Contacts of the helix formed by residues 334 - 340 (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 PHE 334 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617 VAL* 3.3 29.8 - - + -
627 THR* 5.2 4.0 - - - -
657 HIS* 4.5 0.2 - + - -
3109 LYS* 5.4 0.7 - - - +
3319 LEU* 5.2 2.8 - - - +
3329 ASN* 3.7 6.0 - - - +
3339 ASP* 1.9 64.4 - - - +
3359 LEU* 1.3 77.9 + - + +
3369 GLU 2.9 0.2 - - - -
3379 GLN* 2.8 33.1 + - - +
3389 LEU 3.9 0.5 + - - -
3769 MET* 4.5 20.9 - - + -
3809 ILE* 4.6 10.5 - - + -
3889 ARG* 5.7 2.7 - - + -
4209 PHE* 1.9 57.9 - + + -
4239 MET* 6.1 0.9 - - + -
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Residues in contact with LEU 335 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3329 ASN 4.4 0.2 - - - -
3339 ASP 3.7 0.8 - - - +
3349 PHE* 1.3 82.2 - - + +
3369 GLU* 1.3 67.2 + - - +
3389 LEU* 2.7 57.5 - - + +
3399 ARG* 3.8 1.4 + - - +
3769 MET* 4.8 1.3 - - + -
3779 GLU* 3.7 11.4 - - + +
3809 ILE* 1.2 87.9 - - + -
3819 ASN* 3.8 7.0 - - + +
3889 ARG* 2.9 18.2 - - - +
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Residues in contact with GLU 336 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3109 LYS* 5.8 5.1 - - - -
3179 GLU* 4.7 8.0 - - - +
3329 ASN 3.6 4.9 - - - +
3339 ASP* 1.1 165.6 + - - +
3359 LEU* 1.3 74.7 - - - +
3379 GLN* 1.3 66.4 + - - +
3389 LEU 3.0 0.2 + - - -
3399 ARG* 3.3 19.7 + - + +
3409 GLN* 4.1 16.4 + - + +
3889 ARG* 4.6 1.5 - - - +
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Residues in contact with GLN 337 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 THR* 2.2 48.3 + - - +
597 LEU* 5.7 0.2 - - - +
627 THR* 4.4 9.1 + - - -
3109 LYS* 3.0 41.3 + - + +
3339 ASP 2.9 1.8 + - - -
3349 PHE* 2.8 14.9 + - - +
3369 GLU* 1.3 79.8 - - - +
3389 LEU* 1.3 54.1 + - - +
3409 GLN* 3.5 9.1 + - - +
3419 MET* 2.4 48.8 - - + +
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Residues in contact with LEU 338 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3349 PHE 3.9 0.6 + - - -
3359 LEU* 2.7 36.4 + - + +
3379 GLN* 1.3 73.2 - - - +
3399 ARG* 1.3 62.1 - - + +
3419 MET* 1.7 54.1 - - - +
3429 LYS* 3.9 19.5 + - + -
3739 LEU 4.3 14.6 - - - +
3779 GLU* 2.8 57.9 - - + +
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Residues in contact with ARG 339 (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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3359 LEU 4.9 0.9 - - - +
3369 GLU* 3.3 14.8 + - - +
3389 LEU* 1.3 82.2 - - + +
3409 GLN* 1.3 74.0 - - + +
3419 MET* 2.2 22.2 - - - +
3429 LYS* 2.9 4.3 + - - +
3439 ASN* 2.8 43.7 + - + +
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Residues in contact with GLN 340 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3069 ASP* 5.7 3.6 - - - +
3109 LYS* 6.4 3.8 - - + -
3139 ARG* 3.4 29.5 + - - +
3369 GLU* 4.3 17.3 + - + +
3379 GLN* 3.6 11.9 - - - +
3389 LEU 3.1 0.4 + - - -
3399 ARG* 1.3 88.8 - - - +
3419 MET* 2.0 60.8 - - + +
3439 ASN* 2.7 9.5 + - - +
3449 MET* 2.4 68.9 + - + +
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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
------------------------------------------------------------
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