Contacts of the helix formed by residues 422 - 438 (chain A) in PDB entry 2OAT
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 GLU 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A LEU* 3.8 21.6 - - + +
355A ILE* 3.8 22.4 - - + +
421A LYS* 1.3 72.9 - - - +
423A ASP* 1.3 58.3 + - - +
425A LEU* 3.6 4.2 - - + +
426A ARG* 2.8 67.0 + - + +
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Residues in contact with ASP 423 (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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421A LYS* 3.2 40.0 + - - +
422A GLU* 1.3 74.2 + - - +
424A GLU* 1.3 68.5 + - - +
426A ARG* 3.2 7.8 + - - +
427A GLU* 2.9 23.5 + - - +
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Residues in contact with GLU 424 (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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68A ILE* 3.4 29.4 - - + +
69A TYR* 3.9 16.6 + - - +
79A PHE* 3.9 4.5 - - + -
419A VAL 4.7 0.2 - - - +
420A ILE* 3.6 11.3 - - + +
421A LYS* 2.7 57.5 + - - +
423A ASP* 1.3 82.8 + - - +
425A LEU* 1.3 63.7 + - - +
427A GLU* 3.1 12.7 + - - +
428A SER* 3.0 26.5 + - - -
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Residues in contact with LEU 425 (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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81A PHE* 4.2 19.7 - - + -
352A LEU* 3.5 39.5 - - + +
355A ILE* 4.0 23.8 - - + -
356A LEU* 4.0 25.6 - - + +
376A LEU* 5.2 4.3 - - + -
416A PRO* 4.8 6.3 - - + -
420A ILE* 3.7 17.6 - - + +
421A LYS 2.8 20.5 + - - +
422A GLU* 3.6 5.8 - - + +
424A GLU* 1.3 72.5 - - - +
426A ARG* 1.4 59.1 + - + +
428A SER* 3.1 5.2 + - - -
429A ILE* 2.8 34.2 + - + +
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Residues in contact with ARG 426 (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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355A ILE* 3.6 32.0 - - + +
359A GLU* 3.3 29.0 + - + -
422A GLU* 2.8 53.8 + - + +
423A ASP* 3.8 6.3 - - - +
425A LEU* 1.4 73.5 - - + +
427A GLU* 1.3 63.6 + - - +
429A ILE* 3.2 14.6 + - + +
430A GLU* 3.0 29.7 + - + +
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Residues in contact with GLU 427 (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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69A TYR* 4.8 3.7 + - - -
79A PHE* 3.6 27.4 - - + -
423A ASP 2.9 13.1 + - - +
424A GLU* 3.1 14.4 + - - +
426A ARG* 1.3 76.1 - - - +
428A SER* 1.3 62.9 + - - +
430A GLU* 3.2 10.9 + - - +
431A ILE* 3.0 26.8 + - + +
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Residues in contact with SER 428 (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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79A PHE* 3.4 24.8 - - - -
81A PHE* 3.4 20.9 - - - -
402A LEU* 3.4 25.1 - - - +
420A ILE* 4.5 0.3 - - - +
424A GLU 3.0 16.9 + - - -
425A LEU* 3.6 4.6 - - - -
427A GLU* 1.3 75.8 - - - +
429A ILE* 1.3 52.5 + - - +
431A ILE* 3.1 9.6 + - - +
432A ILE* 2.7 39.7 + - - +
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Residues in contact with ILE 429 (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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81A PHE* 6.2 0.2 - - + -
355A ILE* 4.2 4.0 - - + -
356A LEU* 3.9 30.5 - - + -
359A GLU* 3.7 42.6 - - + +
360A LEU* 5.5 4.5 - - + +
425A LEU* 2.8 42.1 + - + +
426A ARG* 3.2 10.1 + - + +
428A SER* 1.3 75.8 - - - +
430A GLU* 1.3 55.2 + - - +
432A ILE* 3.0 10.1 + - + +
433A ASN* 2.7 54.4 + - - +
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 3.0 20.8 + - + +
427A GLU* 3.2 10.7 + - + +
429A ILE* 1.3 79.4 - - - +
431A ILE* 1.3 57.1 + - + +
433A ASN* 3.5 19.4 + - - +
434A LYS* 2.8 33.8 + - - +
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Residues in contact with ILE 431 (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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79A PHE* 3.8 35.4 - - + -
397A LEU* 4.7 2.7 - - + -
400A ASN* 3.4 42.2 - - + +
401A GLY* 4.5 4.0 - - - +
402A LEU* 4.0 18.2 - - + -
427A GLU* 3.0 22.2 + - + +
428A SER* 3.1 7.6 + - - +
430A GLU* 1.3 76.1 - - + +
432A ILE* 1.3 60.5 + - - +
434A LYS* 3.8 7.8 - - - +
435A THR* 2.7 35.6 + - - +
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Residues in contact with ILE 432 (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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81A PHE* 4.4 9.0 - - + -
356A LEU* 5.2 4.3 - - + -
360A LEU* 4.1 21.3 - - + -
363A LEU* 4.9 4.5 - - + -
380A ILE* 5.3 0.7 - - + -
397A LEU* 4.1 11.0 - - + -
402A LEU* 4.1 20.9 - - + -
414A PHE* 3.6 51.4 - - + -
428A SER 2.7 26.2 + - - +
429A ILE* 3.5 10.5 - - + +
431A ILE* 1.3 72.7 - - - +
433A ASN* 1.3 64.7 + - - +
435A THR* 3.7 1.4 - - - -
436A ILE* 2.9 35.8 + - + +
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Residues in contact with ASN 433 (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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359A GLU* 4.6 7.7 + - - +
360A LEU* 5.6 1.9 - - - +
363A LEU* 3.2 33.8 - - + +
429A ILE* 2.7 44.0 + - - +
430A GLU* 3.5 23.0 + - - +
432A ILE* 1.3 73.4 - - - +
434A LYS* 1.3 67.0 + - - +
437A LEU* 2.9 37.9 + - + +
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Residues in contact with LYS 434 (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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400A ASN* 3.8 38.7 + - - +
430A GLU 2.8 20.4 + - - +
431A ILE* 3.8 7.4 - - - +
433A ASN* 1.3 72.9 - - - +
435A THR* 1.3 63.8 + - - +
437A LEU* 3.8 4.6 - - - +
438A SER* 2.9 28.3 + - - -
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Residues in contact with THR 435 (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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393A VAL* 4.0 6.7 - - + +
396A ARG* 3.5 34.3 - - + -
397A LEU* 3.4 35.8 - - + +
400A ASN* 3.2 21.7 + - - +
431A ILE 2.7 21.2 + - - -
432A ILE 3.7 0.7 - - - -
434A LYS* 1.3 76.6 - - - +
436A ILE* 1.3 65.5 + - - +
438A SER* 2.9 23.5 + - - -
439A PHE* 3.4 13.9 - - + -
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Residues in contact with ILE 436 (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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363A LEU* 4.3 25.6 - - + -
367A VAL* 3.4 27.9 - - + +
368A VAL* 4.6 2.5 - - + -
380A ILE* 4.3 11.4 - - + -
382A ILE* 4.3 17.3 - - + -
388A TRP* 4.2 17.5 - - + -
393A VAL* 3.9 25.8 - - + -
397A LEU* 5.8 0.7 - - + -
432A ILE* 2.9 28.9 + - + +
433A ASN* 4.0 1.8 - - - +
435A THR* 1.3 75.4 - - - +
437A LEU* 1.3 69.8 - - + +
438A SER 3.3 0.7 + - - -
439A PHE* 3.5 20.8 + - - +
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Residues in contact with LEU 437 (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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363A LEU* 4.4 12.8 - - + -
364A PRO* 3.9 33.0 - - + -
367A VAL* 5.6 3.6 - - + -
433A ASN* 2.9 33.4 + - + +
434A LYS* 4.1 3.4 - - - +
436A ILE* 1.3 78.7 - - + +
438A SER* 1.3 60.2 + - - +
439A PHE* 3.2 10.1 + - - +
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Residues in contact with SER 438 (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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396A ARG* 2.7 36.6 + - - -
400A ASN* 5.9 0.7 - - - -
434A LYS* 2.9 23.0 + - - -
435A THR* 2.9 12.5 + - - -
437A LEU* 1.3 75.1 - - - +
439A PHE* 1.3 57.6 + - - +
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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