Contacts of the helix formed by residues 422 - 438 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LEU* 3.9 25.4 - - + +
355B ILE* 4.0 15.4 - - + +
421B LYS* 1.3 73.2 - - - +
423B ASP* 1.3 62.6 + - - +
425B LEU* 3.3 5.2 + - + +
426B ARG* 2.9 62.1 + - + +
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Residues in contact with ASP 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS* 3.4 31.8 + - - +
422B GLU* 1.3 74.2 - - - +
424B GLU* 1.3 65.0 + - - +
426B ARG* 3.3 8.6 + - - +
427B GLU* 2.9 29.0 + - - +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.5 27.6 - - + +
69B TYR* 4.1 17.5 + - - +
79B PHE* 3.6 4.6 - - + -
419B VAL 4.4 1.0 - - - +
420B ILE* 3.7 11.8 - - + -
421B LYS* 2.8 52.2 + - - +
423B ASP* 1.3 82.5 + - - +
425B LEU* 1.3 59.4 + - - +
427B GLU* 3.3 12.2 + - - +
428B SER* 2.9 32.1 + - - -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 4.7 8.5 - - + -
352B LEU* 3.5 43.3 - - + +
355B ILE* 3.8 25.1 - - + -
356B LEU* 3.7 30.3 - - + +
376B LEU* 5.0 3.1 - - + -
416B PRO* 5.0 4.5 - - + -
420B ILE* 4.0 22.3 - - + +
421B LYS 2.9 13.5 + - - +
422B GLU* 3.5 10.1 - - - +
424B GLU* 1.3 75.5 - - - +
426B ARG* 1.3 60.6 + - + +
428B SER* 3.1 5.2 + - - -
429B ILE* 2.8 36.8 + - + +
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ILE* 3.6 30.5 - - + +
359B GLU* 3.3 28.3 + - - +
422B GLU* 2.9 50.7 + - + +
423B ASP* 3.8 5.6 - - - +
425B LEU* 1.3 76.3 - - + +
427B GLU* 1.3 62.1 + - - +
429B ILE* 3.3 14.8 + - + +
430B GLU* 3.0 30.2 + - + +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 4.5 4.4 + - - -
79B PHE* 3.5 28.0 - - + -
423B ASP 2.9 15.5 + - - +
424B GLU* 3.5 13.6 - - - +
426B ARG* 1.3 77.9 - - - +
428B SER* 1.4 63.0 + - - +
430B GLU* 3.2 10.4 + - + +
431B ILE* 3.1 26.0 + - + +
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Residues in contact with SER 428 (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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79B PHE* 3.2 13.7 - - - -
81B PHE* 3.2 42.9 - - - -
402B LEU* 3.8 8.4 - - - +
420B ILE* 4.3 0.7 - - - +
424B GLU 2.9 18.1 + - - -
425B LEU* 3.3 8.7 - - - -
427B GLU* 1.4 79.3 - - - +
429B ILE* 1.3 57.9 + - - +
431B ILE* 3.1 12.9 + - - +
432B ILE* 2.9 31.5 + - - +
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Residues in contact with ILE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ILE* 4.4 3.4 - - + -
356B LEU* 3.8 36.1 - - + -
359B GLU* 3.6 43.1 - - + +
360B LEU* 5.6 3.8 - - + +
425B LEU* 2.8 30.3 + - + +
426B ARG* 3.6 15.9 - - + +
427B GLU 3.3 0.2 - - - -
428B SER* 1.3 73.6 - - - +
430B GLU* 1.3 64.6 + - - +
432B ILE* 3.0 9.7 + - + +
433B ASN* 2.8 49.4 + - - +
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ARG* 3.0 21.7 + - + +
427B GLU* 3.2 10.3 + - + +
429B ILE* 1.3 80.4 - - - +
431B ILE* 1.3 56.4 + - + +
433B ASN* 3.8 16.8 + - - +
434B LYS* 2.8 33.6 + - - +
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Residues in contact with ILE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.7 36.8 - - + -
397B LEU* 4.3 4.5 - - + -
400B ASN* 3.5 40.1 - - + +
401B GLY* 4.3 5.6 - - - +
402B LEU* 4.0 18.8 - - + +
427B GLU* 3.1 20.7 + - + +
428B SER* 3.1 8.5 + - - +
430B GLU* 1.3 77.7 - - + +
432B ILE* 1.3 61.8 + - - +
434B LYS* 3.5 8.8 + - - +
435B THR* 2.8 32.1 + - - +
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Residues in contact with ILE 432 (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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81B PHE* 4.6 8.5 - - + -
356B LEU* 4.8 5.6 - - + -
360B LEU* 3.9 26.7 - - + -
363B LEU* 4.8 2.7 - - + -
380B ILE* 5.4 0.9 - - + -
397B LEU* 4.0 14.1 - - + +
402B LEU* 3.9 19.3 - - + -
414B PHE* 3.8 43.7 - - + -
428B SER* 2.9 22.4 + - - +
429B ILE* 3.0 10.1 + - - +
431B ILE* 1.3 76.0 - - - +
433B ASN* 1.3 66.2 + - - +
435B THR* 3.3 1.4 + - - -
436B ILE* 2.9 35.8 + - + +
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Residues in contact with ASN 433 (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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359B GLU* 4.9 7.5 + - - +
360B LEU* 5.1 2.4 - - - +
363B LEU* 3.6 34.3 - - + +
429B ILE* 2.8 42.2 + - - +
430B GLU* 3.9 17.3 + - - +
432B ILE* 1.3 74.3 - - - +
434B LYS* 1.3 64.8 + - - +
437B LEU* 2.8 38.3 + - + +
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Residues in contact with LYS 434 (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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400B ASN* 3.8 33.6 - - - +
430B GLU 2.8 18.8 + - - +
431B ILE* 3.7 8.3 - - - +
433B ASN* 1.3 77.4 - - - +
435B THR* 1.3 62.1 + - - +
437B LEU* 3.9 3.1 - - - +
438B SER* 3.0 27.6 + - - -
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Residues in contact with THR 435 (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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393B VAL* 3.8 9.0 - - + +
396B ARG* 3.6 30.7 - - + +
397B LEU* 3.5 33.0 - - + +
400B ASN* 2.8 25.9 + - - +
431B ILE 2.8 19.2 + - - -
432B ILE 3.7 0.4 - - - -
434B LYS* 1.3 77.3 - - - +
436B ILE* 1.3 64.5 + - - +
438B SER* 2.6 25.0 + - - -
439B PHE* 3.4 10.1 - - + -
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Residues in contact with ILE 436 (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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363B LEU* 4.0 37.2 - - + -
367B VAL* 4.3 18.5 - - + +
368B VAL* 4.4 7.4 - - + -
380B ILE* 4.7 6.3 - - + -
382B ILE* 4.2 17.9 - - + -
388B TRP* 3.8 27.7 - - + -
393B VAL* 4.2 19.3 - - + -
397B LEU* 6.2 0.9 - - + -
432B ILE* 2.9 25.2 + - + +
433B ASN 3.9 0.7 - - - +
435B THR* 1.3 78.4 - - - +
437B LEU* 1.3 70.2 + - + +
438B SER 3.3 0.5 + - - -
439B PHE* 3.6 17.8 + - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 4.2 15.9 - - + -
364B PRO* 3.9 33.2 - - + -
367B VAL* 5.7 3.6 - - + -
433B ASN* 2.8 31.1 + - + +
434B LYS* 4.3 2.7 - - - +
436B ILE* 1.3 77.7 - - + +
438B SER* 1.3 60.7 + - - +
439B PHE* 3.2 9.3 + - - +
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ARG* 2.8 35.3 + - - -
400B ASN* 5.8 0.7 - - - -
434B LYS* 3.0 20.8 + - - -
435B THR* 2.6 17.5 + - - -
437B LEU* 1.3 76.1 - - - +
439B PHE* 1.3 58.7 + - - +
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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