Contacts of the helix formed by residues 385 - 390 (chain 9) in PDB entry 2J28
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 MET 385 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638 A 4.5 1.6 + - - -
648 G 4.5 9.8 + - - +
3309 ASP* 3.3 25.6 - - - +
3329 ASN* 4.8 8.0 - - - +
3839 MET 3.7 0.2 + - - -
3849 THR* 1.3 79.7 + - - +
3869 LYS* 1.3 56.5 + - - +
3879 GLU 2.6 15.2 + - - -
3889 ARG* 2.9 29.2 + - - +
3899 ALA 4.1 0.7 + - - -
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Residues in contact with LYS 386 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388 U 4.4 15.8 + - - +
398 A 4.4 20.5 + - - +
3849 THR* 4.1 11.1 + - + +
3859 MET* 1.3 79.8 - - - +
3879 GLU* 1.3 66.5 + - - +
3899 ALA* 2.7 25.3 + - + +
3909 LYS* 3.1 45.9 + - + +
3939 ILE* 5.2 4.7 - - + -
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Residues in contact with GLU 387 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398 A 4.5 8.3 + - - -
3839 MET* 2.7 41.5 - - + +
3849 THR* 2.2 55.7 + - + +
3859 MET 2.6 3.8 + - - -
3869 LYS* 1.3 75.5 - - - +
3889 ARG* 1.3 56.9 - - - +
3909 LYS 2.9 30.3 - - - +
3919 PRO* 3.4 2.8 - - - +
3939 ILE* 4.1 13.3 - - + +
3949 ILE* 6.0 0.5 - - - +
3989 ARG* 5.4 7.0 - - - +
4019 ARG* 3.8 8.2 + - - -
4029 ILE* 3.0 17.2 - - - +
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Residues in contact with ARG 388 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638 A 6.0 0.2 + - - -
3309 ASP* 5.6 0.4 - - - +
3319 LEU 1.6 30.6 - - - +
3329 ASN* 2.8 49.3 + - + +
3349 PHE* 5.7 2.5 - - + -
3359 LEU* 2.9 17.4 - - - +
3369 GLU* 4.6 1.6 - - - +
3809 ILE* 2.7 60.5 + - + +
3819 ASN* 5.9 1.2 - - - +
3839 MET* 3.9 23.4 + - + -
3849 THR 4.8 3.4 + - - -
3859 MET* 2.9 25.4 + - - +
3879 GLU* 1.3 72.9 - - + +
3899 ALA* 1.3 52.6 + - - +
3919 PRO* 3.0 19.7 - - - +
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Residues in contact with ALA 389 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3309 ASP* 4.1 24.4 + - + +
3319 LEU* 3.0 18.8 - - - +
3859 MET 4.1 0.6 + - - -
3869 LYS* 2.7 26.1 + - + +
3889 ARG* 1.3 70.5 - - - +
3909 LYS* 1.3 60.4 + - + +
3919 PRO* 2.7 18.9 - - - +
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Residues in contact with LYS 390 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3869 LYS* 3.1 37.6 + - + +
3879 GLU 2.9 8.3 + - - +
3899 ALA* 1.3 81.7 - - + +
3919 PRO* 1.3 51.5 - - - +
3929 GLU* 2.6 22.2 + - + +
3939 ILE* 2.6 55.0 - - + +
3949 ILE* 4.2 0.3 - - - +
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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