Contacts of the helix formed by residues 392 - 408 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381D TRP* 4.8 4.0 - - + -
384D TRP* 4.4 7.9 - - + -
385D ALA* 4.0 29.5 + - + -
388D VAL* 4.1 7.6 - - + +
390D PRO 3.2 1.0 - - - -
391D ASP* 1.3 76.6 - - - +
393D GLN* 1.3 65.7 + - - +
394D ASP 3.3 2.9 - - - -
395D ILE* 3.1 18.3 + - + +
396D LEU* 3.0 21.8 + - - +
503D EDO 3.7 18.4 - - - +
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Residues in contact with GLN 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ALA* 5.2 2.7 - - - +
389D HIS* 4.1 21.3 - - - -
390D PRO* 3.2 21.0 + - + +
391D ASP 3.4 1.2 + - - -
392D ALA* 1.3 76.3 - - - +
394D ASP* 1.3 61.1 + - - +
396D LEU* 3.3 23.4 + - - +
397D ASP* 2.8 49.3 + - - +
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Residues in contact with ASP 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D ASP 5.0 1.9 + - - +
392D ALA 3.3 0.8 - - - -
393D GLN* 1.3 81.3 - - - +
395D ILE* 1.3 56.8 + - - +
397D ASP* 3.7 13.4 - - - +
398D THR* 2.8 35.1 + - - +
515D PEG 5.4 4.7 - - - +
516D PEG 3.5 23.1 + - - +
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Residues in contact with ILE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TRP* 3.8 32.1 - - + +
323D THR* 3.4 33.2 - - + +
381D TRP* 3.9 26.5 - - + -
392D ALA* 3.1 15.2 + - + +
394D ASP* 1.3 76.9 - - - +
396D LEU* 1.3 62.8 + - - +
398D THR* 3.2 8.3 + - - -
399D LEU* 3.1 21.7 + - - +
503D EDO 3.8 37.5 - - - +
516D PEG 3.4 15.7 - - - +
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Residues in contact with LEU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D HIS* 3.8 23.6 - - + +
381D TRP* 4.1 13.6 - - + -
382D GLU* 3.8 36.6 - - + +
385D ALA* 4.1 19.3 - - + -
392D ALA 3.0 11.7 + - - +
393D GLN* 3.6 26.5 - - - +
395D ILE* 1.3 74.6 - - - +
397D ASP* 1.3 67.1 + - - +
399D LEU* 3.2 8.8 + - + +
400D GLU* 3.1 38.1 + - - +
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Residues in contact with ASP 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D GLN* 2.8 40.9 + - - +
394D ASP* 3.7 13.3 - - - +
395D ILE 3.3 0.2 - - - -
396D LEU* 1.3 76.0 - - - +
398D THR* 1.3 63.7 + - - +
400D GLU* 3.2 14.1 + - - +
401D ASP* 3.0 30.8 + - - +
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Residues in contact with THR 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TRP* 6.1 0.4 - - - -
323D THR 3.3 21.8 - - - +
324D LYS 3.6 20.2 - - - +
325D PRO* 4.3 7.2 - - + -
394D ASP* 2.8 22.3 + - - +
395D ILE* 3.6 5.7 - - - -
396D LEU 3.2 0.2 - - - -
397D ASP* 1.3 76.1 - - - +
399D LEU* 1.3 58.5 + - - +
401D ASP* 3.2 10.2 + - + +
402D ASN* 2.9 34.7 + - - +
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Residues in contact with LEU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D PRO* 3.4 42.8 - - + +
323D THR* 4.2 7.4 - - + +
373D ILE* 3.7 22.9 - - + -
377D VAL* 4.0 11.9 - - + -
378D HIS* 3.7 42.8 - - + +
381D TRP* 4.1 15.9 - - + -
395D ILE 3.1 12.2 + - - +
396D LEU* 3.4 11.9 - - + +
398D THR* 1.3 78.1 - - - +
400D GLU* 1.3 56.7 + - - +
402D ASN* 3.2 1.4 + - - +
403D ARG* 2.9 27.9 + - - +
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Residues in contact with GLU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D ILE* 6.1 0.2 - - - -
378D HIS* 2.9 37.5 + - + +
396D LEU* 3.1 27.2 + - - +
397D ASP* 3.7 14.6 - - - +
399D LEU* 1.3 75.2 - - - +
401D ASP* 1.3 67.3 + - - +
403D ARG* 3.2 8.6 + - - +
404D GLU* 3.1 28.0 + - + +
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Residues in contact with ASP 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D ASP* 3.0 19.2 + - - +
398D THR* 3.4 12.1 - - + +
400D GLU* 1.3 79.1 - - - +
402D ASN* 1.3 64.9 + - - +
404D GLU* 3.4 6.2 + - - +
405D TRP* 3.2 20.6 + - - +
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Residues in contact with ASN 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D PRO 2.9 22.7 + - - +
324D LYS 2.8 27.1 + - - -
326D LEU* 3.4 27.5 + - + +
329D TYR* 3.7 24.3 - - + +
373D ILE* 4.6 2.2 - - + -
398D THR* 2.9 23.9 + - - +
399D LEU 3.2 4.2 + - - +
401D ASP* 1.3 77.6 - - - +
403D ARG* 1.3 66.4 + - - +
405D TRP* 3.3 7.4 + - - +
406D TYR* 3.2 26.7 + - - -
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Residues in contact with ARG 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D VAL* 3.4 25.7 - - + +
373D ILE* 3.7 38.1 - - + +
374D ASP* 3.1 34.0 + - - +
399D LEU 2.9 14.0 + - - +
400D GLU* 3.2 13.2 + - - +
402D ASN* 1.3 77.4 - - - +
404D GLU* 1.3 94.0 + - - +
405D TRP 3.3 0.3 + - - -
406D TYR* 3.3 2.3 + - - +
407D GLN* 3.1 43.0 + - - +
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Residues in contact with GLU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D GLU* 3.1 14.3 + - + +
401D ASP* 3.8 8.7 - - - +
402D ASN 3.3 0.2 - - - -
403D ARG* 1.3 109.3 + - - +
405D TRP* 1.3 64.0 + - - +
407D GLN* 3.3 10.7 + - - +
408D SER* 3.0 22.9 + - - -
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Residues in contact with TRP 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D LEU* 3.7 36.2 - - + +
330D ARG* 3.3 45.5 - - - -
401D ASP 3.2 13.4 + - - +
402D ASN* 3.6 9.2 - - - +
403D ARG 3.2 1.0 - - - -
404D GLU* 1.3 77.6 - - - +
406D TYR* 1.3 92.6 + + - +
408D SER* 2.9 28.3 + - - -
409D THR* 3.5 27.1 + - + +
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Residues in contact with TYR 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D LEU* 5.0 2.2 - - + -
329D TYR* 3.4 42.8 - + - -
330D ARG* 3.7 19.5 + - - +
333D THR* 3.1 34.6 + - + +
334D ASP* 5.5 0.7 + - - -
365D VAL* 4.9 3.4 - - + -
366D GLU* 3.5 49.5 - - + +
369D GLN* 3.9 17.9 - - + -
370D VAL* 4.1 6.7 - - + +
373D ILE* 5.5 1.1 - - + -
402D ASN 3.2 12.9 + - - +
403D ARG* 4.0 6.5 - - - +
405D TRP* 1.3 100.3 - + - +
407D GLN* 1.3 63.9 + - - +
409D THR* 2.9 18.0 + - - -
410D ILE* 3.2 8.5 + - - +
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Residues in contact with GLN 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D VAL* 3.6 28.8 - - + +
403D ARG* 3.1 35.8 + - - +
404D GLU* 3.4 16.2 - - - +
405D TRP 3.2 0.2 - - - -
406D TYR* 1.3 78.2 - - - +
408D SER* 1.3 57.5 + - - +
409D THR 3.1 4.0 + - - -
410D ILE* 3.5 29.8 + - - +
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Residues in contact with SER 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D GLU 3.0 13.1 + - - -
405D TRP* 2.9 23.7 + - - -
407D GLN* 1.3 75.5 - - - +
409D THR* 1.3 65.0 + - - +
410D ILE 3.6 2.2 - - - +
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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