Contacts of the helix formed by residues 411 - 422 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D GLY* 1.3 70.1 - - - -
412D ALA* 1.3 57.7 + - - +
414D ILE* 4.2 3.8 - - - +
415D LEU* 2.9 31.9 + - - +
437D TYR* 4.8 3.7 + - - -
438D TRP* 3.0 14.4 - - - +
439D SER* 2.4 48.3 + - - -
441D GLU* 5.2 0.7 - - - +
442D MET* 3.4 21.6 - - + +
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Residues in contact with ALA 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP* 4.5 12.8 - - + -
410D GLY* 2.9 1.3 - - - -
411D ASP* 1.3 79.5 - - - +
413D GLY* 1.3 65.3 + - - +
415D LEU* 3.6 11.1 + - - +
416D GLN* 3.2 31.8 + - - +
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Residues in contact with GLY 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP* 4.0 11.4 - - - +
386D CYS* 3.5 32.9 - - - +
409D LEU* 5.2 0.2 - - - -
410D GLY 2.7 16.6 + - - +
412D ALA* 1.3 74.4 - - - +
414D ILE* 1.3 64.8 + - - -
416D GLN* 3.1 14.9 + - - +
417D LEU* 3.2 14.2 + - - +
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Residues in contact with ILE 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D LEU* 3.5 26.0 - - + +
410D GLY 2.6 31.0 + - - +
411D ASP* 4.1 3.8 - - - +
413D GLY* 1.3 71.5 - - - -
415D LEU* 1.3 63.2 + - - +
417D LEU* 3.0 14.0 + - + +
418D VAL* 2.9 27.6 + - + +
433D LEU* 5.2 10.5 - - + -
436D ILE* 3.8 5.6 - - + -
437D TYR 4.2 0.2 - - - +
438D TRP* 3.3 42.2 - - + -
442D MET* 3.2 27.4 - - + -
446D LEU* 4.3 15.0 - - + -
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ASP 2.9 20.3 + - - +
412D ALA* 3.7 12.6 - - - +
414D ILE* 1.3 77.5 - - - +
416D GLN* 1.3 68.1 + - + +
418D VAL* 3.0 16.0 + - - +
419D GLU* 3.0 38.0 + - - +
442D MET* 4.0 11.0 - - - -
445D ARG* 2.9 32.3 - - - +
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Residues in contact with GLN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ASP* 4.0 18.8 + - - +
386D CYS* 4.0 12.0 - - + +
387D SER* 3.1 34.7 - - - +
390D ALA* 3.5 15.5 - - + +
412D ALA* 3.2 22.1 + - - +
413D GLY 3.1 6.7 + - - +
415D LEU* 1.3 85.3 - - + +
417D LEU* 1.3 61.7 + - - +
419D GLU* 3.4 18.4 + - - +
420D SER 3.5 7.6 + - - -
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D CYS* 3.8 25.8 - - + +
389D LEU* 3.9 19.3 - - + -
390D ALA* 4.0 9.0 - - - +
393D LEU* 4.4 11.6 - - + +
402D LEU* 5.9 0.2 - - + -
404D LEU* 3.7 28.5 - - + -
409D LEU* 4.5 12.8 - - + -
413D GLY 3.2 11.0 + - - +
414D ILE* 3.0 14.6 + - + +
416D GLN* 1.3 77.6 - - - +
418D VAL* 1.3 65.0 + - + +
420D SER* 3.2 4.8 + - - -
421D VAL* 3.0 27.0 + - + +
431D LEU* 5.1 15.9 - - + -
433D LEU* 4.9 9.4 - - + -
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Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D ILE* 2.9 26.8 + - + +
415D LEU* 3.0 8.9 + - - +
417D LEU* 1.3 76.5 - - + +
419D GLU* 1.3 67.2 + - + +
421D VAL* 4.2 5.1 - - - +
422D ARG* 3.1 24.6 + - + +
431D LEU* 6.4 1.3 - - + -
442D MET* 4.1 8.3 - - + -
445D ARG* 4.0 25.4 - - + +
446D LEU* 3.6 28.5 - - + -
449D LEU* 4.2 24.0 - - + -
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Residues in contact with GLU 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D LEU* 3.0 38.5 + - - +
416D GLN* 3.7 13.2 - - - +
417D LEU 3.2 0.4 - - - -
418D VAL* 1.3 80.3 - - - +
420D SER* 1.3 61.7 + - - +
422D ARG* 3.5 9.9 - - - +
423D GLN* 3.4 20.2 + - - +
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Residues in contact with SER 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D ALA* 2.6 46.2 + - - +
393D LEU* 4.3 9.9 - - - -
394D LEU* 3.3 23.0 - - - +
416D GLN 3.5 2.3 + - - -
417D LEU 3.2 7.5 + - - -
419D GLU* 1.3 81.0 - - - +
421D VAL* 1.3 57.9 + - - +
422D ARG 3.1 0.2 - - - -
423D GLN* 3.0 26.9 + - - +
426D CYS* 3.4 11.4 - - - +
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Residues in contact with VAL 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D LEU* 4.2 12.8 - - + -
417D LEU* 3.0 18.3 + - + +
418D VAL* 4.2 1.3 - - - +
420D SER* 1.3 75.0 - - - +
422D ARG* 1.3 56.9 + - - +
423D GLN 3.3 0.4 - - - -
426D CYS* 3.8 13.9 - - - -
428D LEU* 3.9 28.5 - - + -
431D LEU* 4.8 13.5 - - + -
449D LEU* 3.8 16.8 - - + -
453D LYS* 2.9 29.9 + - - +
456D LEU* 3.1 33.6 - - + +
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Residues in contact with ARG 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D VAL* 3.1 22.1 + - + +
419D GLU* 3.5 8.5 - - - +
420D SER 3.1 0.2 - - - -
421D VAL* 1.3 75.3 - - - +
423D GLN* 1.3 68.4 + - + +
424D PRO* 3.6 3.3 - - - +
449D LEU* 3.7 19.7 - - + -
453D LYS* 3.7 10.2 - - - +
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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