Contacts of the helix formed by residues 319 - 327 (chain j) in PDB entry 5JPQ
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 ASN 319 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116j LEU* 5.7 6.1 - - + -
117j GLY* 5.6 11.7 - - - +
292j SER* 5.4 4.7 - - - -
318j GLU* 1.3 72.5 - - - +
320j LEU* 1.3 58.5 + - - +
321j LYS* 3.1 13.4 + - + +
322j THR* 4.1 13.0 + - - +
323j LEU* 4.8 3.6 + - - +
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Residues in contact with LEU 320 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314j SER* 6.2 2.9 - - - -
317j PRO* 4.9 5.6 - - + +
318j GLU* 2.7 10.4 + - - +
319j ASN* 1.3 70.5 - - - +
321j LYS* 1.3 61.8 + - - +
322j THR 3.4 0.8 + - - -
323j LEU* 3.5 8.8 + - - +
324j PHE* 3.3 24.7 + - + +
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Residues in contact with LYS 321 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117j GLY* 6.1 4.9 - - - -
319j ASN* 3.1 8.7 - - + -
320j LEU* 1.3 75.6 - - - +
322j THR* 1.3 65.3 + - - +
324j PHE* 4.5 1.9 - - - +
325j GLU* 2.9 28.3 + - + +
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Residues in contact with THR 322 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292j SER* 4.2 16.4 - - - -
293j ALA* 5.5 2.7 - - - -
319j ASN* 4.1 10.4 + - - +
320j LEU 3.4 0.8 - - - -
321j LYS* 1.3 77.0 - - - +
323j LEU* 1.4 53.2 + - - +
325j GLU* 3.0 6.1 + - - +
326j PHE* 2.7 37.5 + - - +
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Residues in contact with LEU 323 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292j SER* 4.0 30.3 - - - +
295j MET* 5.1 6.1 - - + +
296j GLY* 3.4 12.6 - - - +
319j ASN 4.8 2.1 + - - +
320j LEU* 3.5 11.1 + - - +
321j LYS 3.4 0.4 - - - -
322j THR* 1.4 74.9 - - - +
324j PHE* 1.3 59.3 + - - +
326j PHE* 2.9 7.8 + - - +
327j VAL* 2.8 23.1 + - - +
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Residues in contact with PHE 324 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320j LEU* 3.3 13.2 + - + +
321j LYS* 4.5 2.0 - - - +
323j LEU* 1.3 76.9 - - - +
325j GLU* 1.3 63.4 + - - +
327j VAL* 2.7 34.3 + - - +
369j ILE* 4.0 21.5 - - + +
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Residues in contact with GLU 325 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321j LYS* 2.9 21.6 + - + +
322j THR* 3.6 4.9 - - - +
324j PHE* 1.3 77.8 - - - +
326j PHE* 1.3 61.1 + - - +
327j VAL 4.2 2.8 - - - -
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Residues in contact with PHE 326 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293j ALA* 4.2 21.1 - - + +
296j GLY* 3.9 19.8 - - - +
297j VAL* 4.6 3.2 + - - +
300j ALA* 5.7 1.0 - - - +
322j THR 2.7 12.4 + - - +
323j LEU 3.4 8.7 - - - +
325j GLU* 1.3 76.0 - - - +
327j VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 327 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296j GLY 3.7 10.1 - - - -
299j ILE* 3.9 21.1 - - + -
300j ALA* 3.8 21.5 + - - +
323j LEU 2.8 6.9 + - - +
324j PHE* 2.7 33.1 + - + +
325j GLU 4.2 3.1 - - - -
326j PHE* 1.3 79.8 - - - +
368j THR 5.7 3.8 - - - +
369j ILE* 4.1 16.8 - - + +
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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