Contacts of the helix formed by residues 424 - 437 (chain B) in PDB entry 1ASZ
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 THR 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B HIS* 5.3 2.5 - - + +
333B ARG* 4.2 20.0 + - - +
423B SER* 1.3 73.4 - - - +
425B GLU* 1.3 65.3 + - - +
427B GLU* 3.1 11.2 + - - +
428B LYS* 3.0 55.1 + - + +
672S A 3.6 19.7 - - - +
673S G 2.4 34.0 + - - +
675S C 5.2 4.7 + - - -
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LYS* 4.1 19.3 + - - +
423B SER* 3.3 7.0 + - - +
424B THR* 1.3 80.0 - - - +
426B ASN* 1.3 63.2 + - - +
428B LYS* 3.7 6.1 + - - +
429B PHE* 3.0 25.7 + - + +
672S A 4.1 19.6 + - - +
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B LEU* 3.0 31.1 - - + +
414B LYS* 3.9 18.5 - - - +
416B ILE* 3.2 24.1 - - - +
421B ASP 5.2 1.4 + - - -
422B LEU* 4.2 8.5 - - + +
423B SER* 3.1 32.9 + - - +
425B GLU* 1.3 78.2 - - - +
427B GLU* 1.3 67.4 + - - +
429B PHE* 2.9 6.8 + - - +
430B LEU* 2.7 26.4 + - - +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ARG* 2.8 45.4 + - - -
422B LEU* 4.4 20.8 - - + +
423B SER 2.7 17.1 + - - +
424B THR* 3.1 11.5 + - - +
426B ASN* 1.3 73.8 - - - +
428B LYS* 1.3 67.3 + - - +
430B LEU* 3.1 4.3 + - - +
431B GLY* 3.1 13.3 + - - -
443B TYR* 4.5 3.5 + - - -
473B PHE* 3.9 22.2 - - + -
476B GLY 3.4 14.0 - - - +
477B GLU* 3.2 5.5 - - - -
478B GLU* 3.0 21.6 + - - +
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B HIS* 4.6 8.3 + - - -
424B THR* 3.0 36.3 + - + +
425B GLU* 4.0 4.9 - - - +
427B GLU* 1.3 76.3 - - + +
429B PHE* 1.3 57.7 + - - +
431B GLY* 2.8 20.1 + - - -
432B LYS* 2.9 12.7 + - - +
475B ARG 6.0 0.2 - - - +
476B GLY* 3.8 13.2 - - - -
477B GLU* 4.5 28.7 - - + +
671S G 4.3 7.7 + - - -
672S A 2.7 32.9 + - - +
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 3.5 20.4 - - + -
412B ALA* 4.1 13.7 - - + -
414B LYS* 3.3 43.7 - - + +
425B GLU* 3.0 20.2 + - + +
426B ASN* 2.9 6.5 + - - +
428B LYS* 1.3 71.7 - - - +
430B LEU* 1.3 67.9 + - - +
432B LYS* 3.1 44.9 + - + +
433B LEU* 3.1 44.0 + - + +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B LEU* 5.4 2.7 - - + -
405B GLY* 3.8 33.4 - - - +
408B MET* 4.1 26.2 - - + -
409B LEU* 3.9 19.2 - - + +
422B LEU* 4.3 17.7 - - + -
426B ASN 2.7 15.5 + - - +
427B GLU* 3.6 9.2 - - - +
429B PHE* 1.3 70.8 - - - +
431B GLY* 1.3 65.7 + - - +
433B LEU* 2.9 16.7 + - + -
434B VAL* 2.9 27.5 + - + +
443B TYR* 4.0 15.9 - - + +
445B LEU* 4.1 14.8 - - + -
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Residues in contact with GLY 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B GLU 3.1 6.7 + - - -
428B LYS 2.8 9.8 + - - -
430B LEU* 1.3 78.4 - - - +
432B LYS* 1.3 54.1 + - - +
434B VAL* 3.0 14.3 + - - +
435B ARG* 2.9 27.3 + - - +
440B THR 5.2 1.0 - - - +
443B TYR* 4.4 9.6 + - - -
476B GLY* 4.1 19.7 - - - -
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B LYS 2.9 10.1 + - - +
429B PHE* 3.3 37.5 - - + +
431B GLY* 1.3 75.2 - - - +
433B LEU* 1.3 63.4 + - + +
435B ARG* 2.9 24.8 - - + +
436B ASP* 3.3 20.0 - - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B MET* 3.9 38.4 - - + +
409B LEU* 4.6 2.2 - - + -
412B ALA* 4.2 9.6 - - + -
429B PHE* 3.1 65.6 + - + +
430B LEU* 2.9 17.5 + - + +
432B LYS* 1.3 74.3 - - + +
434B VAL* 1.3 54.0 + - - +
436B ASP* 3.1 10.7 + - - +
437B LYS* 2.7 39.9 + - + +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B VAL* 4.1 3.8 - - + -
400B LEU* 4.5 4.0 - - + -
408B MET* 5.5 2.2 - - - -
430B LEU* 2.9 37.6 + - + +
431B GLY* 3.0 13.0 + - - +
433B LEU* 1.3 73.4 - - - +
435B ARG* 1.3 58.7 + - - +
437B LYS* 4.3 5.2 - - - -
438B TYR* 2.8 56.3 + - + +
439B ASP 3.2 4.7 + - - -
440B THR* 4.0 8.4 + - + +
443B TYR* 3.9 44.0 - - + -
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Residues in contact with ARG 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B GLU* 3.6 28.9 + - - +
388B GLU 4.6 0.8 + - - -
390B LYS* 2.7 44.8 - - - +
431B GLY 2.9 11.9 + - - +
432B LYS* 2.9 20.4 - - + +
434B VAL* 1.3 76.2 - - - +
436B ASP* 1.3 63.2 + - - +
439B ASP* 2.8 32.1 - - - +
440B THR 4.0 13.0 + - - -
441B ASP* 2.8 42.5 + - - +
475B ARG* 4.1 6.7 - - - +
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Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LYS* 3.3 26.1 - - - +
433B LEU* 3.1 9.6 + - - +
435B ARG* 1.3 84.7 - - - +
437B LYS* 1.3 68.6 + - - +
438B TYR 3.4 0.7 + - - -
439B ASP* 3.5 12.7 + - - +
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Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B MET* 3.2 35.1 - - + +
433B LEU* 2.7 25.2 + - + +
434B VAL* 4.2 1.1 - - - +
436B ASP* 1.3 75.5 - - - +
438B TYR* 1.3 90.8 + - + +
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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