Contacts of the helix formed by residues 332 - 342 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D PRO* 2.7 44.3 + - + +
329D GLU 4.1 0.4 - - - -
331D ARG* 1.3 110.3 + - + +
333D GLU* 1.3 54.0 + - - +
335D GLN* 3.1 28.7 + - - +
336D LEU* 2.8 37.9 + - + +
351D VAL* 4.4 8.1 - - + -
354D LEU* 4.0 31.3 + - + -
355D ARG* 3.7 37.6 - - + +
358D GLY 5.3 0.5 - - - -
359D GLY* 3.9 20.1 + - - -
333I GLU* 5.1 3.3 - - - +
337I ARG* 4.0 12.4 + - - -
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Residues in contact with GLU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LEU* 4.6 5.0 - - - +
331C ARG* 2.7 46.0 + - - -
332C TYR* 3.2 22.5 + - - +
358C GLY* 3.4 28.7 - - - +
329D GLU 3.3 18.9 + - - +
330D GLU* 3.3 14.8 + - - +
331D ARG 3.5 0.8 - - - -
332D TYR* 1.3 75.9 - - - +
334D HIS* 1.3 71.0 + - - +
335D GLN* 3.7 0.6 - - - +
336D LEU* 4.6 3.6 - - - -
337D ARG 3.1 17.3 + - - -
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Residues in contact with HIS 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C GLY 5.2 0.2 - - - -
331D ARG 5.0 6.1 - - - -
333D GLU* 1.3 87.1 + - + +
335D GLN* 1.3 90.7 + - + +
337D ARG* 3.5 10.7 + - - +
338D GLN* 3.2 27.5 + - - +
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Residues in contact with GLN 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ARG 3.9 3.0 + - - +
332D TYR* 3.1 41.8 - - - +
333D GLU 3.7 0.4 - - - +
334D HIS* 1.3 101.6 + - + +
336D LEU* 1.3 58.7 + - - +
338D GLN* 3.3 3.3 + - - +
339D LEU* 3.0 35.6 + - - +
354D LEU* 3.6 17.0 - - + -
359D GLY* 3.2 30.4 - - - +
361D VAL* 3.5 26.2 - - + +
337I ARG* 5.2 5.0 + - - -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ARG 4.0 19.5 - - - +
356C ARG 3.9 14.6 - - - +
357C SER 3.5 2.7 - - - -
358C GLY* 3.8 10.3 - - - +
328D PRO 4.0 15.7 - - - +
329D GLU* 4.0 6.1 - - - +
332D TYR* 2.8 33.4 + - + +
333D GLU* 3.6 4.5 - - - +
335D GLN* 1.3 70.1 - - - +
337D ARG* 1.3 60.7 + - - +
339D LEU* 3.4 4.1 + - - +
340D ASN* 2.6 36.3 + - - +
347D PHE* 4.0 21.8 - - + -
350D ASN* 3.9 30.1 - - + +
351D VAL* 4.3 9.2 - - + -
354D LEU* 4.4 6.0 - - + +
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Residues in contact with ARG 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ARG 5.6 1.0 + - - -
332C TYR* 5.1 4.6 - - - -
335C GLN* 3.2 26.5 - - - +
357C SER 3.3 9.1 + - - -
358C GLY 3.2 25.5 + - - +
359C GLY* 3.8 11.4 + - - -
360C SER* 3.9 13.7 - - - +
333D GLU 3.1 8.4 + - - +
334D HIS* 3.5 13.1 - - - +
335D GLN 3.2 0.2 - - - -
336D LEU* 1.3 76.9 - - - +
338D GLN* 1.3 58.8 + - - +
340D ASN* 3.4 0.7 + - - +
341D ASP* 2.9 49.0 + - - +
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Residues in contact with GLN 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D HIS* 3.2 15.1 + - - +
335D GLN* 3.3 8.0 + - - +
337D ARG* 1.3 82.2 - - - +
339D LEU* 1.3 62.5 + - - +
341D ASP* 3.4 8.7 + - - +
342D MET* 3.2 35.1 + - - +
361D VAL* 3.5 35.5 - - + +
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D GLN 3.0 21.5 + - - +
336D LEU* 3.8 4.9 - - - +
338D GLN* 1.3 77.0 - - - +
340D ASN* 1.3 59.0 + - - +
342D MET* 3.2 10.1 + - - -
343D GLY 3.3 0.3 + - - -
344D PHE* 2.9 30.5 + - + +
350D ASN* 3.6 35.2 - - + +
354D LEU* 3.7 31.0 - - + -
361D VAL* 4.0 20.4 - - + -
364D ALA* 4.4 8.1 - - + -
365D LEU* 4.1 16.6 - - + -
368D LEU* 3.8 21.8 - - + -
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Residues in contact with ASN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ARG 4.1 5.3 + - - +
357C SER* 3.4 23.9 + - - +
360C SER* 3.4 24.3 + - - +
362C GLN* 4.6 2.8 - - - +
363C GLY* 3.4 20.7 - - - -
336D LEU* 2.6 31.5 + - - +
339D LEU* 1.3 71.5 - - - +
341D ASP* 1.3 61.1 + - - +
342D MET 3.1 1.8 - - - -
343D GLY 3.0 14.2 + - - -
344D PHE 3.5 14.8 + - - -
345D PHE* 3.1 36.3 + - + +
350D ASN* 3.8 10.9 - - - +
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Residues in contact with ASP 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C SER* 3.0 25.4 + - - -
362C GLN* 5.5 4.3 - - - +
337D ARG* 2.9 36.3 + - - +
338D GLN* 3.6 9.2 - - - +
340D ASN* 1.3 75.2 - - - +
342D MET* 1.3 62.0 + - + +
343D GLY 3.3 1.0 + - - -
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Residues in contact with MET 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D GLN* 3.2 24.6 + - - +
339D LEU 3.2 6.6 + - - +
340D ASN 3.1 0.6 - - - -
341D ASP* 1.3 78.9 - - + +
343D GLY* 1.3 58.5 + - - +
344D PHE* 3.5 20.2 + - + -
361D VAL* 5.4 2.0 - - - -
365D LEU* 3.8 39.7 - - + -
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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