Contacts of the helix formed by residues 332 - 342 (chain F) in PDB entry 2BWB
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 TYR 332 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328F PRO* 2.7 44.7 + - + +
329F GLU 4.1 0.4 - - - -
331F ARG* 1.3 111.8 + - + +
333F GLU* 1.3 58.1 + - - +
335F GLN* 3.3 26.2 + - - +
336F LEU* 2.8 34.3 + - + +
351F VAL* 4.4 7.6 - - + -
354F LEU* 3.8 32.8 + - + -
355F ARG* 3.7 36.7 + - + +
358F GLY* 5.3 0.5 - - - -
359F GLY* 3.9 21.3 + - - -
333G GLU* 4.2 9.2 + - - +
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Residues in contact with GLU 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E ARG* 3.1 40.1 + - - -
332E TYR* 3.8 15.2 + - - +
355E ARG 5.7 0.7 - - - +
358E GLY* 3.5 26.7 - - - +
329F GLU 3.3 19.8 + - - +
330F GLU* 3.4 14.5 + - - +
331F ARG 3.5 1.2 + - - -
332F TYR* 1.3 76.7 - - - +
334F HIS* 1.3 83.7 + - + +
335F GLN* 4.0 0.2 - - - +
336F LEU* 3.4 3.3 + - - -
337F ARG* 3.1 19.9 + - - +
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Residues in contact with HIS 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F TYR 3.4 0.4 - - - -
333F GLU* 1.3 97.8 + - + +
335F GLN* 1.3 69.4 + - + +
337F ARG* 3.3 9.0 - - - +
338F GLN* 3.2 34.3 + - - +
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Residues in contact with GLN 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F ARG 3.9 6.2 + - - +
332F TYR* 3.3 34.5 - - - +
334F HIS* 1.3 87.6 - - + +
336F LEU* 1.3 59.0 + - - +
338F GLN* 3.4 4.7 + - - +
339F LEU* 3.0 34.8 + - - +
354F LEU* 3.7 17.7 - - + -
359F GLY* 2.9 35.5 - - - +
361F VAL* 3.5 25.0 - - + +
337G ARG* 3.0 17.9 + - - +
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Residues in contact with LEU 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E ARG 4.3 5.6 - - - +
356E ARG 4.0 20.0 - - - +
357E SER 3.4 3.6 - - - -
358E GLY 4.0 9.6 - - - +
328F PRO 4.0 16.2 - - - +
329F GLU* 4.1 11.4 - - - +
332F TYR* 2.8 25.4 + - + +
333F GLU* 3.7 5.2 - - - +
335F GLN* 1.3 73.7 - - - +
337F ARG* 1.3 60.0 + - - +
339F LEU* 3.4 3.4 + - - -
340F ASN* 2.6 37.0 + - - +
347F PHE* 4.0 23.1 - - + -
350F ASN* 3.8 32.5 - - + +
351F VAL* 4.4 5.4 - - + -
354F LEU* 4.4 8.1 - - + -
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Residues in contact with ARG 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E GLN* 3.1 20.4 - - - +
357E SER 3.3 9.8 + - - -
358E GLY 2.9 30.6 + - - +
359E GLY* 2.7 29.6 + - - -
360E SER* 3.8 4.6 - - - +
361E VAL* 5.4 0.8 - - - +
333F GLU 3.1 8.5 + - - +
334F HIS* 3.3 14.4 - - - +
336F LEU* 1.3 76.8 - - - +
338F GLN* 1.3 58.6 + - + +
341F ASP* 3.0 57.7 + - - +
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Residues in contact with GLN 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F HIS* 3.2 26.3 + - - +
335F GLN* 3.7 7.0 - - - +
337F ARG* 1.3 81.1 - - + +
339F LEU* 1.3 62.2 + - - +
341F ASP* 3.4 8.5 + - - +
342F MET* 3.1 31.9 + - + +
361F VAL* 3.7 36.7 - - + +
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Residues in contact with LEU 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F GLN 3.0 22.5 + - - +
336F LEU* 3.8 4.0 - - - +
338F GLN* 1.3 75.6 - - - +
340F ASN* 1.3 60.7 + - - +
342F MET* 3.1 12.0 + - - +
343F GLY 3.3 0.3 + - - -
344F PHE* 2.9 27.4 + - + +
350F ASN* 3.8 37.7 - - + +
354F LEU* 3.9 24.2 - - + -
361F VAL* 4.2 11.2 - - + -
364F ALA* 4.5 4.0 - - + -
365F LEU* 3.6 39.3 - - + +
368F LEU* 3.7 17.9 - - + -
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Residues in contact with ASN 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E ARG 4.1 4.9 + - - -
357E SER* 3.3 24.1 + - - +
360E SER* 3.2 25.7 + - - +
362E GLN* 4.0 3.8 - - - +
363E GLY* 3.3 20.7 - - - -
336F LEU* 2.6 32.3 + - - +
339F LEU* 1.3 70.3 - - - +
341F ASP* 1.3 58.3 + - - +
342F MET 3.1 4.7 - - - -
343F GLY 3.1 14.2 + - - -
344F PHE 3.4 8.3 - - - -
345F PHE* 3.2 37.2 + - - +
350F ASN* 3.6 15.8 - - - +
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Residues in contact with ASP 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E SER* 3.0 17.4 + - - -
362E GLN* 2.8 39.0 + - - +
337F ARG* 3.0 41.8 + - - +
338F GLN* 3.4 9.0 + - - +
340F ASN* 1.3 75.4 - - - +
342F MET* 1.3 59.5 + - + +
343F GLY 3.4 1.5 + - - -
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Residues in contact with MET 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F GLN* 3.1 17.6 + - - +
339F LEU 3.5 8.5 - - - +
340F ASN 3.1 1.0 - - - -
341F ASP* 1.3 79.1 - - + +
343F GLY* 1.3 59.1 + - - +
344F PHE* 3.5 22.2 - - + -
361F VAL* 5.3 1.6 - - - -
365F LEU* 3.6 37.9 - - + -
369F LEU* 6.5 0.4 - - + -
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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