Contacts of the helix formed by residues 412 - 423 (chain A) in PDB entry 2JDQ
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 SER 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ARG* 3.8 30.1 - - - +
411A GLY* 1.3 72.1 - - - -
413A ALA* 1.3 65.6 + - - +
414A GLU* 3.4 16.7 + - - +
415A GLN* 2.9 35.6 + - - +
416A ILE* 3.0 25.7 + - - +
453A LEU* 4.5 2.7 - - - -
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Residues in contact with ALA 413 (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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412A SER* 1.3 74.2 - - - +
414A GLU* 1.3 59.6 + - - +
416A ILE* 3.5 3.1 + - - +
417A LYS* 2.9 29.8 + - - +
453A LEU* 4.2 22.3 - - + +
456A GLN* 4.1 9.1 + - + +
457A GLU* 3.2 27.4 - - + +
460A ARG* 3.6 30.3 - - - +
468A TYR* 4.6 0.5 + - - -
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Residues in contact with GLU 414 (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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412A SER* 3.5 17.6 + - - +
413A ALA* 1.3 79.5 + - - +
415A GLN* 1.3 57.6 + - + +
417A LYS* 3.5 14.3 - - + +
418A TYR* 3.1 25.3 + - - +
457A GLU* 5.2 0.4 - - - +
460A ARG* 2.9 30.6 + - - +
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Residues in contact with GLN 415 (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 ARG* 3.1 32.5 + - - +
373A ILE* 4.0 10.2 - - + +
374A GLN* 2.7 38.2 + - - +
377A ILE* 3.6 16.4 - - + +
411A GLY* 3.1 11.9 - - - -
412A SER* 2.9 41.6 + - - +
414A GLU* 1.3 75.8 - - + +
416A ILE* 1.3 64.4 + - + +
418A TYR* 3.4 7.8 + - - +
419A LEU* 3.0 31.8 + - + +
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Residues in contact with ILE 416 (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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407A ALA 4.2 2.5 - - - +
408A THR* 3.9 34.3 - - + +
411A GLY* 3.9 17.3 - - - +
412A SER 3.0 17.1 + - - +
413A ALA 3.8 3.6 - - - +
415A GLN* 1.3 76.4 - - + +
417A LYS* 1.3 59.3 + - - +
419A LEU* 3.1 10.4 + - + +
420A VAL* 2.9 33.5 + - + +
450A ILE* 4.2 22.7 - - + -
453A LEU* 3.5 27.1 - - + -
468A TYR* 4.0 21.8 - - + +
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Residues in contact with LYS 417 (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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413A ALA 2.9 22.3 + - - +
414A GLU* 3.5 14.1 - - + +
415A GLN 3.4 0.2 - - - -
416A ILE* 1.3 72.3 - - - +
418A TYR* 1.3 58.6 + - - +
420A VAL* 3.2 5.7 + - - +
421A GLU* 3.0 51.9 + - + +
457A GLU* 4.2 23.1 + - - +
468A TYR* 3.7 16.8 + - + +
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Residues in contact with TYR 418 (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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377A ILE* 3.6 45.8 + - + -
380A ASN* 3.9 20.4 + - - -
382A PHE* 4.5 4.4 - + - +
383A PRO* 4.1 3.3 - - - +
414A GLU 3.1 11.2 + - - +
415A GLN* 3.5 9.2 - - - +
416A ILE 3.2 0.2 - - - -
417A LYS* 1.3 78.3 - - - +
419A LEU* 1.3 74.1 + - + +
421A GLU* 3.2 19.0 + - + +
422A LEU* 3.1 61.3 + - + +
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Residues in contact with LEU 419 (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 ILE* 6.1 1.6 - - + -
377A ILE* 5.0 2.2 - - + -
382A PHE* 3.4 49.1 - - + -
386A ILE* 4.2 2.9 - - + +
404A ILE* 4.5 6.7 - - + +
407A ALA* 3.9 28.0 - - + -
408A THR* 4.4 19.3 - - + +
415A GLN* 3.0 19.5 + - + +
416A ILE* 3.1 13.0 + - + +
418A TYR* 1.3 85.0 - - + +
420A VAL* 1.3 61.8 + - - +
422A LEU* 3.4 6.7 + - + +
423A GLY 3.3 5.7 + - - -
424A CYS* 3.1 37.8 + - + +
450A ILE* 6.2 0.2 - - + -
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Residues in contact with VAL 420 (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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416A ILE* 2.9 21.5 + - + +
417A LYS 3.5 4.9 - - - +
419A LEU* 1.3 79.2 - - - +
421A GLU* 1.3 59.0 + - + +
423A GLY* 3.1 19.2 + - - -
424A CYS* 3.9 10.0 + - - +
425A ILE* 3.9 23.6 + - + +
450A ILE* 4.2 11.7 - - + -
468A TYR* 3.8 26.2 - - + -
471A LEU* 3.7 30.7 - - + -
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Residues in contact with GLU 421 (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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417A LYS* 3.0 37.5 + - + +
418A TYR* 3.2 21.9 + - + +
420A VAL* 1.3 78.5 - - + +
422A LEU* 1.3 61.1 + - + +
423A GLY* 3.2 0.4 - - - -
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Residues in contact with LEU 422 (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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382A PHE* 3.8 21.8 - - + -
383A PRO* 3.8 24.9 - - + -
386A ILE* 3.6 26.4 - - + +
418A TYR* 3.1 58.0 + - + +
419A LEU* 3.8 4.5 - - + +
420A VAL 3.3 0.2 - - - -
421A GLU* 1.3 78.2 - - + +
423A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 423 (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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386A ILE* 4.1 5.6 - - - +
390A GLN* 5.4 0.5 + - - -
419A LEU 3.3 0.4 + - - -
420A VAL 3.1 13.6 + - - -
421A GLU 3.2 0.9 - - - -
422A LEU* 1.3 81.6 - - - +
424A CYS* 1.3 60.8 + - - +
425A ILE 3.3 3.5 + - - -
426A LYS* 4.0 3.3 + - - +
427A PRO* 3.1 25.1 - - - +
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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