Contacts of the helix formed by residues 322 - 330 (chain A) in PDB entry 2ZJ4
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 SER 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A LYS* 3.7 9.3 - - - +
320A PHE* 3.3 12.4 - - - +
321A SER* 1.3 83.2 + - - +
323A PHE* 1.3 63.5 + - - +
325A GLN* 3.1 21.4 + - - +
326A LYS* 3.3 16.1 + - - +
657A PHE* 3.3 20.2 - - - -
667A VAL* 3.4 26.9 - - - +
668A ASP* 3.7 7.0 - - - -
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Residues in contact with PHE 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 MET* 4.3 24.0 - - + -
317A LYS* 3.8 39.0 - - + -
322A SER* 1.3 68.5 - - - +
324A MET* 1.3 60.5 + - - +
326A LYS* 3.2 24.5 + - - +
327A GLU* 2.8 46.1 + - - +
469A ILE* 3.6 43.5 - - + -
470A GLY 4.1 1.3 - - - +
668A ASP* 3.0 27.4 + - - +
669A PHE* 4.9 8.1 - + - -
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Residues in contact with MET 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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322A SER* 3.4 3.6 - - - +
323A PHE* 1.3 73.6 - - - +
325A GLN* 1.3 62.1 + - - +
327A GLU* 3.3 12.5 + - - +
328A ILE* 2.9 33.7 + - + +
470A GLY* 4.7 3.8 - - - -
472A ALA* 4.0 24.9 - - + +
474A THR* 3.6 29.4 - - + -
557A LYS* 4.2 9.6 - - + -
561A ILE* 3.5 33.7 - - + -
653A GLN 3.9 20.0 - - - +
657A PHE* 4.5 9.4 - - + -
667A VAL* 4.2 15.9 - - + +
668A ASP* 2.8 21.4 + - - +
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Residues in contact with GLN 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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320A PHE* 3.7 22.4 - - + +
321A SER* 4.9 8.0 + - - -
322A SER* 3.1 19.7 + - - +
324A MET* 1.3 77.0 - - - +
326A LYS* 1.3 62.9 + - - +
328A ILE* 3.4 7.7 + - - +
329A PHE* 3.1 50.4 + - + -
523A ASP* 3.9 19.4 + - - -
654A LEU* 5.0 3.4 - - + -
657A PHE* 3.6 39.0 - - + -
658A HIS* 4.3 2.2 - - - -
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Residues in contact with LYS 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 MET 3.0 26.5 + - - -
317A LYS* 3.5 28.6 - - - +
318A GLY 5.4 0.9 - - - +
320A PHE* 3.7 29.9 - - + -
322A SER 3.3 12.6 + - - +
323A PHE* 3.2 25.4 + - - +
325A GLN* 1.3 78.7 - - - +
327A GLU* 1.3 60.8 + - - +
329A PHE* 3.3 2.3 + - - +
330A GLU* 2.9 38.7 + - + +
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Residues in contact with GLU 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 PHE* 2.8 32.2 + - - +
324A MET* 3.6 5.8 - - - +
326A LYS* 1.3 73.0 - - + +
328A ILE* 1.3 65.9 + - - +
330A GLU* 3.4 23.0 + - - +
331A GLN* 3.6 11.4 - - - +
467A PRO 4.0 2.3 - - - +
468A GLU* 3.6 13.5 - - + +
469A ILE* 2.8 35.9 + - - +
470A GLY* 3.0 23.6 + - - -
472A ALA 5.2 1.2 - - - +
474A THR* 3.4 17.0 + - - +
475A LYS* 3.8 27.4 - - + +
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Residues in contact with ILE 328 (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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324A MET* 2.9 36.6 + - + +
325A GLN* 3.7 7.9 - - - +
327A GLU* 1.3 76.6 - - - +
329A PHE* 1.3 62.5 + - + +
330A GLU 3.2 0.2 - - - -
331A GLN* 2.8 43.0 + - - +
474A THR* 3.7 19.3 + - + -
520A LEU* 3.8 22.1 - - + +
650A ILE* 4.4 1.8 - - + -
653A GLN* 3.8 35.9 - - + +
654A LEU* 4.1 23.8 - - + +
657A PHE* 4.3 11.2 - - + -
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Residues in contact with PHE 329 (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 PHE* 3.7 26.7 - + + -
325A GLN* 3.1 53.1 + - + +
326A LYS 3.6 1.1 - - - +
328A ILE* 1.3 77.6 - - + +
330A GLU* 1.3 59.2 - - - +
331A GLN 3.3 1.3 - - - -
332A PRO* 3.5 12.3 - - - +
333A GLU* 5.3 2.3 - - - +
520A LEU* 3.9 47.9 - - + +
523A ASP* 4.0 22.2 - - + -
654A LEU* 3.9 15.9 - - + -
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Residues in contact with GLU 330 (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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326A LYS* 2.9 22.9 + - + +
327A GLU* 3.5 15.8 + - - +
328A ILE 3.2 0.8 - - - -
329A PHE* 1.3 76.0 - - - +
331A GLN* 1.3 56.2 + - - +
332A PRO* 3.4 3.1 - - - -
333A GLU* 3.0 27.8 + - + +
334A SER* 2.9 34.4 + - - +
337A ASN* 5.3 4.5 - - - +
465A ALA 4.0 6.1 - - - +
466A GLY* 5.4 1.0 - - - -
475A LYS* 2.9 37.9 + - + +
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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
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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