Contacts of the helix formed by residues 399 - 406 (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 LYS 399 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3799 ILE* 5.3 0.2 - - + -
3949 ILE* 3.0 31.4 + - + +
3959 LYS 3.9 4.9 - - - +
3969 GLY* 4.1 1.9 - - - +
3979 SER 2.6 5.3 + - - -
3989 ARG* 1.3 76.2 - - - +
4009 ARG* 1.3 50.0 + - - +
4019 ARG* 2.8 12.9 - - - +
4029 ILE* 2.5 30.2 + - + +
4039 ALA* 2.4 34.8 + - + +
4109 VAL* 5.7 0.4 - - - -
4139 VAL* 3.4 30.7 - - + -
4149 ASN* 2.2 35.0 + - - +
4179 LEU* 2.5 27.9 - - + +
486B C 3.5 16.2 - - - -
487B C 5.9 0.2 + - - -
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Residues in contact with ARG 400 (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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3969 GLY 2.8 21.8 + - - +
3979 SER* 3.1 12.7 + - - +
3999 LYS* 1.3 76.5 - - - +
4019 ARG* 1.3 51.1 + - - +
4039 ALA* 2.7 12.8 - - + +
4049 ALA* 2.5 36.2 + - - +
4109 VAL* 5.1 6.5 - - + -
485B C 4.0 7.6 - - - +
486B C 3.1 34.7 - - - +
59S GLU* 3.9 18.1 + - - +
60S HIS* 2.1 59.9 + - - +
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Residues in contact with ARG 401 (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 3.0 39.5 + - - -
408 C 3.8 31.5 + - - +
628 C 3.8 41.1 + - - -
638 A 5.8 0.2 - - - -
3829 SER 4.5 0.4 + - - -
3839 MET* 5.9 0.4 - - - +
3879 GLU* 3.8 9.3 + - - -
3979 SER 4.2 2.8 + - - +
3989 ARG* 3.4 9.5 + - - +
3999 LYS 3.1 18.5 - - - +
4009 ARG* 1.3 77.4 - - - +
4029 ILE* 1.3 91.4 + - - +
4049 ALA* 4.3 2.9 - - - +
4059 GLY* 2.1 43.3 + - - +
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Residues in contact with ILE 402 (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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628 C 4.8 0.4 - - - -
3799 ILE* 2.5 55.9 - - + -
3829 SER* 3.1 21.8 - - - +
3839 MET* 3.2 7.6 - - + -
3879 GLU* 3.0 20.9 - - - +
3949 ILE* 5.9 1.8 - - + -
3989 ARG 4.6 1.1 - - - +
3999 LYS* 2.5 27.5 + - + +
4019 ARG* 1.3 106.8 - - - +
4039 ALA* 1.3 52.8 + - - +
4059 GLY* 4.2 1.3 - - - +
4069 CYS* 2.4 44.5 + - - +
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Residues in contact with ALA 403 (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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3799 ILE* 4.9 0.8 - - - +
3999 LYS* 2.4 22.0 + - + +
4009 ARG* 2.7 29.6 - - + +
4029 ILE* 1.3 64.9 - - - +
4049 ALA* 1.3 51.7 + - - +
4069 CYS* 2.8 12.3 - - - -
4079 GLY 2.9 0.3 + - - -
4089 MET 2.6 49.4 + - - +
4109 VAL* 4.0 20.9 - - + +
4139 VAL* 4.4 11.2 - - + -
486B C 6.0 0.2 - - - +
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Residues in contact with ALA 404 (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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498 G 4.1 2.4 + - - -
4009 ARG 2.5 17.8 + - - +
4019 ARG* 4.0 2.9 - - - +
4039 ALA* 1.3 70.3 - - - +
4059 GLY* 1.3 59.9 + - - +
4069 CYS 2.9 1.8 - - - -
4079 GLY* 2.3 32.7 + - - +
4089 MET 4.5 1.6 - - - +
4099 GLN* 6.1 0.7 - - - +
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Residues in contact with GLY 405 (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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488 G 3.9 7.8 + - - +
498 G 3.1 17.6 + - - -
618 G 3.9 15.2 + - - -
628 C 3.6 27.8 - - - +
3829 SER* 4.6 0.2 - - - -
4019 ARG* 2.1 30.6 + - - -
4049 ALA* 1.3 68.7 - - - +
4069 CYS* 1.3 55.9 + - - +
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Residues in contact with CYS 406 (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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488 G 3.9 5.8 - - - +
498 G 3.0 36.7 + - - +
3789 ALA 3.9 1.6 - - - -
3799 ILE* 3.5 16.4 - - + +
3829 SER* 3.2 26.4 + - - +
4029 ILE 2.4 42.9 + - - +
4039 ALA* 2.8 21.5 - - - -
4059 GLY* 1.3 69.3 - - - -
4079 GLY* 1.3 56.4 + - - +
4089 MET* 3.2 31.8 + - + -
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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