Contacts of the helix formed by residues 346 - 357 (chain K) in PDB entry 2BWE
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 346 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344K PHE* 3.5 3.4 - - - +
345K PHE* 1.3 73.9 - - - +
347K PHE* 1.3 61.7 + - - +
348K ASP* 3.1 17.4 + - - +
349K ARG* 3.2 28.0 + - + +
350K ASN* 2.9 32.4 + - - +
63T GLN* 3.2 22.2 + - - +
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Residues in contact with PHE 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356J ARG* 3.3 73.1 - - + +
367J SER* 5.9 0.7 - - - +
328K PRO* 4.2 9.6 - - + -
329K GLU* 3.8 39.9 - - + -
336K LEU* 3.9 15.0 - - + -
340K ASN* 6.2 0.2 - - - +
345K PHE 3.2 7.4 + - - +
346K ASP* 1.3 73.6 + - - +
348K ASP* 1.3 69.5 + - - +
350K ASN* 2.9 9.7 + - - +
351K VAL* 2.8 56.8 + - + +
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Residues in contact with ASP 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356J ARG* 4.3 9.8 + - - -
346K ASP* 3.1 7.3 + - - +
347K PHE* 1.3 94.7 - - - +
349K ARG* 1.3 63.0 + - - +
351K VAL* 4.0 4.0 - - - +
352K ALA* 3.0 25.0 + - - +
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Residues in contact with ARG 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344K PHE* 5.3 4.6 - - - -
346K ASP* 3.2 28.6 + - + +
348K ASP* 1.3 75.7 - - - +
350K ASN* 1.3 58.4 + - - +
352K ALA* 3.3 7.7 + - - +
353K ALA* 2.8 29.6 + - - +
368K LEU* 3.2 51.1 + - + +
371K GLY* 3.3 32.1 - - - -
372K ASP* 3.3 17.2 + - - +
46T TYR* 5.6 3.0 + - - -
61T HIS* 4.7 7.7 + - - +
63T GLN* 2.8 48.5 - - - +
66T HIS* 5.7 3.2 - - - -
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Residues in contact with ASN 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336K LEU* 3.8 14.8 - - + +
339K LEU* 3.6 24.0 - - + +
340K ASN* 3.7 15.6 - - - +
344K PHE* 2.8 32.0 + - - +
345K PHE 4.3 0.2 - - - -
346K ASP* 2.9 22.1 + - - +
347K PHE* 2.9 8.7 + - - +
349K ARG* 1.3 76.6 - - - +
351K VAL* 1.3 57.5 + - - +
353K ALA* 3.2 5.5 + - - +
354K LEU* 2.8 35.5 + - - +
368K LEU* 3.6 22.1 - - - +
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Residues in contact with VAL 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K PRO* 4.1 22.9 - - + -
332K TYR* 4.2 15.7 - - + -
336K LEU* 4.6 8.7 - - + -
347K PHE* 2.8 58.5 + - + +
348K ASP* 4.0 4.5 - - - +
350K ASN* 1.3 70.3 - - - +
352K ALA* 1.3 58.1 + - - +
354K LEU* 3.1 7.5 + - - +
355K ARG* 2.8 44.0 + - - +
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Residues in contact with ALA 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348K ASP 3.0 18.7 + - - +
349K ARG* 3.4 7.2 - - - +
351K VAL* 1.3 78.5 - - - +
353K ALA* 1.3 61.5 + - - +
355K ARG* 3.5 10.7 + - - +
356K ARG* 3.3 31.5 + - - +
372K ASP* 4.8 7.2 - - - +
329L GLU* 5.4 0.2 - - - +
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Residues in contact with ALA 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349K ARG 2.8 19.3 + - - +
350K ASN 3.6 3.8 - - - +
352K ALA* 1.3 73.4 - - - +
354K LEU* 1.3 58.2 + - - +
356K ARG* 3.4 10.4 + - - +
357K SER* 3.1 26.7 + - - -
364K ALA* 3.8 24.4 - - + +
367K SER* 4.2 12.0 + - - -
368K LEU* 3.9 22.9 - - + -
372K ASP* 4.3 8.4 + - - +
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Residues in contact with LEU 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332K TYR* 4.0 29.8 - - + -
335K GLN* 3.8 24.9 - - + -
336K LEU* 4.3 8.3 - - + +
339K LEU* 3.8 20.0 - - + -
350K ASN 2.8 22.7 + - - +
351K VAL* 3.6 4.7 - - - +
353K ALA* 1.3 72.7 - - - +
355K ARG* 1.3 64.5 + - - +
356K ARG 3.1 1.6 - - - -
357K SER* 3.1 2.8 + - - -
358K GLY 2.9 4.5 + - - -
359K GLY* 2.8 55.0 + - - +
360K SER 4.0 3.8 - - - +
361K VAL* 4.4 3.4 - - - -
364K ALA* 3.8 19.1 - - + -
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Residues in contact with ARG 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332K TYR* 3.5 28.3 - - + +
351K VAL* 2.8 33.6 + - - +
352K ALA* 3.9 7.8 - - - +
354K LEU* 1.3 71.1 - - - +
356K ARG* 1.3 62.4 + - - +
358K GLY* 3.2 13.0 + - - +
327L ASP* 3.2 27.3 + - - -
329L GLU* 3.5 50.4 + - + +
330L GLU* 2.6 38.6 + - - +
333L GLU* 5.7 0.5 - - - +
336L LEU* 4.4 1.2 - - - +
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Residues in contact with ARG 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352K ALA* 3.3 20.5 + - - +
353K ALA* 3.5 11.0 - - - +
354K LEU 3.1 0.4 - - - -
355K ARG* 1.3 78.2 - - - +
357K SER* 1.3 58.5 + - - +
358K GLY 3.2 1.2 + - - -
367K SER* 4.3 11.1 + - - +
372K ASP* 3.8 38.5 - - - +
329L GLU* 3.9 15.7 + - - +
336L LEU* 3.8 14.0 - - - +
340L ASN* 4.1 2.4 + - - -
347L PHE* 3.3 81.6 - - + +
348L ASP* 4.2 15.0 + - - -
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Residues in contact with SER 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353K ALA 3.1 9.1 + - - -
354K LEU* 3.1 10.7 + - - -
356K ARG* 1.3 76.2 - - - +
358K GLY* 1.3 60.6 + - - +
359K GLY 3.8 0.3 - - - -
360K SER* 2.7 45.5 + - - -
363K GLY 3.9 0.9 - - - -
364K ALA 3.7 13.9 + - - -
367K SER* 5.9 0.7 - - - -
336L LEU 4.5 2.0 - - - -
337L ARG* 3.8 5.2 - - - -
340L ASN* 3.3 35.8 - - - +
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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