Contacts of the helix formed by residues 319 - 327 (chain A) in PDB entry 1JRX
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A THR* 6.1 3.2 - - - +
316A PHE* 3.0 13.9 + - + +
318A LYS* 1.3 74.9 - - - +
320A ASN* 1.3 55.6 + - - +
321A GLU* 3.3 13.0 + - - +
322A ARG* 2.9 35.4 + - + +
323A VAL* 2.9 27.4 + - - +
341A ALA 3.7 1.2 + - - -
342A VAL* 3.1 39.3 + - + +
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Residues in contact with ASN 320 (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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317A ALA 5.3 0.4 - - - -
318A LYS 3.1 9.1 + - - +
319A ASN* 1.3 72.1 + - - +
321A GLU* 1.3 54.6 + - - +
323A VAL* 3.9 7.7 - - - +
324A ALA* 2.6 37.8 + - - +
330A LEU 3.0 24.4 + - - -
331A LYS* 3.3 9.9 - - - +
332A GLY* 2.7 28.0 + - - +
333A PHE 4.0 14.7 + - - +
503A VAL* 4.1 12.5 - - - +
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Residues in contact with GLU 321 (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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319A ASN* 3.3 9.6 - - - +
320A ASN* 1.3 79.0 - - - +
322A ARG* 1.3 63.1 + - + +
324A ALA* 3.6 5.5 - - - +
325A LYS* 3.1 53.1 + - - +
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Residues in contact with ARG 322 (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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316A PHE* 4.0 20.6 - - + -
319A ASN* 2.9 34.4 + - + +
321A GLU* 1.3 75.8 - - + +
323A VAL* 1.3 66.3 + - - +
325A LYS* 3.2 10.1 + - + +
326A LEU* 3.2 27.9 + - + +
342A VAL 4.6 0.8 + - - -
343A GLY* 3.5 22.0 + - - -
346A LEU* 4.0 10.1 - - - +
347A ASP* 3.2 30.0 + - - -
350A GLU* 4.4 4.9 + - - -
356A LEU* 3.9 16.0 - - - +
359A MET* 3.4 29.9 - - - +
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Residues in contact with VAL 323 (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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316A PHE* 3.7 28.0 - - + +
317A ALA* 4.2 3.8 - - - +
319A ASN 2.9 20.7 + - - +
320A ASN* 3.6 12.8 - - - +
322A ARG* 1.3 75.8 - - - +
324A ALA* 1.3 52.2 + - - +
326A LEU* 3.1 2.6 + - - +
327A ASP* 2.6 35.2 + - - +
330A LEU* 3.6 39.3 - - + -
362A ILE* 3.8 14.5 - - + +
503A VAL* 4.0 22.4 - - + -
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Residues in contact with ALA 324 (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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320A ASN 2.6 23.0 + - - +
321A GLU* 3.6 7.4 - - - +
323A VAL* 1.3 75.1 - - - +
325A LYS* 1.3 63.7 + - + +
327A ASP 3.5 8.7 - - - -
328A PRO* 3.1 29.2 - - + +
331A LYS* 3.6 40.4 - - + +
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Residues in contact with LYS 325 (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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321A GLU* 3.1 43.1 + - - +
322A ARG* 3.2 10.9 + - + +
324A ALA* 1.3 77.4 - - + +
326A LEU* 1.3 63.7 + - + +
328A PRO* 4.7 5.2 - - - +
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Residues in contact with LEU 326 (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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316A PHE* 3.5 32.5 - - + -
322A ARG* 3.2 19.7 + - + +
323A VAL 3.1 1.6 + - - -
325A LYS* 1.3 84.1 - - + +
327A ASP* 1.3 58.4 + - - +
328A PRO* 3.9 5.2 - - - +
359A MET* 3.6 39.7 - - + +
360A GLN* 4.1 22.9 - - + +
362A ILE* 3.6 14.8 - - + -
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Residues in contact with ASP 327 (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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323A VAL 2.6 18.9 + - - +
324A ALA* 3.3 7.1 - - - -
326A LEU* 1.3 75.7 - - - +
328A PRO* 1.4 69.1 - - - +
329A SER* 3.0 28.9 + - - -
330A LEU* 2.9 38.2 + - + +
360A GLN 4.5 8.3 - - - +
362A ILE* 4.2 15.4 + - + +
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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