Contacts of the helix formed by residues 400 - 415 (chain A) in PDB entry 4AY6
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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395A LEU* 3.1 40.5 + - + +
398A MET* 2.9 10.5 + - + +
399A GLN* 1.3 74.1 - - - +
401A VAL* 1.3 62.2 + - - +
402A GLN* 3.6 10.7 + - - +
403A GLY* 3.1 21.7 + - - -
404A ALA* 3.3 13.3 + - - +
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Residues in contact with VAL 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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396A LYS* 5.1 6.7 + - + +
399A GLN 3.4 9.3 + - - +
400A ASP* 1.3 71.2 - - - +
402A GLN* 1.3 70.2 + - + +
404A ALA* 3.2 7.3 + - - +
405A LEU* 2.9 28.7 + - + +
428A ILE* 4.1 30.5 - - + +
432A SER* 5.7 2.0 - - - +
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASP* 3.6 8.7 - - - +
401A VAL* 1.3 83.6 - - + +
403A GLY* 1.3 63.1 + - - +
405A LEU* 3.3 11.9 + - - +
406A GLN* 3.2 39.4 + - - +
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Residues in contact with GLY 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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395A LEU* 3.5 11.0 - - - +
400A ASP* 3.1 20.4 + - - -
402A GLN* 1.3 78.1 - - - +
404A ALA* 1.3 64.6 + - - +
406A GLN* 3.2 17.9 - - - +
407A CYS* 3.1 24.8 + - - -
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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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392A GLY* 3.1 31.2 - - - +
395A LEU* 3.6 9.8 - - + +
396A LYS* 3.6 22.4 - - + +
400A ASP 3.3 6.7 + - - +
401A VAL* 3.2 8.9 + - - +
403A GLY* 1.3 73.9 - - - +
405A LEU* 1.3 65.0 + - - +
407A CYS* 3.2 3.6 + - - +
408A TYR* 3.2 34.5 + - + -
428A ILE* 4.9 2.2 - - + -
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Residues in contact with LEU 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 VAL* 2.9 16.5 + - + +
402A GLN* 3.4 16.6 - - - +
403A GLY 3.2 0.2 - - - -
404A ALA* 1.3 77.0 - - - +
406A GLN* 1.3 62.5 + - - +
408A TYR* 3.4 8.5 + - + +
409A THR* 3.1 29.9 + - + +
425A LEU* 3.9 26.7 - - + -
428A ILE* 3.9 31.2 - - + +
429A HIS* 5.6 4.3 - - + +
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A GLN* 3.2 28.6 + - - +
403A GLY* 3.2 16.7 - - - +
405A LEU* 1.3 75.9 - - - +
407A CYS* 1.3 58.7 + - - +
409A THR* 3.0 8.1 + - - +
410A ARG* 2.9 71.8 + - - +
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Residues in contact with CYS 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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388A TYR* 3.4 26.1 - - - +
391A MET* 3.4 37.0 - - - -
392A GLY* 3.8 18.2 - - - -
395A LEU* 4.0 7.6 - - - -
403A GLY 3.1 18.2 + - - -
404A ALA 3.2 8.5 + - - +
406A GLN* 1.3 72.7 - - - +
408A TYR* 1.3 56.5 + - - +
410A ARG* 3.1 6.9 + - - +
411A ALA* 2.8 35.7 + - - +
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Residues in contact with TYR 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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389A SER* 3.2 31.2 - - - -
392A GLY* 3.1 17.1 + - - -
393A ASN* 2.8 29.5 + - - -
396A LYS* 4.1 10.6 + - - +
404A ALA 3.2 15.1 + - - -
405A LEU* 3.4 8.3 + - + +
407A CYS* 1.3 77.6 - - - +
409A THR* 1.3 62.4 + - - +
411A ALA* 3.1 8.2 + - - +
412A ILE* 3.0 27.8 + - - +
421A ALA* 4.1 6.9 - - - +
424A ASN* 3.4 46.2 + - + +
425A LEU* 3.9 18.8 - - + -
428A ILE* 3.6 25.4 - - + -
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Residues in contact with THR 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 LEU* 3.1 18.3 + - + +
406A GLN* 3.0 18.0 + - - +
408A TYR* 1.3 75.4 - - - +
410A ARG* 1.3 62.9 + - - +
412A ILE* 3.1 11.6 + - + +
413A GLN* 3.0 26.4 + - - +
425A LEU* 4.2 21.8 - - + -
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Residues in contact with ARG 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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388A TYR* 3.9 33.1 - - + +
406A GLN* 2.9 59.3 + - - +
407A CYS* 3.4 4.9 - - - +
409A THR* 1.3 76.7 + - - +
411A ALA* 1.3 61.5 + - - +
413A GLN* 3.4 17.8 + - + +
414A ILE* 3.2 33.8 + - + +
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Residues in contact with ALA 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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385A ALA* 3.9 16.0 - - - +
388A TYR* 3.7 23.2 - - + +
389A SER 4.3 4.5 - - - +
407A CYS 2.8 16.5 + - - +
408A TYR* 3.1 10.3 + - - +
410A ARG* 1.3 74.3 - - - +
412A ILE* 1.3 57.6 + - - +
414A ILE* 3.2 7.3 + - - +
415A ASN* 2.9 30.1 + - - +
418A PHE* 4.7 3.5 - - + +
421A ALA* 4.1 15.5 - - + -
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Residues in contact with ILE 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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408A TYR 3.0 18.3 + - - +
409A THR* 3.1 10.9 + - + +
411A ALA* 1.3 76.0 - - - +
413A GLN* 1.3 62.7 + - - +
415A ASN 3.8 5.8 - - - -
416A PRO* 3.1 27.2 - - + +
421A ALA* 3.4 24.2 - - + +
422A HIS* 3.6 56.5 - - + +
425A LEU* 4.4 17.5 - - + -
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Residues in contact with GLN 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 THR 3.0 10.5 + - - +
410A ARG* 3.5 23.9 + - - +
412A ILE* 1.3 79.2 - - - +
414A ILE* 1.3 63.3 + - + +
416A PRO* 4.0 8.9 - - - +
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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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382A PRO 4.0 9.2 - - - +
383A THR* 4.1 31.4 - - + +
385A ALA* 4.6 4.0 - - + -
388A TYR* 3.7 36.6 - - + +
410A ARG* 3.2 23.1 + - + +
411A ALA* 3.6 6.7 - - - +
413A GLN* 1.3 84.3 - - + +
415A ASN* 1.3 63.0 + - + +
416A PRO* 3.4 7.2 - - - +
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Residues in contact with ASN 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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385A ALA* 4.0 17.9 - - + +
411A ALA 2.9 9.6 + - - +
412A ILE* 3.2 10.0 - - - +
414A ILE* 1.3 79.0 - - + +
416A PRO* 1.3 64.9 - - - +
417A ALA* 2.9 23.9 + - - +
418A PHE* 3.0 43.9 + - + +
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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