Contacts of the helix formed by residues 382 - 396 (chain A) in PDB entry 2OCA
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 ASP 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLU 2.6 11.5 + - - -
381A VAL* 1.3 97.6 - - - +
383A THR* 1.3 70.2 + - - +
384A GLU 3.3 1.1 - - - -
385A THR* 2.8 2.4 + - - -
386A ARG* 2.8 51.2 + - - +
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Residues in contact with THR 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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380A GLU* 3.9 1.9 + - - -
382A ASP* 1.3 79.6 - - - +
384A GLU* 1.3 61.8 + - + +
386A ARG* 4.7 1.7 - - - +
387A ASN* 3.3 21.0 + - - +
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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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376A TYR 4.6 10.9 - - - +
380A GLU* 3.8 38.7 + - + +
382A ASP 3.3 0.4 - - - -
383A THR* 1.3 79.4 - - + +
385A THR* 1.3 59.9 + - - +
387A ASN* 3.4 12.9 - - + +
388A ILE* 3.0 32.6 - - + +
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Residues in contact with THR 385 (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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377A VAL* 4.0 20.0 - - + +
379A GLY 3.6 6.6 + - - -
380A GLU 3.3 4.2 + - - -
381A VAL* 2.5 40.0 + - - +
382A ASP* 2.8 5.8 + - - -
384A GLU* 1.3 75.4 - - - +
386A ARG* 1.3 64.0 + - + +
387A ASN 3.1 1.5 + - - -
388A ILE* 3.4 10.5 + - - +
389A MET* 3.0 45.2 + - + +
407A VAL* 4.5 7.2 - - + +
411A GLY* 5.8 3.1 - - - +
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Residues in contact with ARG 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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382A ASP* 2.8 36.8 + - - +
383A THR* 4.7 1.6 - - - +
385A THR* 1.3 76.0 - - + +
387A ASN* 1.3 56.9 + - - +
388A ILE 3.2 0.2 - - - -
389A MET* 3.8 11.2 - - + -
390A LYS* 2.8 59.3 + - + +
411A GLY* 5.8 8.9 - - - -
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Residues in contact with ASN 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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383A THR* 3.3 21.6 + - - +
384A GLU* 3.4 14.7 - - - +
386A ARG* 1.3 80.0 - - - +
388A ILE* 1.3 60.3 + - - +
390A LYS* 3.6 8.6 - - - +
391A THR* 2.9 35.9 + - - -
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Residues in contact with ILE 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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375A TYR* 3.8 46.9 - - + -
376A TYR 4.3 4.5 - - - +
377A VAL* 3.4 32.3 - - + -
384A GLU* 3.0 30.1 - - + +
385A THR* 3.4 5.8 + - - +
386A ARG 3.2 0.2 - - - -
387A ASN* 1.3 74.4 - - + +
389A MET* 1.3 59.8 + - + +
390A LYS 2.9 4.5 - - - -
391A THR* 2.8 29.3 + - - -
392A LEU* 3.0 15.1 + - + +
399A ILE* 5.3 3.4 - - + -
401A ILE* 4.9 12.6 - - + -
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Residues in contact with MET 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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351A PHE* 4.2 19.3 - - + -
377A VAL* 5.0 5.2 - - + -
385A THR* 3.0 42.3 + - + +
386A ARG* 3.3 13.9 + - + +
388A ILE* 1.3 78.3 - - + +
390A LYS* 1.3 58.2 - - + +
392A LEU* 4.1 10.9 - - - +
393A ALA* 3.3 22.7 + - - +
401A ILE* 6.0 2.7 - - + -
407A VAL* 4.4 16.8 - - + -
408A PHE* 5.5 1.8 - - - -
411A GLY 4.4 15.0 - - - +
412A ILE 5.3 0.4 - - - -
413A SER* 3.0 32.0 + - - +
414A VAL* 3.8 25.9 + - + +
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Residues in contact with LYS 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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386A ARG* 2.8 40.8 + - + +
387A ASN* 3.6 7.2 - - - +
389A MET* 1.3 80.0 - - + +
391A THR* 1.3 57.8 + - - +
392A LEU 3.0 2.0 - - - -
393A ALA* 3.9 6.0 - - + +
394A GLU* 2.9 42.0 + - - +
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Residues in contact with THR 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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375A TYR* 4.8 15.4 - - + +
387A ASN* 2.9 27.6 + - - -
388A ILE* 2.8 15.0 + - - -
390A LYS* 1.3 78.0 - - - +
392A LEU* 1.3 59.3 + - - +
394A GLU* 3.8 14.2 - - - +
396A GLY* 3.6 18.5 + - - -
399A ILE* 4.0 17.9 - - + -
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Residues in contact with LEU 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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349A ASN* 4.2 17.5 - - + +
351A PHE* 4.3 10.8 - - + -
388A ILE* 3.0 13.5 + - + +
389A MET* 4.3 9.9 - - - +
391A THR* 1.3 75.2 - - - +
393A ALA* 1.3 67.4 + - - +
394A GLU 3.1 2.8 + - - -
395A ASN* 3.4 5.9 + - - -
396A GLY 3.9 2.6 + - - +
399A ILE* 4.3 15.3 - - + -
401A ILE* 4.5 12.1 - - + -
414A VAL* 4.2 18.6 - - + -
415A LYS 3.5 13.5 - - - +
416A ASN* 3.0 56.4 + - - +
417A LEU* 4.1 14.4 - - + +
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Residues in contact with ALA 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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389A MET 3.3 18.2 + - - +
390A LYS* 3.3 9.8 + - + +
392A LEU* 1.3 80.5 - - - +
394A GLU* 1.3 66.9 + - - +
413A SER* 5.4 3.8 - - - +
415A LYS* 3.6 52.5 + - + +
416A ASN* 4.0 4.6 + - - -
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Residues in contact with GLU 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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390A LYS* 2.9 28.4 + - - +
391A THR* 3.8 11.8 - - - +
392A LEU 3.1 0.8 + - - -
393A ALA* 1.3 82.8 - - - +
395A ASN* 1.3 69.7 + - + +
416A ASN* 4.0 2.4 + - - -
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Residues in contact with ASN 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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392A LEU 3.4 0.6 + - - -
394A GLU* 1.3 85.4 - - - +
396A GLY* 1.3 64.9 + - - +
397A LYS* 2.9 30.3 + - - +
416A ASN* 3.3 15.0 + - - +
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Residues in contact with GLY 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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349A ASN* 3.2 25.6 + - - +
373A LYS* 5.8 0.9 - - - -
391A THR* 3.6 11.2 + - - -
392A LEU 3.9 2.9 + - - +
395A ASN* 1.3 78.7 - - - +
397A LYS* 1.3 66.9 + - - +
399A ILE* 3.8 19.8 - - - +
416A ASN* 4.6 0.5 + - - -
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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