Contacts of the helix formed by residues 392 - 408 (chain A) in PDB entry 4OGB
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 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 6.3 0.4 - - + -
381A TRP* 5.0 4.7 - - + -
384A TRP* 4.3 10.1 - - + -
385A ALA* 3.7 31.6 - - + +
388A VAL* 3.9 12.4 - - + +
390A PRO 3.1 1.4 - - - -
391A ASP* 1.3 76.7 - - - +
393A GLN* 1.3 64.7 + - - +
394A ASP 3.3 2.7 - - - -
395A ILE* 3.1 23.1 + - + +
396A LEU* 3.0 22.2 + - - +
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Residues in contact with GLN 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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385A ALA* 5.1 1.6 - - - +
389A HIS* 4.8 13.2 + - - -
390A PRO* 3.1 22.8 + - + +
391A ASP 3.4 1.2 - - - -
392A ALA* 1.3 76.7 - - - +
394A ASP* 1.3 60.5 + - - +
396A LEU* 3.2 22.2 + - - +
397A ASP* 2.6 61.8 + - - +
400A GLU* 6.2 0.2 - - - -
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Residues in contact with ASP 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASP 4.9 5.0 + - - +
392A ALA 3.3 0.4 - - - -
393A GLN* 1.3 80.6 - - - +
395A ILE* 1.3 62.8 + - + +
397A ASP* 3.5 9.7 + - - +
398A THR* 2.9 29.1 + - - -
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Residues in contact with ILE 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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102A TRP* 3.7 47.3 - - + +
174A VAL* 5.9 1.6 - - + -
175A LEU* 4.7 6.3 - - + -
323A THR* 3.5 28.5 - - + +
381A TRP* 3.8 33.4 - - + -
391A ASP 5.3 2.0 - - - +
392A ALA* 3.1 20.6 + - + +
394A ASP* 1.3 79.3 - - + +
396A LEU* 1.3 63.5 + - - +
398A THR* 3.3 8.0 + - - -
399A LEU* 3.0 20.6 + - - +
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Residues in contact with LEU 396 (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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378A HIS* 3.8 24.0 - - + +
381A TRP* 4.1 12.3 - - + -
382A GLU* 3.9 35.0 - - + +
385A ALA* 4.0 19.5 - - + -
392A ALA 3.0 12.3 + - - +
393A GLN* 3.5 25.4 - - - +
395A ILE* 1.3 78.8 - - - +
397A ASP* 1.3 61.9 + - - +
399A LEU* 3.1 8.9 + - + +
400A GLU* 3.0 40.2 + - - +
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Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLN* 2.6 49.2 + - - +
394A ASP* 3.8 9.9 - - - +
396A LEU* 1.3 75.1 - - - +
398A THR* 1.3 58.3 + - - +
400A GLU* 3.3 15.3 + - - +
401A ASP* 2.9 39.8 + - - +
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Residues in contact with THR 398 (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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102A TRP* 6.1 0.3 - - - -
323A THR 3.2 25.6 - - - +
324A LYS 3.8 10.1 - - - +
325A PRO* 4.2 8.7 - - + -
394A ASP 2.9 15.3 + - - -
395A ILE* 3.6 6.0 - - - -
396A LEU 3.3 0.2 - - - -
397A ASP* 1.3 75.7 - - - +
399A LEU* 1.3 58.4 + - - +
401A ASP* 3.7 7.5 - - + +
402A ASN* 2.9 51.4 + - - +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 3.5 41.7 + - + +
323A THR* 4.2 6.5 - - + +
373A ILE* 4.0 16.6 - - + +
377A VAL* 3.9 11.4 - - + -
378A HIS* 3.7 41.5 - - + +
381A TRP* 4.0 22.7 - - + -
395A ILE 3.0 13.6 + - - +
396A LEU* 3.1 12.5 + - + +
398A THR* 1.3 78.2 - - - +
400A GLU* 1.3 56.8 + - - +
402A ASN* 3.5 1.7 + - - +
403A ARG* 2.9 26.3 + - - +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS* 2.9 37.2 + - + +
396A LEU* 3.0 32.8 + - - +
397A ASP* 3.3 14.6 + - - +
399A LEU* 1.3 73.0 - - - +
401A ASP* 1.3 62.1 + - - +
403A ARG* 3.1 7.3 + - - +
404A GLU* 2.8 37.4 + - + +
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Residues in contact with ASP 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASP* 2.9 27.0 + - - +
398A THR* 3.7 8.0 - - + +
400A GLU* 1.3 77.3 - - - +
402A ASN* 1.3 61.0 + - - +
404A GLU* 3.2 9.5 + - - +
405A TRP* 2.8 28.3 + - - +
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Residues in contact with ASN 402 (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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322A PRO 2.8 26.7 + - - +
324A LYS 2.9 23.6 + - - -
326A LEU* 3.8 25.5 + - + +
329A TYR* 3.7 26.0 - - + +
373A ILE* 4.7 1.1 - - + -
398A THR* 2.9 26.1 + - - +
399A LEU 3.8 2.0 - - - +
401A ASP* 1.3 77.2 - - - +
403A ARG* 1.3 62.7 + - - +
405A TRP* 3.6 7.6 - - - +
406A TYR* 3.0 29.9 + - - -
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Residues in contact with ARG 403 (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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370A VAL* 3.8 18.6 - - + +
373A ILE* 3.7 38.1 - - + +
374A ASP* 2.8 38.6 + - - +
378A HIS* 6.3 0.9 - - + -
399A LEU 2.9 17.6 + - - +
400A GLU* 3.1 9.4 + - + +
402A ASN* 1.3 77.6 - - - +
404A GLU* 1.3 79.3 + - - +
406A TYR* 3.3 4.6 + - - +
407A GLN* 3.0 55.9 + - - +
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLU* 2.8 19.0 + - + +
401A ASP* 3.5 10.1 - - - +
403A ARG* 1.3 110.2 + - - +
405A TRP* 1.3 51.8 + - - +
407A GLN* 3.3 6.9 + - - +
408A SER* 2.7 36.8 + - - -
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Residues in contact with TRP 405 (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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326A LEU* 3.6 29.2 - - + +
330A ARG* 3.4 45.3 - - - -
366A GLU* 5.9 0.4 - - + -
401A ASP 2.8 16.8 + - - +
402A ASN* 3.6 10.3 - - - +
404A GLU* 1.3 73.5 - - - +
406A TYR* 1.3 118.7 + + - +
408A SER* 2.7 28.2 + - - -
409A THR* 3.3 27.1 - - + +
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Residues in contact with TYR 406 (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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326A LEU* 4.5 3.4 - - + -
329A TYR* 3.4 39.5 - + - -
330A ARG* 4.0 14.1 - - - +
333A THR* 3.4 26.2 + - - +
365A VAL* 4.5 7.6 - - + +
366A GLU* 3.8 38.6 - - + +
369A GLN* 4.0 19.5 - - + -
370A VAL* 4.1 14.8 - - + +
373A ILE* 5.4 1.6 - - + -
402A ASN 3.0 20.9 + - - +
403A ARG* 3.8 4.5 - - - +
405A TRP* 1.3 107.9 - + - +
407A GLN* 1.3 58.1 + - - +
409A THR* 2.8 29.0 + - - -
410A ILE 3.9 0.3 - - - +
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Residues in contact with GLN 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 3.7 28.5 - - + +
403A ARG* 3.0 42.1 + - - +
404A GLU* 3.6 9.6 - - - +
406A TYR* 1.3 71.4 - - - +
408A SER* 1.3 62.8 + - - +
409A THR 2.9 6.5 + - - -
410A ILE* 3.5 18.3 + - - +
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Residues in contact with SER 408 (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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404A GLU 2.7 21.6 + - - -
405A TRP* 2.7 20.8 + - - -
406A TYR 3.2 0.2 - - - -
407A GLN* 1.3 74.1 - - - +
409A THR* 1.3 65.2 + - - +
410A ILE 3.4 3.0 + - - -
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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