Contacts of the helix formed by residues 424 - 432 (chain B) in PDB entry 5AO4
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 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A LEU* 5.2 1.3 - - + -
146B TYR* 3.0 20.0 + - + +
147B ILE* 3.8 1.1 - - - -
148B LYS* 2.8 53.1 + - - +
212B PRO* 3.4 6.0 - - - +
213B PHE* 3.0 39.6 + - + -
423B THR* 1.3 73.5 - - - +
425B ASN* 1.3 63.9 + - - +
426B ILE* 3.1 4.3 - - - -
427B PHE* 3.2 19.6 + - + +
428B LEU* 4.1 6.4 + - - +
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Residues in contact with ASN 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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425A ASN* 2.6 28.5 - - - +
428A LEU* 3.2 43.6 + - + +
429A GLU* 4.3 3.0 + - - +
432A TYR* 3.7 20.3 - - + +
421B LYS 5.5 0.2 - - - +
423B THR* 3.0 12.6 + - - +
424B ASP* 1.3 78.2 - - - +
426B ILE* 1.3 63.0 + - - +
428B LEU* 3.1 16.4 + - - +
429B GLU* 3.2 31.5 + - - +
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Residues in contact with ILE 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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212B PRO* 4.1 10.5 - - + -
213B PHE* 5.1 0.2 - - + -
390B PHE* 3.3 31.9 - - + -
397B ILE* 3.7 37.2 - - + -
399B ILE* 5.6 2.2 - - + -
409B ILE* 3.8 22.0 - - + -
422B LEU* 4.3 14.6 - - + -
423B THR 3.1 19.5 + - - +
424B ASP* 4.4 1.8 - - - -
425B ASN* 1.3 83.2 - - - +
427B PHE* 1.3 64.3 + - + +
429B GLU* 4.0 10.1 - - - +
430B ILE* 3.3 27.0 + - + +
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Residues in contact with PHE 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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146A TYR* 3.3 27.1 - + - -
155B TYR* 3.2 23.3 - + - -
213B PHE* 3.5 32.5 - + + -
386B ILE* 3.9 25.8 - - + -
390B PHE* 4.6 5.2 - - - -
424B ASP 3.2 12.5 + - - +
426B ILE* 1.3 83.6 - - - +
428B LEU* 1.3 73.5 + - + +
430B ILE 3.5 0.2 + - - -
431B LEU* 3.3 22.7 + - + +
445B LEU* 3.3 54.7 - - + +
448B ILE* 4.3 9.9 - - + -
449B GLU* 4.4 3.1 - - - -
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Residues in contact with LEU 428 (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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146A TYR* 3.9 47.3 - - + -
423A THR* 4.1 0.4 - - - +
425A ASN* 3.5 37.9 - - + +
428A LEU* 6.3 1.6 - - + -
424B ASP 4.9 6.7 - - - +
425B ASN* 3.1 6.0 + - - +
427B PHE* 1.3 83.5 - - + +
429B GLU* 1.3 60.1 + - - +
431B LEU* 3.6 17.4 - - + +
432B TYR* 2.8 66.0 + - + +
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Residues in contact with GLU 429 (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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425A ASN* 4.5 4.4 + - - +
397B ILE* 4.5 27.7 - - + +
398B GLU 5.8 0.2 - - - +
425B ASN* 3.2 32.8 + - - +
426B ILE* 3.7 9.8 + - + +
427B PHE 3.4 0.2 - - - -
428B LEU* 1.3 74.6 - - - +
430B ILE* 1.3 62.5 + - - +
432B TYR* 3.8 4.2 - - - -
433B SER* 3.0 29.2 + - - -
438B LEU* 5.4 4.8 - - + +
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Residues in contact with ILE 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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389B ALA 4.6 2.7 - - - +
390B PHE* 4.1 27.1 - - + -
393B ALA* 3.8 20.6 - - + -
397B ILE* 3.6 23.1 - - + -
409B ILE* 5.1 0.2 - - + -
426B ILE* 3.3 19.0 + - + +
427B PHE 3.8 4.9 - - - +
428B LEU 3.3 0.2 - - - -
429B GLU* 1.3 78.7 - - - +
431B LEU* 1.3 61.5 + - - +
433B SER* 2.5 26.1 + - - +
438B LEU* 4.7 5.6 - - + +
441B ALA* 3.9 12.1 - - + +
442B ARG* 3.4 35.5 - - + +
445B LEU* 3.9 12.3 - - + -
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Residues in contact with LEU 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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146A TYR* 4.9 0.7 - - + -
421A LYS* 5.7 2.1 - - - -
427B PHE* 3.3 18.8 + - + +
428B LEU* 3.2 29.5 + - + +
430B ILE* 1.3 80.8 - - - +
432B TYR* 1.3 72.9 + - + +
433B SER 3.6 0.3 + - - -
442B ARG* 3.7 15.0 - - - +
445B LEU* 4.0 37.2 - - + +
446B LYS* 4.2 18.2 - - + +
449B GLU* 3.4 36.6 - - - +
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Residues in contact with TYR 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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143A ARG* 5.2 0.9 - - - +
146A TYR* 4.3 3.3 - - - -
400A THR* 5.2 0.2 + - - -
420A THR 4.4 3.9 + - - -
421A LYS* 3.0 65.5 + - + +
423A THR* 3.1 36.5 + - - +
425A ASN* 3.6 22.2 - - - -
428B LEU* 2.8 43.3 + - + +
429B GLU* 3.8 4.3 - - - +
431B LEU* 1.3 98.0 - - + +
433B SER* 1.3 64.1 + - - +
434B THR* 3.6 8.5 + - - +
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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