Contacts of the helix formed by residues 392 - 410 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 6.3 0.2 - - + -
381B TRP* 4.7 4.7 - - + -
384B TRP* 4.6 9.4 - - + -
385B ALA* 3.9 30.6 + - + +
388B VAL* 4.1 12.5 - - + +
390B PRO 3.2 1.0 - - - -
391B ASP* 1.3 76.6 - - - +
393B GLN* 1.3 65.4 + - - +
394B ASP 3.3 2.5 - - - -
395B ILE* 3.1 24.9 + - + +
396B LEU* 2.9 24.2 + - + +
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Residues in contact with GLN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ALA* 5.3 3.7 - - - +
389B HIS* 4.6 16.5 + - - -
390B PRO* 3.2 21.1 + - + +
391B ASP 3.3 1.4 - - - -
392B ALA* 1.3 77.6 - - - +
394B ASP* 1.3 62.9 + - - +
396B LEU* 3.4 19.5 + - - +
397B ASP* 2.9 64.1 + - - +
400B GLU* 5.5 0.6 + - - -
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Residues in contact with ASP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASP 4.9 2.3 + - - +
392B ALA 3.3 0.4 - - - -
393B GLN* 1.3 80.6 - - - +
395B ILE* 1.3 57.1 + - + +
397B ASP* 3.7 11.6 - - - +
398B THR* 2.7 39.6 + - - +
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.8 44.9 - - + +
174B VAL* 5.7 2.5 - - + -
175B LEU* 4.8 6.7 - - + -
323B THR* 3.6 29.9 - - + +
381B TRP* 3.6 33.2 - - + -
391B ASP 5.0 3.8 + - - +
392B ALA* 3.1 21.9 + - + +
394B ASP* 1.3 78.8 - - + +
396B LEU* 1.3 58.4 + - - +
398B THR* 3.2 7.8 + - - -
399B LEU* 3.0 25.5 + - - +
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 3.9 22.2 - - + +
381B TRP* 4.0 9.6 - - + -
382B GLU* 3.8 33.9 - - + +
385B ALA* 4.2 19.1 - - + -
392B ALA* 2.9 18.9 + - + +
393B GLN* 3.8 18.6 - - - +
395B ILE* 1.3 75.0 - - + +
397B ASP* 1.3 58.5 + - - +
399B LEU* 3.2 16.0 - - + +
400B GLU* 3.0 43.9 + - - +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLN* 2.9 49.7 + - - +
394B ASP* 3.7 12.7 - - - +
396B LEU* 1.3 72.7 - - - +
398B THR* 1.3 63.0 + - - +
400B GLU* 3.3 15.4 + - - +
401B ASP* 2.9 37.4 + - - +
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 6.1 0.3 - - - -
323B THR 3.6 12.1 - - - +
324B LYS 3.5 28.7 - - - +
325B PRO* 4.2 7.2 - - + -
326B LEU 5.2 0.2 - - - +
394B ASP* 2.7 23.1 + - - +
395B ILE* 3.5 5.1 - - - -
397B ASP* 1.3 72.4 - - - +
399B LEU* 1.3 56.9 + - - +
401B ASP* 3.2 8.6 + - + +
402B ASN* 2.7 46.9 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 3.3 44.1 + - + +
323B THR* 3.9 10.7 - - + +
373B ILE* 3.9 16.4 - - + -
377B VAL* 4.0 11.4 - - + +
378B HIS* 3.6 44.4 - - + +
381B TRP* 4.2 6.7 - - + -
395B ILE 3.0 13.5 + - - +
396B LEU* 3.2 20.2 - - + +
398B THR* 1.3 76.6 - - - +
400B GLU* 1.3 58.8 + - - +
402B ASN* 3.7 0.7 - - - +
403B ARG* 2.9 29.8 + - - +
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 2.8 37.6 + - + +
393B GLN* 5.5 0.5 + - - -
396B LEU* 3.0 35.5 + - - +
397B ASP* 3.7 18.5 - - - +
399B LEU* 1.3 76.3 - - - +
401B ASP* 1.3 64.5 + - - +
403B ARG* 3.3 10.1 - - - +
404B GLU* 3.2 26.6 + - - +
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Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ASP* 2.9 23.3 + - - +
398B THR* 3.5 8.2 - - + +
400B GLU* 1.3 76.2 - - - +
402B ASN* 1.3 63.8 + - - +
404B GLU* 2.9 23.9 + - - +
405B TRP* 3.0 13.3 + - - +
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Residues in contact with ASN 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO 3.0 26.3 + - - +
324B LYS 2.6 29.9 + - - -
326B LEU* 3.5 28.2 + - + +
329B TYR* 3.7 22.4 - - + -
373B ILE* 4.6 2.7 - - + -
398B THR* 2.7 26.7 + - - +
399B LEU 3.7 0.9 - - - +
401B ASP* 1.3 74.5 - - - +
403B ARG* 1.3 62.6 + - - +
405B TRP* 3.3 7.7 + - - +
406B TYR* 3.1 28.5 + - - -
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Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.7 18.8 - - + +
373B ILE* 3.7 39.1 - - + +
374B ASP* 2.9 36.8 + - - +
378B HIS* 6.5 0.4 - - + -
399B LEU 2.9 17.1 + - - +
400B GLU* 3.3 10.8 - - - +
402B ASN* 1.3 77.0 - - - +
404B GLU* 1.3 81.0 + - - +
406B TYR* 3.4 3.5 + - - +
407B GLN* 3.0 53.9 + - - +
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Residues in contact with GLU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLU 3.2 13.2 + - - +
401B ASP* 2.9 11.0 + - - +
403B ARG* 1.3 109.0 + - - +
405B TRP* 1.3 65.6 - - - +
407B GLN* 3.3 8.8 + - - +
408B SER* 3.0 23.4 + - - -
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Residues in contact with TRP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.6 36.3 - - + +
330B ARG* 3.1 49.6 - - - -
401B ASP 3.0 11.0 + - - +
402B ASN* 3.3 10.3 + - - +
404B GLU* 1.3 77.0 - - - +
406B TYR* 1.3 90.0 + + - +
408B SER* 2.7 27.9 + - - -
409B THR* 2.9 34.3 + - + -
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Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 4.6 2.9 - - + -
329B TYR* 3.2 46.2 - + - -
330B ARG* 3.8 14.8 + - + +
333B THR* 3.1 33.1 + - + +
365B VAL* 5.1 2.5 - - + -
366B GLU* 3.9 32.7 - - + +
369B GLN* 4.1 15.5 - - + -
370B VAL* 3.9 15.3 - - + -
373B ILE* 5.2 0.9 - - + -
402B ASN 3.1 17.7 + - - +
403B ARG* 3.9 4.7 - - - +
405B TRP* 1.3 100.9 - + - +
407B GLN* 1.3 61.6 + - - +
409B THR* 2.8 21.2 + - + -
410B ILE* 3.3 12.6 + - - +
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Residues in contact with GLN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.6 22.1 - - + +
403B ARG* 3.0 47.7 + - - +
404B GLU* 3.6 12.3 - - - +
406B TYR* 1.3 75.5 - - - +
408B SER* 1.3 61.4 + - - +
410B ILE* 3.3 37.1 + - - +
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Residues in contact with SER 408 (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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404B GLU 3.0 13.0 + - - -
405B TRP* 2.7 25.8 + - - -
406B TYR 3.1 0.4 - - - -
407B GLN* 1.3 77.2 - - - +
409B THR* 1.3 60.5 + - - +
410B ILE 3.4 3.6 + - - +
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Residues in contact with THR 409 (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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366B GLU* 3.5 28.2 - - + +
405B TRP* 2.9 42.0 + - + -
406B TYR* 2.8 12.0 + - + -
408B SER* 1.3 81.3 + - - +
410B ILE* 1.3 61.0 + - - +
411B PRO* 3.2 11.3 - - - +
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Residues in contact with ILE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLU* 4.0 2.7 - - + -
367B LYS* 3.8 54.5 - - + +
370B VAL* 3.9 10.5 - - + -
406B TYR 3.6 9.0 - - - +
407B GLN* 3.3 46.3 + - - +
408B SER 4.6 3.5 - - - +
409B THR* 1.3 75.5 - - - +
411B PRO* 1.3 81.0 - - + +
412B GLN 3.8 7.0 + - - +
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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
------------------------------------------------------------
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