Contacts of the helix formed by residues 400 - 413 (chain A) in PDB entry 1DQU
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A LEU* 2.8 16.7 + - + +
399A PRO* 1.3 73.7 - - - +
401A TYR* 1.3 60.3 + - - +
402A LYS* 3.1 9.8 + - - +
403A GLN* 2.2 53.8 + - + +
404A ALA* 2.8 22.3 + - - +
422A TYR* 3.6 2.3 + - - -
442A TYR* 3.6 5.7 + - - -
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Residues in contact with TYR 401 (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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399A PRO 4.2 1.2 - - - -
400A ASP* 1.3 70.3 + - - +
402A LYS* 1.3 63.1 + - + +
404A ALA* 3.4 7.9 + - - +
405A LYS* 2.8 48.6 + - + +
442A TYR* 4.2 11.1 + - + -
445A ARG* 3.1 55.0 + - + +
446A LEU* 3.9 13.0 - - + -
449A LEU* 3.3 28.0 - - + +
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Residues in contact with LYS 402 (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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400A ASP* 3.1 11.0 + - - +
401A TYR* 1.3 78.7 - - + +
403A GLN* 1.3 70.4 + - - +
405A LYS* 2.9 14.7 + - + +
406A GLU* 2.9 32.5 + - - +
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Residues in contact with GLN 403 (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 GLU* 3.7 26.1 + - - +
375A THR* 3.7 21.1 + - + +
394A MET* 3.8 16.1 - - + +
396A SER* 4.0 17.4 - - - +
398A LEU* 3.9 21.8 + - - +
400A ASP* 2.2 41.0 + - - +
402A LYS* 1.3 66.9 - - - +
404A ALA* 1.3 58.3 + - - +
406A GLU* 3.5 11.4 - - - +
407A PHE* 3.0 30.2 + - - +
422A TYR* 5.8 0.6 + - - -
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Residues in contact with ALA 404 (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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400A ASP 2.8 16.6 + - - +
401A TYR* 3.5 6.5 - - - +
402A LYS 3.0 0.2 - - - -
403A GLN* 1.3 78.9 - - - +
405A LYS* 1.3 56.0 + - - +
407A PHE* 4.7 1.8 - - - -
408A ALA* 3.1 13.3 + - - +
422A TYR* 4.2 18.2 - - + -
446A LEU* 3.8 26.0 - - + -
449A LEU* 5.2 0.9 - - - -
451A TYR* 2.7 33.9 + - + +
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Residues in contact with LYS 405 (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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401A TYR* 2.8 41.0 + - + +
402A LYS* 2.9 6.0 + - + +
404A ALA* 1.3 75.2 - - - +
406A GLU* 1.3 56.1 + - - +
408A ALA* 3.5 0.3 - - - +
409A ASP* 2.4 83.6 + - - +
449A LEU* 3.2 26.5 - - + -
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Residues in contact with GLU 406 (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 THR* 3.9 25.3 + - + +
376A GLN* 5.5 1.9 - - - +
379A ILE* 4.2 3.1 - - + -
402A LYS* 2.9 32.0 + - - +
403A GLN* 3.5 11.9 - - - +
405A LYS* 1.3 76.1 - - - +
407A PHE* 1.3 53.8 + - - +
409A ASP* 3.0 6.2 + - - +
410A GLY* 2.2 39.7 + - - -
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Residues in contact with PHE 407 (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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244A THR* 5.0 0.9 - - + -
375A THR* 4.4 4.0 - - + +
378A ALA* 3.5 24.7 - - + -
379A ILE* 3.6 27.8 - - + -
382A ALA* 3.8 11.2 - - + -
392A ILE* 4.0 8.1 - - + -
394A MET* 3.3 54.1 - - + -
403A GLN 3.0 14.3 + - - +
404A ALA* 4.3 3.4 - - - +
406A GLU* 1.3 76.7 - - - +
408A ALA* 1.3 74.8 + - - +
410A GLY* 3.5 0.3 - - - -
411A VAL* 2.8 42.6 + - + +
420A LEU* 4.0 18.8 - - + -
451A TYR* 3.8 15.3 - + - +
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Residues in contact with ALA 408 (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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404A ALA 3.1 21.1 + - - +
405A LYS 3.5 4.3 - - - +
407A PHE* 1.3 82.4 - - - +
409A ASP* 1.3 54.9 + - - +
411A VAL* 2.9 2.9 + - - +
412A HIS* 2.8 40.4 + - + +
420A LEU* 4.3 12.1 - - + -
449A LEU* 4.0 26.2 - - + +
451A TYR* 3.5 21.2 + - + +
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Residues in contact with ASP 409 (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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405A LYS* 2.4 67.6 + - - +
406A GLU* 3.3 5.5 - - - +
408A ALA* 1.3 75.6 - - - +
410A GLY* 1.3 62.9 + - - +
412A HIS* 3.2 18.1 + - - +
413A ALA* 3.5 11.6 + - - +
449A LEU* 4.8 3.4 - - - +
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Residues in contact with GLY 410 (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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379A ILE* 3.2 31.2 - - - +
383A VAL* 4.6 2.9 - - - +
406A GLU 2.2 25.9 + - - -
409A ASP* 1.3 69.1 - - - +
411A VAL* 1.3 60.9 + - - +
413A ALA* 3.8 13.0 - - - +
414A VAL* 4.7 1.9 + - - +
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Residues in contact with VAL 411 (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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379A ILE* 3.7 14.1 - - + -
382A ALA* 3.8 14.6 - - + -
383A VAL* 4.5 6.5 - - + +
386A ALA* 5.4 1.3 - - + -
392A ILE* 5.1 4.9 - - + -
407A PHE* 2.8 45.1 + - + +
408A ALA 3.5 5.8 - - - +
410A GLY* 1.3 76.2 - - - +
412A HIS* 1.3 66.4 + - + +
413A ALA 3.2 1.6 + - - -
414A VAL* 3.4 4.3 + - - +
415A TRP* 3.4 26.3 + - + +
418A GLN* 4.2 29.2 - - + -
420A LEU* 4.5 12.6 - - + -
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Residues in contact with HIS 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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67A PHE* 4.2 5.2 - + - -
408A ALA* 2.8 26.4 + - - +
409A ASP* 3.2 11.6 + - - +
411A VAL* 1.3 70.9 - - + +
413A ALA* 1.3 63.5 + - - +
415A TRP 3.1 17.0 - - - -
416A PRO* 3.1 39.9 - - + +
418A GLN* 3.0 30.7 + - + -
420A LEU* 3.7 18.7 - - + +
449A LEU 3.2 26.5 + - - -
450A GLY* 4.8 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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409A ASP 3.5 8.4 + - - +
410A GLY* 3.8 13.2 - - - +
411A VAL 3.2 0.2 + - - -
412A HIS* 1.3 79.8 - - - +
414A VAL* 1.3 66.4 + - + +
416A PRO* 4.3 3.5 - - - +
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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