LEU* 5.5 5.2 - - + -
327B SER* 2.9 27.5 + - - -
331B ALA* 4.0 17.3 - - + -
390B THR* 3.0 25.8 + - + +
391B ALA 3.7 4.0 - - - +
393B VAL* 1.3 79.5 - - - +
395B LEU* 1.3 61.0 + - + +
396B SER 3.0 3.8 + - - -
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Residues in contact with LEU 395 (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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309B LEU* 4.1 25.8 - - + -
310B PRO* 4.8 4.7 - - + +
312B PHE* 4.1 17.3 - - + -
323B LEU* 3.9 19.3 - - + -
391B ALA 3.0 13.2 + - - +
392B ILE 3.4 4.2 + - - -
394B ILE* 1.3 74.8 - - + +
396B SER* 1.3 60.3 + - - +
397B PRO* 3.5 0.3 - - - +
408B VAL* 3.4 14.4 - - + +
411B LEU* 4.1 31.0 - - + +
412B GLN* 3.1 34.2 - - + +
415B LEU* 3.6 29.8 - - + -
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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