Contacts of the helix formed by residues 411 - 422 (chain A) in PDB entry 1A4Y
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 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A GLY* 1.3 70.7 - - - -
412A ALA* 1.3 63.5 + - - +
414A ILE* 4.4 1.6 - - - -
415A LEU* 3.0 25.6 + - - +
437A TYR 4.8 2.0 + - - -
438A TRP* 3.2 9.0 - - - +
439A SER* 2.5 43.9 + - - -
442A MET* 2.9 32.2 - - + +
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Residues in contact with ALA 412 (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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383A ASP* 4.3 13.7 - - + -
410A GLY* 4.8 0.9 - - - -
411A ASP* 1.3 82.4 - - - +
413A GLY* 1.3 61.9 + - - +
415A LEU* 3.4 12.0 + - - +
416A GLN* 3.3 22.7 - - - +
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Residues in contact with GLY 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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383A ASP* 3.9 12.4 - - - +
386A CYS* 3.4 43.0 - - - +
410A GLY 3.2 8.7 + - - -
412A ALA* 1.3 75.9 - - - +
414A ILE* 1.3 67.8 + - - +
416A GLN* 3.3 12.6 + - - -
417A LEU* 3.4 10.3 + - - +
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Residues in contact with ILE 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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409A LEU* 5.1 7.2 - - + +
410A GLY 2.8 27.2 + - - +
411A ASP* 3.8 4.5 - - - +
413A GLY* 1.3 73.3 - - - +
415A LEU* 1.3 66.9 + - - +
417A LEU* 2.8 28.0 + - + +
418A VAL* 2.9 20.4 + - + +
433A LEU* 5.5 9.6 - - + -
436A ILE* 4.5 9.9 - - + -
437A TYR 4.5 0.4 - - - +
438A TRP* 3.2 50.3 - - + -
442A MET* 3.2 27.1 - - + -
446A LEU* 4.8 13.7 - - + -
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Residues in contact with LEU 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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411A ASP 3.0 14.2 + - - +
412A ALA* 3.5 12.8 - - - +
414A ILE* 1.3 75.9 - - - +
416A GLN* 1.3 65.3 + - + +
418A VAL* 2.9 16.0 + - + +
419A GLU* 2.5 41.7 + - + +
442A MET* 3.9 7.8 - - + -
445A ARG* 3.6 52.3 - - - +
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Residues in contact with GLN 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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383A ASP* 3.7 22.6 + - - +
386A CYS* 3.6 12.9 - - - +
387A SER* 3.2 35.5 + - - -
390A ALA* 3.6 8.6 - - + +
412A ALA* 3.3 20.6 + - - +
413A GLY* 3.5 8.1 - - - +
414A ILE 3.2 0.2 - - - -
415A LEU* 1.3 75.8 - - + +
417A LEU* 1.3 61.2 + - - +
419A GLU* 3.2 22.4 + - - +
420A SER* 3.4 12.1 + - - -
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Residues in contact with LEU 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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386A CYS* 4.2 20.2 - - - +
389A LEU* 4.0 27.1 - - + -
390A ALA* 4.4 6.5 - - - +
393A LEU* 4.4 12.1 - - + -
402A LEU* 5.7 0.7 - - + -
404A LEU* 4.0 26.2 - - + -
409A LEU* 4.9 4.0 - - + -
413A GLY 3.5 14.6 - - - +
414A ILE* 2.8 24.3 + - + +
416A GLN* 1.3 67.9 - - - +
418A VAL* 1.3 64.6 + - + +
419A GLU 3.0 2.4 + - - -
420A SER* 3.1 3.6 + - - +
421A VAL* 3.0 35.0 + - + +
431A LEU* 5.2 12.3 - - + -
433A LEU* 4.8 12.8 - - + -
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Residues in contact with VAL 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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414A ILE* 2.9 28.0 + - + +
415A LEU* 3.4 8.5 - - + +
417A LEU* 1.3 77.1 - - + +
419A GLU* 1.3 69.6 + - - +
421A VAL* 4.1 0.6 - - - +
422A ARG* 3.2 27.0 + - + +
442A MET* 3.6 21.1 - - + -
445A ARG* 4.5 23.1 - - + +
446A LEU* 4.6 8.3 - - + -
449A LEU* 3.6 31.0 - - + +
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Residues in contact with GLU 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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415A LEU* 2.5 52.5 + - + +
416A GLN* 3.2 15.3 - - - +
418A VAL* 1.3 85.9 - - - +
420A SER* 1.3 61.5 + - - +
422A ARG* 3.7 5.1 + - - +
423A GLN* 2.9 26.1 + - - +
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Residues in contact with SER 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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390A ALA* 2.8 47.4 + - - +
393A LEU* 4.3 10.5 - - - -
394A LEU* 3.9 16.6 - - - +
416A GLN 3.5 1.0 + - - -
417A LEU 3.1 4.5 + - - -
419A GLU* 1.3 74.2 - - - +
421A VAL* 1.3 65.5 + - - +
422A ARG 3.1 2.0 - - - -
423A GLN* 2.8 32.1 + - - +
426A CYS* 3.4 7.9 - - - +
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Residues in contact with VAL 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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393A LEU* 4.0 22.4 - - + -
417A LEU* 3.0 22.2 + - + +
418A VAL 4.4 1.8 - - - +
420A SER* 1.3 76.4 - - - +
422A ARG* 1.3 56.8 + - - +
423A GLN 3.5 0.2 - - - +
426A CYS* 3.8 15.4 - - - +
428A LEU* 4.5 12.1 - - + +
431A LEU* 4.9 13.0 - - + -
449A LEU* 4.2 11.4 - - + -
453A LYS* 2.8 28.3 + - + +
456A LEU* 3.2 41.7 - - + -
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Residues in contact with ARG 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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418A VAL* 3.2 20.9 + - + +
419A GLU* 3.8 8.3 - - - +
420A SER 3.1 0.8 - - - -
421A VAL* 1.3 77.5 - - - +
423A GLN* 1.3 68.7 + - - +
424A PRO* 3.5 2.9 - - - +
449A LEU* 4.0 18.4 - - + +
453A LYS* 3.2 9.7 + - - +
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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