Contacts of the helix formed by residues 332 - 342 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326C LEU* 5.4 0.4 - - + +
328C PRO* 2.7 37.9 + - + +
331C ARG* 1.3 97.1 - - + +
333C GLU* 1.3 58.6 + - - +
335C GLN* 3.2 24.8 + - - +
336C LEU* 2.8 33.0 + - + +
351C VAL* 5.0 4.5 - - + -
354C LEU* 3.8 46.6 + - + -
355C ARG* 4.3 34.3 + - + -
358C GLY* 4.5 1.4 - - - -
359C GLY* 3.8 19.2 + - - -
333D GLU* 3.2 25.8 + - - +
337D ARG* 5.1 3.8 - - - -
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ARG* 3.3 44.7 + - - +
332B TYR* 4.5 9.4 + - - +
358B GLY* 3.7 24.2 - - - +
329C GLU 3.4 20.9 + - - +
330C GLU* 3.4 13.4 + - - +
331C ARG 3.5 1.4 + - - -
332C TYR* 1.3 77.2 - - - +
334C HIS* 1.3 86.2 + - + +
336C LEU* 3.3 5.7 + - - +
337C ARG* 3.1 19.8 + - - +
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Residues in contact with HIS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C TYR 3.4 0.2 - - - -
333C GLU* 1.3 97.3 + - + +
335C GLN* 1.3 69.7 + - - +
337C ARG* 3.5 8.6 + - - +
338C GLN* 3.2 26.7 + - - +
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Residues in contact with GLN 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ARG 4.1 4.6 + - - +
332C TYR* 3.2 35.3 + - - +
333C GLU 3.9 0.3 + - - -
334C HIS* 1.3 84.0 + - + +
336C LEU* 1.3 60.3 + - - +
338C GLN* 3.4 2.8 + - - +
339C LEU* 3.0 36.2 + - - +
354C LEU* 3.6 17.9 - - + -
359C GLY 3.1 27.9 + - - +
361C VAL* 3.6 25.1 - - + +
337D ARG* 3.2 26.6 - - - +
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ARG 4.3 4.5 - - - +
356B ARG 4.0 13.9 - - - +
357B SER 3.7 2.2 - - - -
358B GLY* 4.0 11.0 - - - +
328C PRO 3.8 18.8 - - - +
329C GLU* 4.1 10.5 - - - +
332C TYR* 2.8 30.4 + - + +
333C GLU* 3.6 4.5 - - - +
335C GLN* 1.3 69.9 - - - +
337C ARG* 1.3 60.6 + - - +
339C LEU* 3.4 3.4 + - - +
340C ASN* 2.6 38.0 + - - +
347C PHE* 4.1 25.8 - - + -
350C ASN* 3.8 32.5 - - + +
351C VAL* 4.5 6.3 - - + -
354C LEU* 4.2 7.9 - - + -
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Residues in contact with ARG 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLN* 3.4 24.5 + - - +
357B SER 3.5 8.0 + - - -
358B GLY 3.5 20.6 + - - +
359B GLY* 3.4 15.9 + - - -
360B SER* 4.3 12.7 - - - +
333C GLU 3.1 9.7 + - - +
334C HIS* 3.7 11.7 - - - +
335C GLN 3.2 0.2 - - - -
336C LEU* 1.3 73.4 - - - +
338C GLN* 1.3 59.6 + - - +
340C ASN* 3.3 1.0 + - - +
341C ASP* 2.9 52.7 + - - +
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Residues in contact with GLN 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C HIS 3.2 15.1 + - - +
335C GLN 3.5 8.1 - - - +
337C ARG* 1.3 79.5 - - + +
339C LEU* 1.3 63.9 + - - +
341C ASP* 3.3 9.0 + - - +
342C MET* 3.1 37.5 + - - +
361C VAL* 4.0 32.4 - - + +
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Residues in contact with LEU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C GLN 3.0 18.3 + - - +
336C LEU* 3.8 4.9 - - - +
338C GLN* 1.3 79.1 - - - +
340C ASN* 1.3 57.6 + - - +
342C MET* 3.1 16.4 + - - +
343C GLY 3.3 0.5 + - - -
344C PHE* 2.9 28.8 + - + +
350C ASN* 4.0 28.7 - - + +
354C LEU* 3.8 31.9 - - + -
361C VAL* 4.6 9.4 - - + -
364C ALA* 4.3 8.7 - - + -
365C LEU* 3.9 31.4 - - + +
368C LEU* 3.6 23.1 - - + -
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Residues in contact with ASN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ARG 4.2 3.6 + - - -
357B SER* 3.5 24.9 + - - +
360B SER* 3.5 23.6 + - - +
362B GLN* 4.8 2.4 - - - +
363B GLY* 3.4 21.1 - - - -
336C LEU* 2.6 31.5 + - - +
337C ARG 3.8 0.4 - - - +
339C LEU* 1.3 71.0 - - - +
341C ASP* 1.3 58.6 + - - +
342C MET 3.1 5.2 - - - -
343C GLY 3.1 14.4 + - - -
344C PHE 3.4 14.6 + - - -
345C PHE* 3.1 34.8 + - + +
350C ASN* 3.7 11.3 - - - +
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Residues in contact with ASP 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B SER* 3.5 20.3 + - - -
362B GLN* 5.5 3.0 - - - +
337C ARG* 2.9 41.8 + - - +
338C GLN* 3.6 10.0 - - - +
340C ASN* 1.3 74.6 - - - +
342C MET* 1.3 60.8 + - + +
343C GLY 3.4 1.5 + - - -
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C GLN* 3.1 28.7 + - - +
339C LEU* 3.1 8.4 + - - +
340C ASN 3.1 1.0 - - - -
341C ASP* 1.3 79.6 - - + +
343C GLY* 1.3 57.2 + - - +
344C PHE* 3.5 20.1 + - + -
361C VAL* 5.1 1.3 - - - -
365C LEU* 3.9 40.2 - - + -
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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