Contacts of the helix formed by residues 382 - 395 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A LYS 4.4 4.9 - - - +
381A MET* 1.3 76.8 - - - +
383A GLN* 1.3 65.2 + - - +
384A GLU* 3.4 12.8 + - - +
385A GLU* 2.9 37.3 + - - +
386A TYR* 3.1 23.8 + - - -
426A HIS* 5.8 10.3 - - + +
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Residues in contact with GLN 383 (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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261A MET* 3.4 15.3 - - + +
264A TYR* 4.1 12.9 - - + -
265A ASN* 2.9 43.1 + - - +
338A GLU* 3.8 22.7 - - - +
342A LYS* 5.1 7.9 + - - +
382A THR* 1.3 74.5 - - - +
384A GLU* 1.3 60.0 + - + +
386A TYR* 3.2 3.4 + - - +
387A ALA* 2.9 27.4 + - - +
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Residues in contact with GLU 384 (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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257A LEU* 3.7 23.7 - - + +
258A HIS* 6.1 0.9 - - - -
261A MET* 3.8 33.4 - - + +
382A THR* 3.2 10.5 + - - +
383A GLN* 1.3 77.6 - - + +
385A GLU* 1.3 58.0 + - + +
387A ALA* 3.2 2.1 + - - +
388A LEU* 2.9 36.5 + - - +
422A LEU* 4.0 28.7 - - + +
426A HIS* 4.4 11.3 - - - -
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Residues in contact with GLU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LYS 4.1 2.1 - - - +
381A MET* 3.3 25.1 - - + -
382A THR* 2.9 38.5 + - - +
384A GLU* 1.3 75.7 - - + +
386A TYR* 1.3 59.9 + - - +
388A LEU* 4.1 0.3 - - - +
389A LEU* 2.7 34.1 + - - +
419A LEU* 4.1 22.6 - - + +
422A LEU* 5.6 7.1 - - + -
423A CYS* 4.2 5.2 + - - -
427A GLN* 5.4 0.7 - - - +
433A HIS* 2.6 37.2 + - - -
437A LEU* 3.9 9.5 - - + +
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Residues in contact with TYR 386 (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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264A TYR* 3.7 15.9 - - - +
334A LEU* 3.5 46.2 - - + -
337A ALA* 3.7 2.5 + - + -
338A GLU* 3.5 51.2 + - + +
341A ASN* 4.4 3.6 + - + +
376A ILE* 3.6 25.6 - - + +
381A MET* 3.3 37.7 - - + +
382A THR 3.1 22.2 + - - -
383A GLN* 3.7 6.7 - - - +
385A GLU* 1.3 75.4 - - - +
387A ALA* 1.3 56.7 + - - +
389A LEU* 3.9 1.8 - - - +
390A THR* 2.8 37.3 + - - -
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Residues in contact with ALA 387 (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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260A ILE* 3.9 9.0 - - + -
261A MET* 3.5 30.5 - - - -
264A TYR* 3.4 37.7 - - + -
305A PHE* 3.7 5.5 - - - -
383A GLN 2.9 13.4 + - - +
384A GLU 3.2 0.6 + - - +
386A TYR* 1.3 73.7 - - - +
388A LEU* 1.3 62.7 + - - +
390A THR* 3.4 2.8 + - - -
391A ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 388 (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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256A LEU* 5.9 0.9 - - + -
257A LEU* 4.1 12.8 - - + -
260A ILE* 4.4 14.1 - - + -
384A GLU 2.9 18.8 + - - +
385A GLU 4.1 1.6 - - - +
387A ALA* 1.3 73.6 - - - +
389A LEU* 1.3 67.7 + - - +
391A ALA* 3.2 4.8 + - - +
392A ILE* 2.9 31.0 + - + +
415A LEU* 3.8 32.8 - - + +
418A VAL* 3.9 23.1 - - + -
419A LEU* 4.0 28.0 - - + -
422A LEU* 3.3 33.2 - - + -
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Residues in contact with LEU 389 (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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334A LEU* 3.9 18.2 - - + -
376A ILE* 4.9 3.1 - - + -
381A MET* 3.7 28.0 - - + -
385A GLU 2.7 14.3 + - - +
386A TYR 3.9 2.9 - - - +
388A LEU* 1.3 78.4 - - - +
390A THR* 1.3 62.5 + - - +
392A ILE* 3.2 5.7 + - + +
393A VAL* 2.9 26.2 + - - +
419A LEU* 3.6 25.5 - - + +
437A LEU* 4.1 30.1 - - + +
438A LEU* 4.9 2.5 - - + -
440A ARG* 5.8 0.9 - - + -
441A LEU* 3.6 39.3 - - + -
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Residues in contact with THR 390 (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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264A TYR* 4.0 17.0 + - + -
302A LEU* 4.3 5.4 - - + -
305A PHE* 3.9 14.6 - - + -
331A ALA* 4.3 17.9 + - + +
334A LEU* 3.6 20.0 - - - +
335A ARG* 5.4 1.7 + - - +
386A TYR* 2.8 30.2 + - - +
387A ALA 3.7 3.8 - - - -
388A LEU 3.3 0.2 - - - -
389A LEU* 1.3 73.7 - - - +
391A ALA* 1.3 62.7 + - - +
393A VAL* 3.3 5.4 + - - +
394A ILE* 3.0 46.0 + - + +
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Residues in contact with ALA 391 (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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260A ILE* 4.7 1.8 - - + -
305A PHE* 3.9 10.3 - - + -
309A LEU* 3.9 22.9 - - + -
387A ALA 3.1 13.9 + - - +
388A LEU* 3.2 8.0 + - - +
390A THR* 1.3 76.9 - - - +
392A ILE* 1.3 56.5 + - - +
394A ILE* 3.3 4.1 + - - +
395A LEU* 3.0 34.8 + - - +
415A LEU* 3.7 30.3 - - + -
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Residues in contact with ILE 392 (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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388A LEU 2.9 22.4 + - - +
389A LEU* 3.7 6.1 - - + +
391A ALA* 1.3 71.9 - - - +
393A VAL* 1.3 66.6 + - - +
394A ILE 3.5 0.2 + - - -
395A LEU 3.5 0.9 + - - -
396A SER* 3.4 7.6 + - - -
412A GLN* 3.0 42.5 + - + +
415A LEU* 3.8 35.7 - - + +
416A LEU* 3.9 30.3 - - + +
419A LEU* 3.6 30.1 - - + -
438A LEU* 5.5 0.7 - - + -
441A LEU* 4.1 18.6 - - + -
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Residues in contact with VAL 393 (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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327A SER* 3.5 7.3 - - - +
330A GLU* 3.7 27.1 - - + +
331A ALA* 3.8 15.0 - - + +
334A LEU* 4.4 7.4 - - + -
389A LEU 2.9 18.5 + - - +
390A THR* 3.5 9.4 - - - +
392A ILE* 1.3 77.7 - - - +
394A ILE* 1.3 61.7 + - - +
396A SER* 3.0 20.7 + - - -
399A ARG* 3.0 29.7 + - - +
441A LEU* 3.6 34.3 - - + -
444A LEU* 5.8 0.2 - - + -
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Residues in contact with ILE 394 (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 LEU* 3.6 23.3 - - + -
305A PHE* 4.1 12.6 - - + -
306A THR* 3.5 34.8 - - + +
309A LEU* 3.7 23.6 - - + -
312A PHE* 4.6 8.7 - - + -
323A LEU* 3.7 25.0 - - + +
324A LEU* 5.1 2.9 - - + -
327A SER* 3.5 22.8 + - - +
331A ALA* 4.4 7.6 - - + -
390A THR* 3.0 32.0 + - + +
391A ALA 3.3 4.5 + - - +
393A VAL* 1.3 76.7 - - - +
395A LEU* 1.3 58.2 + - + +
396A SER 3.2 4.4 + - - -
399A ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 395 (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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309A LEU* 4.3 22.4 - - + -
310A PRO* 5.1 3.4 - - + +
312A PHE* 4.1 25.4 - - + -
323A LEU* 4.5 9.4 - - + -
391A ALA 3.0 13.5 + - - +
392A ILE 3.6 4.9 - - - -
393A VAL 3.3 0.4 - - - -
394A ILE* 1.3 78.0 - - - +
396A SER* 1.3 60.9 + - - +
397A PRO* 3.3 3.6 - - - +
408A VAL* 3.4 13.7 - - + +
411A LEU* 3.9 37.2 - - + +
412A GLN* 3.3 29.9 + - + +
415A LEU* 3.7 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