Contacts of the helix formed by residues 369 - 380 (chain A) in PDB entry 1BJ4
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 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A LEU* 3.4 7.0 - - - +
368A THR* 1.3 82.5 + - - +
370A GLY* 1.3 62.4 + - - +
371A GLY* 2.8 26.3 + - - -
372A ARG* 2.9 42.7 + - - +
373A ALA* 3.2 22.9 + - - +
397A ARG* 3.7 33.0 + - + +
398A PRO 3.3 15.2 - - - +
399A SER* 3.9 7.4 - - - +
436A GLN* 4.0 1.4 + - - -
445A LEU* 5.6 0.2 - - - +
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Residues in contact with GLY 370 (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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363A LEU* 3.8 10.5 - - - -
369A ASP* 1.3 71.8 - - - +
371A GLY* 1.3 57.0 + - - -
373A ALA 3.8 0.2 - - - -
374A GLU* 2.9 32.2 + - - +
386A LYS* 3.5 8.2 - - - +
398A PRO 2.8 13.4 + - - -
399A SER 3.5 5.7 + - - -
400A GLY 3.2 24.0 - - - -
401A LEU* 3.6 4.7 - - - +
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Residues in contact with GLY 371 (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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369A ASP* 2.8 8.8 + - - -
370A GLY* 1.3 78.2 - - - +
372A ARG* 1.3 61.9 + - - +
374A GLU* 3.6 12.0 - - - +
375A LYS* 3.6 17.2 - - - +
386A LYS* 3.8 22.2 - - - +
398A PRO* 3.7 9.8 + - - +
445A LEU* 4.4 16.1 - - - +
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Residues in contact with ARG 372 (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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368A THR* 4.5 0.7 - - - +
369A ASP* 2.9 29.5 + - - +
371A GLY* 1.3 71.7 - - - +
373A ALA* 1.3 66.6 + - - +
374A GLU 3.3 0.2 + - - -
375A LYS* 3.3 3.0 + - - +
376A VAL* 3.3 24.3 + - - +
397A ARG* 3.3 34.7 - - - +
432A THR* 4.1 7.6 - - + -
436A GLN* 3.3 29.0 - - - +
439A THR* 5.4 1.4 - - - +
443A ALA* 3.6 21.2 + - - +
444A THR* 3.6 11.5 + - - +
445A LEU* 3.8 30.4 - - + +
448A PHE* 3.5 58.0 - - + +
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Residues in contact with ALA 373 (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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363A LEU* 3.4 32.5 - - + -
368A THR* 5.1 0.4 - - + -
369A ASP 3.2 7.0 + - - +
370A GLY 4.0 0.9 - - - +
372A ARG* 1.3 78.8 - - - +
374A GLU* 1.3 62.0 + - - +
376A VAL* 3.5 1.2 + - - +
377A LEU* 3.0 32.9 + - - +
401A LEU* 3.8 12.3 - - + -
429A ILE* 4.0 13.7 - - + -
432A THR* 3.8 17.9 - - + +
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Residues in contact with GLU 374 (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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370A GLY 2.9 20.3 + - - +
371A GLY 3.6 3.1 - - - +
372A ARG 3.2 0.2 - - - -
373A ALA* 1.3 76.6 - - - +
375A LYS* 1.3 79.4 + - + +
377A LEU* 3.6 2.1 + - - +
378A GLU* 3.1 31.9 + - + +
382A ILE 4.9 0.3 - - - +
384A CYS* 4.0 21.3 + - - +
385A ASN* 3.4 11.6 - - - +
386A LYS* 3.1 51.5 + - - +
401A LEU* 4.1 12.1 - - + +
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Residues in contact with LYS 375 (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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371A GLY 3.6 14.8 + - - +
372A ARG* 3.3 8.3 + - - +
374A GLU* 1.3 97.9 - - + +
376A VAL* 1.3 64.6 + - - +
378A GLU* 3.2 20.1 + - - +
379A ALA* 3.0 23.2 + - - +
445A LEU* 5.1 6.2 - - + +
448A PHE* 5.0 4.9 - - + -
449A LYS* 3.1 49.5 - - + +
452A LEU* 3.9 17.3 - - + +
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Residues in contact with VAL 376 (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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372A ARG 3.3 12.6 + - - +
373A ALA 3.9 1.8 - - - +
375A LYS* 1.3 74.5 - - - +
377A LEU* 1.3 65.4 + - - +
379A ALA* 3.0 14.4 + - - +
380A CYS* 3.2 14.4 + - - -
428A GLY* 3.5 26.2 - - - +
431A LEU* 4.2 22.9 - - + -
432A THR* 3.3 23.1 - - - +
435A ILE* 4.3 2.2 - - + -
448A PHE* 3.6 24.0 - - + -
452A LEU* 3.9 23.6 - - + -
461A VAL* 5.9 0.2 - - + -
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Residues in contact with LEU 377 (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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373A ALA* 3.0 24.3 + - + +
374A GLU 3.9 3.1 - - - +
376A VAL* 1.3 76.1 - - + +
378A GLU* 1.3 55.1 + - - +
380A CYS* 3.1 9.3 + - + +
382A ILE* 2.7 68.5 + - + +
384A CYS* 3.5 26.2 - - - -
401A LEU* 3.8 19.5 - - + -
403A LEU* 5.6 0.7 - - + -
424A PHE 5.0 0.4 - - - +
425A ILE* 3.9 20.6 - - + +
428A GLY* 3.9 28.3 - - - -
429A ILE* 4.7 5.6 - - + -
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Residues in contact with GLU 378 (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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374A GLU* 3.1 20.4 + - + +
375A LYS* 3.4 24.9 - - - +
376A VAL 3.1 0.2 - - - -
377A LEU* 1.3 77.2 - - - +
379A ALA* 1.3 56.5 + - - +
381A SER* 2.9 20.0 + - - +
382A ILE 3.4 9.4 + - - +
383A ALA* 5.5 2.9 - - + +
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Residues in contact with ALA 379 (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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375A LYS 3.0 12.2 + - - +
376A VAL* 3.0 13.9 + - - +
378A GLU* 1.3 75.0 - - - +
380A CYS* 1.3 58.4 + - - +
381A SER 3.4 0.4 - - - -
452A LEU* 4.5 15.5 - - + -
461A VAL* 3.5 27.4 - - + +
465A ARG* 3.5 22.4 + - - +
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Residues in contact with CYS 380 (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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376A VAL* 3.5 17.0 - - - +
377A LEU* 3.1 8.9 + - + +
378A GLU 3.0 1.4 - - - -
379A ALA* 1.3 78.5 - - - +
381A SER* 1.3 70.5 + - - +
382A ILE* 3.2 10.7 + - + -
428A GLY* 5.6 0.7 - - - -
431A LEU* 4.4 10.5 - - - -
461A VAL* 4.0 23.1 - - - -
464A LEU* 3.8 29.4 - - + -
465A ARG* 3.7 18.4 - - - +
468A VAL* 3.5 20.5 - - + +
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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