Contacts of the helix formed by residues 392 - 408 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C TRP* 4.9 3.1 - - + -
384C TRP* 4.2 13.0 - - + -
385C ALA* 4.2 16.0 + - + +
388C VAL* 4.0 15.5 - - + +
390C PRO 2.9 1.2 + - - -
391C ASP* 1.3 78.2 - - - +
393C GLN* 1.3 58.3 + - - +
394C ASP 3.4 2.5 - - - -
395C ILE* 3.3 15.5 + - + +
396C LEU* 3.0 28.6 + - - +
513C EDO 3.6 19.7 - - - -
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Residues in contact with GLN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C ALA* 5.6 4.4 - - + +
389C HIS* 4.4 23.6 + - + +
390C PRO* 3.1 21.4 + - + +
391C ASP 3.5 1.2 + - - -
392C ALA* 1.3 78.1 - - - +
394C ASP* 1.3 58.7 + - - +
396C LEU* 3.5 17.6 + - - +
397C ASP* 2.8 52.0 + - - +
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Residues in contact with ASP 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ASP 5.2 0.8 + - - -
392C ALA 3.4 0.2 - - - -
393C GLN* 1.3 76.0 - - - +
395C ILE* 1.3 57.3 + - + +
397C ASP* 3.8 15.9 - - - +
398C THR* 2.7 37.1 + - - +
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Residues in contact with ILE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C TRP* 3.7 45.1 - - + +
175C LEU* 4.6 1.1 - - + -
323C THR* 3.6 28.3 - - + +
381C TRP* 3.8 32.8 - - + -
391C ASP 5.5 0.2 - - - +
392C ALA* 3.3 12.9 + - + +
393C GLN 3.3 0.4 - - - -
394C ASP* 1.3 77.9 - - - +
396C LEU* 1.3 63.3 + - - +
398C THR* 3.2 8.0 + - - -
399C LEU* 3.1 20.8 + - - +
513C EDO 4.0 30.3 - - - -
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Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C THR* 6.1 0.2 - - - -
378C HIS* 3.9 19.1 - - + +
381C TRP* 4.1 7.6 - - + -
382C GLU* 4.0 39.5 - - + +
385C ALA* 4.4 12.3 - - + -
392C ALA 3.0 16.7 + - - +
393C GLN* 3.8 20.9 - - - +
395C ILE* 1.3 77.9 - - - +
397C ASP* 1.3 61.6 + - - +
399C LEU* 3.2 23.5 + - + +
400C GLU* 3.1 44.3 + - - +
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Residues in contact with ASP 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C GLN* 2.8 44.7 + - - +
394C ASP* 3.8 17.0 - - - +
396C LEU* 1.3 76.4 - - - +
398C THR* 1.3 61.9 - - - +
400C GLU* 3.6 16.3 + - - +
401C ASP* 3.1 33.5 + - - +
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Residues in contact with THR 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 5.8 1.6 - - - -
323C THR 3.4 21.9 + - - +
324C LYS 3.8 9.9 - - - +
325C PRO* 4.3 7.4 - - + -
394C ASP* 2.7 23.5 + - - +
395C ILE* 3.2 5.7 + - - -
397C ASP* 1.3 75.8 - - - +
399C LEU* 1.3 57.5 + - - +
401C ASP* 3.4 7.6 + - + +
402C ASN* 2.8 44.3 + - - +
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Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C PRO* 3.6 38.8 - - + +
323C THR* 4.2 7.8 - - + +
373C ILE* 3.6 26.0 - - + -
377C VAL* 4.0 13.9 - - + +
378C HIS* 3.7 43.7 - - + +
381C TRP* 4.2 7.0 - - + -
395C ILE 3.1 12.7 + - - +
396C LEU* 3.3 20.2 - - + +
398C THR* 1.3 76.2 - - - +
400C GLU* 1.3 54.0 + - - +
402C ASN* 2.9 4.9 + - - +
403C ARG* 2.7 34.1 + - - +
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C HIS* 3.0 36.6 + - + +
396C LEU* 3.1 28.9 + - - +
397C ASP* 4.0 17.3 - - - +
399C LEU* 1.3 75.5 - - - +
401C ASP* 1.3 65.2 + - - +
403C ARG* 3.3 9.6 + - - +
404C GLU* 3.1 28.5 + - + +
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Residues in contact with ASP 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C ASP* 3.1 23.6 + - - +
398C THR* 3.5 7.8 - - + +
400C GLU* 1.3 78.7 - - - +
402C ASN* 1.3 62.9 + - - +
404C GLU* 3.1 9.2 + - - +
405C TRP* 3.0 21.7 + - - +
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Residues in contact with ASN 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C PRO 2.6 27.5 + - - +
324C LYS 2.9 23.8 + - - +
326C LEU* 3.2 30.1 + - + +
329C TYR* 3.8 17.9 - - + -
373C ILE* 4.6 2.5 - - + -
398C THR* 2.8 29.3 + - - +
399C LEU 3.3 6.5 - - - +
401C ASP* 1.3 69.2 - - - +
403C ARG* 1.3 66.3 + - - +
405C TRP* 3.2 7.8 + - - +
406C TYR* 3.1 27.5 + - - -
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Residues in contact with ARG 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C VAL* 3.8 20.2 - - + +
373C ILE* 3.7 39.4 - - + +
374C ASP* 2.9 37.3 + - - +
399C LEU 2.7 15.6 + - - +
400C GLU* 3.4 13.5 - - - +
401C ASP 3.2 0.2 - - - -
402C ASN* 1.3 73.2 - - - +
404C GLU* 1.3 80.5 + - - +
406C TYR* 3.6 2.0 + - - +
407C GLN* 3.1 48.5 + - - +
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Residues in contact with GLU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C GLU* 3.1 14.3 + - + +
401C ASP* 3.1 10.3 + - - +
403C ARG* 1.3 108.2 + - - +
405C TRP* 1.3 65.7 + - - +
407C GLN* 3.2 10.9 + - - +
408C SER* 3.0 24.8 + - - -
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Residues in contact with TRP 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LEU* 3.4 34.9 - - + +
330C ARG* 3.6 35.7 - - + -
401C ASP 3.0 12.1 + - - +
402C ASN* 3.6 11.2 - - - +
404C GLU* 1.3 77.1 - - - +
406C TYR* 1.3 97.1 + + - +
408C SER* 2.7 24.6 + - - -
409C THR* 2.8 34.6 + - + -
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Residues in contact with TYR 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LEU* 4.6 3.1 - - + -
329C TYR* 3.4 44.0 - + - -
330C ARG* 3.9 18.9 - - + +
333C THR* 3.2 33.6 + - + +
334C ASP* 5.6 0.5 + - - -
365C VAL* 5.0 3.4 - - + -
366C GLU* 3.9 36.2 - - + +
369C GLN* 4.1 16.6 - - + -
370C VAL* 4.3 12.8 - - + +
373C ILE* 5.6 0.9 - - + -
402C ASN 3.1 14.0 + - - +
403C ARG* 4.1 4.7 - - - +
405C TRP* 1.3 102.7 - + - +
407C GLN* 1.3 66.0 + - - +
409C THR* 2.9 20.8 + - + -
410C ILE* 3.6 8.5 + - - +
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Residues in contact with GLN 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C VAL* 3.7 22.2 - - + +
403C ARG* 3.1 39.0 + - - +
404C GLU* 3.5 15.0 - - - +
406C TYR* 1.3 75.3 - - - +
408C SER* 1.3 61.8 + - - +
409C THR 3.1 1.4 + - - -
410C ILE* 3.2 49.2 + - - +
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Residues in contact with SER 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C GLU 3.0 12.1 + - - -
405C TRP* 2.7 28.2 + - - -
407C GLN* 1.3 77.1 - - - +
409C THR* 1.3 60.0 + - - +
410C ILE 3.3 2.1 + - - -
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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
------------------------------------------------------------
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