Contacts of the helix formed by residues 345 - 362 (chain A) in PDB entry 2BYL
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN 4.1 13.7 - - - +
90A GLN* 4.3 5.4 - - - -
270A ALA* 4.0 3.1 - - + -
339A VAL* 4.3 12.3 - - + -
340A LEU* 3.2 35.7 + - + +
343A GLU* 3.4 33.2 - - + +
344A ASN* 1.3 73.1 - - - +
346A ALA* 1.3 60.1 + - - +
348A ASN* 3.4 8.3 + - + +
349A ALA* 2.8 31.0 + - - +
418A LEU* 3.8 31.7 - - + +
419A VAL* 4.0 28.3 - - + -
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Residues in contact with ALA 346 (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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270A ALA* 3.5 26.2 - - + +
273A GLY* 3.4 30.3 - - - +
274A ARG* 3.9 10.8 - - - +
275A TRP* 4.6 4.9 - - + +
340A LEU 4.8 1.6 + - - -
344A ASN 3.3 0.8 - - - -
345A LEU* 1.3 76.9 - - - +
347A GLU* 1.3 71.8 + - - +
349A ALA 3.1 1.2 + - - -
350A ASP* 3.0 21.5 + - - +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLY 5.3 0.2 - - - -
344A ASN* 2.8 48.5 + - + +
346A ALA* 1.3 80.5 - - - +
348A ASN* 1.3 64.0 + - - +
350A ASP* 3.4 5.3 + - - +
351A LYS* 3.2 32.0 + - + +
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU 5.4 0.9 - - - +
344A ASN 3.1 10.7 + - - +
345A LEU* 3.5 13.9 - - + +
347A GLU* 1.3 78.5 - - - +
349A ALA* 1.3 56.9 + - - +
351A LYS* 3.3 4.4 + - - +
352A LEU* 3.0 53.4 + - - +
376A LEU* 5.2 0.4 - - - +
418A LEU* 2.7 27.0 + - - +
419A VAL 4.4 1.4 - - - -
420A ILE* 2.9 23.3 + - - +
421A LYS* 5.5 0.9 - - - -
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA 3.3 26.0 - - - +
271A ARG 4.0 11.9 - - - +
273A GLY* 4.2 2.7 - - - -
345A LEU 2.8 17.5 + - - +
346A ALA 3.1 2.7 + - - +
348A ASN* 1.3 73.5 - - - +
350A ASP* 1.3 57.0 + - - +
353A GLY 3.0 21.0 + - - -
375A GLY* 3.2 16.0 - - - -
376A LEU* 3.6 23.1 + - + +
418A LEU* 4.1 6.3 + - + -
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Residues in contact with ASP 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLY* 4.1 8.9 - - - +
274A ARG* 3.4 17.9 + - - +
280A TYR* 3.6 20.7 + - - -
346A ALA 3.0 15.3 + - - +
347A GLU* 3.7 6.7 - - - +
348A ASN 3.2 0.2 - - - -
349A ALA* 1.3 76.2 - - - +
351A LYS* 1.3 67.5 + - + +
353A GLY* 3.9 0.5 - - - -
354A ILE* 3.2 36.3 + - - +
357A ARG* 5.0 1.9 + - - -
375A GLY* 4.3 9.9 + - - -
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Residues in contact with LYS 351 (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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347A GLU* 3.2 20.0 + - + +
348A ASN* 4.1 3.6 - - - +
350A ASP* 1.3 78.9 - - + +
352A LEU* 1.3 69.8 + - + +
354A ILE* 3.3 18.6 + - - +
355A ILE* 3.4 17.5 + - + +
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Residues in contact with LEU 352 (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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348A ASN* 3.0 36.2 + - - +
351A LYS* 1.3 76.9 - - + +
353A GLY* 1.3 60.0 + - - +
355A ILE* 3.3 15.6 + - + +
356A LEU* 2.9 24.6 + - - +
376A LEU* 4.0 11.7 - - + -
420A ILE* 3.1 40.4 - - + +
421A LYS 4.2 8.5 - - - +
422A GLU* 4.0 35.4 - - + +
425A LEU* 3.5 17.7 - - + +
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Residues in contact with GLY 353 (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 ALA 3.0 15.0 + - - -
350A ASP 3.9 0.2 - - - -
351A LYS 3.3 0.2 - - - -
352A LEU* 1.3 73.5 - - - +
354A ILE* 1.3 64.0 + - - +
356A LEU* 3.2 5.1 + - - +
357A ARG* 3.0 37.0 + - - +
375A GLY* 3.2 24.7 - - - -
376A LEU* 3.6 9.0 - - - +
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Residues in contact with ILE 354 (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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350A ASP* 3.2 32.3 + - - +
351A LYS* 3.5 11.4 - - + +
353A GLY* 1.3 76.7 - - - +
355A ILE* 1.3 63.7 + - + +
357A ARG* 3.7 19.6 + - - +
358A ASN* 3.0 46.9 + - - +
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Residues in contact with ILE 355 (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 LYS* 3.4 11.4 + - + +
352A LEU* 3.3 24.5 + - + +
354A ILE* 1.3 79.6 - - + +
356A LEU* 1.3 62.7 + - - +
358A ASN* 3.3 7.8 + - - +
359A GLU* 3.0 31.3 + - + +
422A GLU* 3.9 22.0 - - + +
425A LEU* 4.0 13.9 - - + -
426A ARG* 3.6 42.2 - - + +
429A ILE* 4.3 3.8 - - + -
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Residues in contact with LEU 356 (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* 4.8 13.2 - - + -
352A LEU 2.9 13.8 + - - +
353A GLY* 3.2 10.3 + - - +
355A ILE* 1.3 77.8 - - - +
357A ARG* 1.3 58.4 + - - +
359A GLU* 3.3 1.6 + - - +
360A LEU* 2.9 56.7 + - + +
376A LEU* 4.6 8.3 - - + -
378A ASN* 3.5 33.2 - - + +
414A PHE* 4.5 15.3 - - + +
416A PRO* 5.3 2.2 - - + -
425A LEU* 4.1 16.6 - - + +
429A ILE* 4.0 27.1 - - + -
432A ILE* 5.1 4.0 - - + -
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Residues in contact with ARG 357 (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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350A ASP* 5.0 2.6 + - - -
353A GLY 3.0 15.1 + - - +
354A ILE* 3.7 33.2 - - - +
356A LEU* 1.3 80.1 - - - +
358A ASN* 1.3 62.5 + - - +
360A LEU* 3.2 3.1 + - + +
361A MET* 2.9 40.3 + - + +
371A VAL* 4.1 21.8 - - + -
372A ARG* 4.1 4.9 - - - +
373A GLY 3.6 28.5 + - - +
374A LYS* 4.3 1.2 - - - +
375A GLY 3.1 32.5 + - - +
378A ASN* 3.0 38.1 + - + +
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Residues in contact with ASN 358 (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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354A ILE* 3.0 40.1 + - - +
355A ILE* 3.6 8.0 - - - +
357A ARG* 1.3 77.4 - - - +
359A GLU* 1.3 66.5 + - + +
361A MET* 3.4 25.1 + - - +
362A LYS* 3.6 19.9 + - - +
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Residues in contact with GLU 359 (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* 3.0 28.6 + - + +
356A LEU 3.8 2.9 - - - +
358A ASN* 1.3 76.8 - - - +
360A LEU* 1.3 65.2 + - - +
362A LYS* 3.0 55.6 + - - +
363A LEU 4.0 2.3 + - - -
426A ARG* 4.0 16.0 + - - +
429A ILE* 3.8 39.3 - - + +
433A ASN* 4.5 14.4 + - - +
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Residues in contact with LEU 360 (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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356A LEU* 2.9 48.7 + - + +
357A ARG* 3.2 4.7 + - - +
359A GLU* 1.3 77.4 - - + +
361A MET* 1.3 61.5 + - - +
363A LEU* 3.3 36.8 + - + +
368A VAL* 4.7 2.4 - - - +
371A VAL* 3.8 26.4 - - + +
378A ASN* 5.3 4.9 - - + -
380A ILE* 3.9 24.2 - - + -
414A PHE* 4.3 15.7 - - + -
429A ILE* 5.9 3.8 - - + -
432A ILE* 4.0 28.3 - - + -
433A ASN* 5.4 2.0 - - - +
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Residues in contact with MET 361 (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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357A ARG* 2.9 39.7 + - + +
358A ASN* 3.8 21.3 - - - +
359A GLU 3.3 0.4 - - - -
360A LEU* 1.3 76.3 - - - +
362A LYS* 1.3 61.9 + - - +
363A LEU 3.2 9.2 + - - +
371A VAL* 3.6 29.2 - - + +
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Residues in contact with LYS 362 (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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358A ASN* 3.6 15.7 - - - +
359A GLU* 3.0 50.0 + - - +
360A LEU 3.2 0.8 - - - -
361A MET* 1.3 75.9 - - - +
363A LEU* 1.3 63.7 + - - +
364A PRO* 3.6 3.3 - - - +
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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