Contacts of the helix formed by residues 345 - 362 (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 LEU 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B ASN 4.2 5.4 - - - +
90B GLN* 4.3 6.7 - - - -
270B ALA* 3.9 6.5 - - + +
339B VAL* 4.3 9.0 - - + -
340B LEU* 3.1 34.4 + - + +
343B GLU* 3.6 28.3 - - + +
344B ASN* 1.3 75.5 - - - +
346B ALA* 1.3 61.0 + - - +
348B ASN* 3.3 7.4 + - + +
349B ALA* 2.9 30.5 + - - +
418B LEU* 3.7 40.3 - - + +
419B VAL* 4.0 27.4 - - + -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 3.6 20.6 - - + +
273B GLY* 3.3 34.9 - - - +
274B ARG* 3.7 12.8 - - - +
275B TRP* 4.6 6.7 - - + +
340B LEU 4.7 1.2 + - - -
344B ASN* 3.2 0.8 - - - -
345B LEU* 1.3 77.5 - - - +
347B GLU* 1.3 63.1 + - - +
349B ALA 3.2 1.6 + - - -
350B ASP* 3.0 19.9 + - - +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY 5.1 0.7 - - - -
344B ASN* 3.4 21.6 + - + +
345B LEU 3.3 0.2 - - - -
346B ALA* 1.3 77.9 - - - +
348B ASN* 1.3 57.8 + - - +
350B ASP* 3.2 7.0 + - + +
351B LYS* 2.9 63.9 + - + +
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU 5.4 0.9 - - - +
344B ASN 3.3 11.2 + - - +
345B LEU* 3.7 12.0 - - + +
346B ALA 3.2 0.6 - - - -
347B GLU* 1.3 78.9 - - - +
349B ALA* 1.3 57.7 + - - +
351B LYS* 3.9 14.1 + - - +
352B LEU* 2.9 50.5 + - - +
376B LEU* 5.2 0.2 - - - +
418B LEU 3.0 19.7 + - - +
419B VAL* 4.5 1.2 - - - +
420B ILE* 2.9 27.9 + - - +
421B LYS* 5.6 0.5 - - - -
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 3.4 25.4 - - - +
271B ARG 4.0 1.3 - - - +
273B GLY 4.2 2.5 - - - +
345B LEU 2.9 13.7 + - - +
346B ALA 3.2 2.4 + - - +
348B ASN* 1.3 76.1 - - - +
350B ASP* 1.3 54.1 + - - +
353B GLY* 2.8 31.7 + - - -
375B GLY* 3.4 8.8 - - - -
376B LEU* 3.5 36.7 - - + +
418B LEU* 4.1 5.6 + - + -
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Residues in contact with ASP 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY* 4.0 7.8 - - - +
274B ARG* 3.1 23.2 + - - -
280B TYR* 3.6 19.2 + - - -
346B ALA 3.0 16.5 + - - +
347B GLU* 3.5 7.4 - - - +
349B ALA* 1.3 78.8 - - - +
351B LYS* 1.3 64.4 + - + +
353B GLY* 4.0 0.2 - - - -
354B ILE* 3.4 19.1 + - - +
357B ARG* 5.2 4.0 + - - -
375B GLY* 4.2 10.9 + - - -
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU* 2.9 62.5 + - - +
348B ASN* 3.9 14.9 + - - +
350B ASP* 1.3 76.6 - - + +
352B LEU* 1.3 68.9 + - + +
354B ILE* 3.3 23.5 - - - +
355B ILE* 3.6 10.8 - - + +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN* 2.9 40.2 + - - +
351B LYS* 1.3 75.7 - - + +
353B GLY* 1.3 65.1 + - - +
355B ILE* 3.1 25.8 + - + +
356B LEU* 3.0 20.3 + - - +
376B LEU* 4.0 11.2 - - + -
420B ILE* 3.3 38.6 - - + +
421B LYS 3.9 12.3 - - - +
422B GLU* 3.9 25.4 - - + +
425B LEU* 3.5 16.0 - - + +
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Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ALA 2.8 18.9 + - - -
350B ASP 4.0 0.4 - - - -
351B LYS 3.3 0.2 - - - -
352B LEU* 1.3 74.0 - - - +
354B ILE* 1.3 61.3 + - - +
356B LEU* 3.3 5.1 + - - +
357B ARG* 3.0 35.3 + - - +
375B GLY* 3.1 26.7 - - - -
376B LEU* 3.5 8.4 - - - +
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Residues in contact with ILE 354 (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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350B ASP* 3.4 11.8 + - - +
351B LYS* 3.3 15.7 - - - +
352B LEU 3.3 0.8 - - - -
353B GLY* 1.3 74.6 - - - +
355B ILE* 1.3 73.0 + - + +
357B ARG* 3.7 24.7 - - + +
358B ASN* 2.9 52.1 + - - +
361B MET* 5.6 1.8 - - + -
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Residues in contact with ILE 355 (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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351B LYS* 3.6 17.7 + - + +
352B LEU* 3.1 27.4 + - + +
354B ILE* 1.3 83.1 - - + +
356B LEU* 1.3 63.6 + - - +
358B ASN* 3.8 4.9 - - - +
359B GLU* 2.9 31.4 + - + +
422B GLU* 4.0 21.5 - - + +
425B LEU* 3.8 13.2 - - + -
426B ARG* 3.6 34.3 - - + +
429B ILE* 4.4 2.9 - - + -
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Residues in contact with LEU 356 (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* 4.7 8.1 - - + -
352B LEU 3.0 12.3 + - - +
353B GLY* 3.5 9.6 - - - +
355B ILE* 1.3 78.1 - - - +
357B ARG* 1.3 57.7 + - - +
359B GLU* 3.3 1.0 + - - +
360B LEU* 2.9 52.6 + - + +
376B LEU* 4.8 5.6 - - + -
378B ASN* 3.7 28.0 - - + +
414B PHE* 4.2 21.3 - - + +
416B PRO* 5.1 2.0 - - + -
425B LEU* 3.7 21.5 - - + +
428B SER* 6.5 0.2 - - - -
429B ILE* 3.8 28.3 - - + -
432B ILE* 4.8 9.6 - - + -
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Residues in contact with ARG 357 (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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350B ASP* 5.2 4.2 + - - -
353B GLY 3.0 16.6 + - - +
354B ILE* 3.7 34.4 - - + +
356B LEU* 1.3 78.7 - - - +
358B ASN* 1.3 62.0 + - - +
360B LEU* 3.3 2.3 + - + +
361B MET* 2.9 43.9 + - + +
371B VAL* 3.9 16.8 - - + +
372B ARG* 4.0 5.8 - - - +
373B GLY 3.5 28.2 + - - +
374B LYS* 3.6 4.0 - - - +
375B GLY 3.1 33.9 + - - +
378B ASN* 2.9 39.7 + - + +
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Residues in contact with ASN 358 (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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354B ILE* 2.9 44.9 + - - +
355B ILE* 3.9 5.1 - - - +
357B ARG* 1.3 76.5 - - - +
359B GLU* 1.3 65.9 + - + +
361B MET* 3.4 28.8 + - - +
362B LYS* 3.7 18.6 + - - +
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Residues in contact with GLU 359 (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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355B ILE* 2.9 21.7 + - + +
356B LEU 3.8 0.2 - - - +
358B ASN* 1.3 77.6 - - - +
360B LEU* 1.3 65.0 + - - +
362B LYS* 2.9 57.0 + - - +
363B LEU* 4.1 3.6 + - - +
426B ARG* 3.3 26.4 + - - +
429B ILE* 3.6 41.9 - - + +
433B ASN* 4.9 5.5 + - - +
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Residues in contact with LEU 360 (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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356B LEU* 2.9 48.1 + - + +
357B ARG* 3.9 2.7 - - - +
359B GLU* 1.3 75.8 - - + +
361B MET* 1.3 63.0 + - - +
362B LYS 3.1 1.4 + - - -
363B LEU* 3.1 32.6 + - + +
368B VAL* 4.6 2.9 - - - +
371B VAL* 3.8 26.6 - - + +
378B ASN* 5.3 6.3 - - + -
380B ILE* 3.7 23.3 - - + -
414B PHE* 3.9 18.8 - - + -
429B ILE* 5.6 3.8 - - + -
432B ILE* 3.9 30.7 - - + -
433B ASN* 5.1 3.6 - - - +
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Residues in contact with MET 361 (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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354B ILE* 5.6 1.6 - - + -
357B ARG* 2.9 43.3 + - + +
358B ASN* 3.5 29.4 - - - +
359B GLU 3.2 0.8 - - - -
360B LEU* 1.3 75.7 - - - +
362B LYS* 1.3 61.1 + - - +
363B LEU 3.2 8.5 + - - +
365B SER* 5.6 1.2 + - - -
368B VAL* 6.0 0.2 - - - -
371B VAL* 3.8 27.6 - - + +
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Residues in contact with LYS 362 (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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358B ASN* 3.7 16.2 - - - +
359B GLU* 2.9 47.9 + - - +
361B MET* 1.3 74.1 - - + +
363B LEU* 1.3 66.4 + - - +
364B PRO* 3.6 2.6 - - - +
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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
------------------------------------------------------------
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