Contacts of the helix formed by residues 422 - 429 (chain A) in PDB entry 5A86
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 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.9 24.0 - - - +
244A ALA* 4.0 11.7 - - + +
245A ASP* 4.2 5.8 - - - +
248A THR* 2.7 36.4 + - + +
420A PHE 3.5 0.4 + - - -
421A ALA* 1.3 76.3 - - - +
423A PRO* 1.3 77.5 - - + +
424A LEU 3.8 3.4 + - - -
425A MET* 3.1 18.5 + - - +
426A GLN* 3.0 20.4 + - - +
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Residues in contact with PRO 423 (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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421A ALA 4.7 0.2 - - - +
422A THR* 1.3 87.0 - - + +
424A LEU* 1.3 61.6 + - - +
426A GLN* 3.3 20.9 + - - +
427A GLU* 3.2 24.1 + - - +
689C ILE* 3.5 23.5 - - + +
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Residues in contact with LEU 424 (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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248A THR* 4.2 25.6 - - + +
251A PHE* 4.2 9.0 - - + -
252A LYS* 3.9 30.5 - - + -
255A ILE* 4.1 24.2 - - + -
422A THR* 3.3 1.8 + - - -
423A PRO* 1.3 77.7 - - - +
425A MET* 1.3 57.2 + - - +
427A GLU* 3.2 7.3 + - - +
428A LEU* 3.0 42.3 + - + +
689C ILE* 4.0 27.1 - - + +
690C LEU* 4.6 12.1 - - + +
693C LEU* 4.2 7.4 - - + -
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Residues in contact with MET 425 (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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243A MET* 4.7 7.2 - - + -
244A ALA* 3.7 28.5 - - - +
247A SER* 4.5 8.5 - - - -
248A THR* 3.7 6.1 - - - +
251A PHE* 4.1 19.5 - - + -
411A LEU* 4.0 30.5 - - + -
420A PHE* 4.3 10.8 - - + -
421A ALA* 3.8 14.4 - - + -
422A THR* 3.1 32.8 + - - +
424A LEU* 1.3 74.1 - - - +
426A GLN* 1.3 68.1 + - - +
428A LEU* 3.2 3.5 + - - +
429A PHE* 3.0 40.4 + - + +
431A ILE* 4.5 0.2 - - - +
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Residues in contact with GLN 426 (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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415A GLN* 4.9 4.9 - - - +
421A ALA* 3.1 31.5 + - + +
422A THR 3.0 19.8 + - - +
423A PRO* 3.3 18.9 + - - +
425A MET* 1.3 74.7 - - - +
427A GLU* 1.3 62.2 + - + +
430A GLY* 3.1 4.7 + - - -
431A ILE* 2.8 59.9 + - + +
432A THR 3.9 16.5 - - - +
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Residues in contact with GLU 427 (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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277A LYS* 3.0 23.0 + - - -
423A PRO 3.2 9.1 + - - +
424A LEU* 3.2 11.9 + - + +
425A MET 3.2 0.4 - - - -
426A GLN* 1.3 81.1 - - + +
428A LEU* 1.3 57.4 + - + +
429A PHE 3.5 0.3 + - - -
430A GLY* 3.6 1.6 + - - -
686C ARG 4.0 12.1 - - - +
687C HIS* 3.2 36.0 + - + -
688C LYS* 3.3 6.4 + - - +
689C ILE* 2.8 40.8 + - + +
690C LEU* 2.9 30.6 + - + +
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Residues in contact with LEU 428 (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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251A PHE* 3.5 44.2 - - + -
255A ILE* 5.1 5.2 - - + -
276A LEU* 4.1 22.4 - - + +
277A LYS* 3.5 38.4 + - - +
280A ALA* 4.3 8.3 - - + -
424A LEU* 3.0 34.9 + - + +
425A MET 3.2 3.6 + - - +
427A GLU* 1.3 75.6 - - - +
429A PHE* 1.3 73.2 + - + +
690C LEU* 4.1 28.3 - - + -
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Residues in contact with PHE 429 (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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251A PHE* 3.4 43.3 - + - -
277A LYS* 4.7 9.0 - - - -
280A ALA* 5.0 1.8 - - + -
281A PHE* 4.5 22.0 - + + -
404A ASN* 4.9 1.6 - - - -
407A HIS* 5.8 5.4 - + - -
408A THR* 4.0 34.7 - - + +
411A LEU* 3.4 34.1 - - + -
412A LEU* 3.8 15.9 - - + +
425A MET* 3.0 35.3 + - + +
428A LEU* 1.3 88.3 - - + +
430A GLY* 1.3 63.1 + - - +
431A ILE* 3.6 5.6 - - + -
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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