Contacts of the helix formed by residues 351 - 361 (chain A) in PDB entry 1BRW
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 ALA 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.4 20.1 - - + +
204A ALA* 4.3 1.6 - - - +
205A GLY* 3.6 11.7 - - - +
239A MET* 3.4 26.9 - - - +
240A SER 3.1 10.9 + - - +
241A GLN 3.9 15.0 - - - +
242A PRO* 4.0 9.9 - - - -
349A MET 3.2 3.7 + - - -
350A ALA* 1.3 70.7 - - - +
352A ASP* 1.3 57.7 + - - +
354A ILE* 3.3 2.3 + - - +
355A GLY 2.7 26.3 + - - -
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Residues in contact with ASP 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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116A HIS* 3.6 28.2 - - + +
204A ALA* 3.3 31.8 + - - +
205A GLY* 3.9 2.6 - - - -
209A LYS* 4.9 5.6 - - - -
350A ALA* 3.5 17.5 - - - +
351A ALA* 1.3 74.0 - - - +
353A ASP* 1.3 70.2 + - - +
355A GLY* 3.3 0.9 + - - -
356A THR* 2.9 33.9 + - - +
410A LYS* 5.4 0.2 - - - -
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Residues in contact with ASP 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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350A ALA* 3.2 12.4 + - - +
352A ASP* 1.3 87.5 + - - +
354A ILE* 1.3 66.3 + - - +
356A THR* 3.2 3.3 + - - -
357A ALA* 2.9 23.8 + - - +
410A LYS* 3.0 43.1 + - + +
413A ALA* 3.3 25.9 - - - +
414A ALA* 3.5 22.0 - - + -
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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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87A VAL* 4.6 0.2 - - + -
242A PRO* 4.0 27.8 - - + -
247A VAL* 4.1 18.4 - - + -
349A MET* 4.0 24.7 - - + +
350A ALA 3.1 16.4 + - - +
351A ALA 3.7 5.6 - - - +
353A ASP* 1.3 74.6 - - - +
355A GLY* 1.3 62.8 + - - +
357A ALA* 3.2 6.1 + - - +
358A ALA* 3.0 22.3 + - - +
378A ILE* 3.8 13.4 - - + +
380A LEU* 4.3 14.4 - - + -
411A ILE* 4.3 21.1 - - + -
414A ALA* 3.9 17.9 - - + -
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Residues in contact with GLY 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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87A VAL* 4.0 10.9 - - - +
116A HIS* 3.5 28.2 - - - +
247A VAL* 5.1 0.9 - - - -
351A ALA 2.7 16.5 + - - -
352A ASP 3.7 2.2 - - - -
354A ILE* 1.3 78.6 - - - +
356A THR* 1.3 60.2 + - - +
358A ALA* 3.5 6.4 + - - +
359A MET* 3.2 21.5 + - - +
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Residues in contact with THR 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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116A HIS* 3.6 13.5 - - - +
352A ASP* 2.9 18.5 + - - +
353A ASP 3.7 4.0 - - - -
355A GLY* 1.3 73.5 - - - +
357A ALA* 1.3 66.7 + - - +
359A MET* 3.2 17.4 + - + +
360A TRP* 3.0 53.7 + - + +
410A LYS* 4.1 18.6 + - - +
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Residues in contact with ALA 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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353A ASP 2.9 12.9 + - - +
354A ILE 3.2 8.3 + - - +
356A THR* 1.3 77.8 - - - +
358A ALA* 1.3 61.2 + - - +
360A TRP* 3.3 9.6 + - - +
361A LEU* 3.2 20.4 + - - +
378A ILE* 3.8 14.6 - - + -
407A VAL* 3.8 13.2 - - + +
410A LYS* 3.8 24.1 - - + +
411A ILE* 3.9 15.9 - - + -
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Residues in contact with ALA 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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247A VAL* 3.9 28.0 - - + +
248A GLY* 5.6 0.2 - - - -
354A ILE 3.0 16.3 + - - +
355A GLY 3.7 4.7 - - - +
357A ALA* 1.3 75.6 - - - +
359A MET* 1.3 63.2 + - - +
361A LEU* 3.1 19.2 + - - +
363A ALA* 3.1 31.9 + - + +
377A GLY* 4.9 0.9 - - - -
378A ILE* 3.6 15.1 - - + +
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Residues in contact with MET 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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115A GLY* 3.2 40.4 - - - +
116A HIS* 5.4 0.2 - - - -
355A GLY 3.2 11.6 + - - +
356A THR* 3.2 18.8 + - + +
358A ALA* 1.3 80.3 - - - +
360A TRP* 1.3 80.2 + - + +
362A GLY* 3.1 14.7 + - - -
364A GLY* 3.7 35.0 - - - +
365A ARG 4.0 1.3 - - - +
366A ALA* 4.3 26.5 - - + -
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Residues in contact with TRP 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 THR* 3.0 33.5 + - + +
357A ALA* 3.6 7.6 - - - +
359A MET* 1.3 92.4 - - - +
361A LEU* 1.3 61.3 + - - +
362A GLY* 3.3 1.0 + - - -
401A ARG* 3.1 21.8 + - - -
406A ASP* 3.2 48.0 - - + +
407A VAL* 4.1 9.0 - - + -
409A GLU* 4.0 10.5 - - - -
410A LYS* 3.3 34.1 - - + -
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Residues in contact with LEU 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 ALA 3.2 9.1 + - - +
358A ALA* 3.1 13.0 + - - +
360A TRP* 1.3 77.0 - - - +
362A GLY* 1.3 56.5 + - - +
363A ALA 3.6 0.4 - - - -
373A ASP* 5.0 1.4 - - - +
376A VAL* 3.4 20.4 - - + +
377A GLY* 3.1 37.9 - - - +
378A ILE* 4.2 8.7 - - + -
397A ILE* 3.8 16.8 - - + -
398A HIS 3.2 14.8 - - - +
399A SER* 3.6 24.4 - - - -
400A ASN 5.7 0.5 + - - -
401A ARG* 3.8 15.8 + - - +
404A VAL* 4.1 7.4 - - + -
407A VAL* 3.8 20.6 - - + +
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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