Contacts of the helix formed by residues 325 - 330 (chain A) in PDB entry 3ZXR
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A MET* 3.4 24.5 - - + +
264A PRO* 3.2 19.0 - - + +
265A LYS* 2.8 46.7 + - - +
323A THR* 3.3 8.8 + - - +
324A VAL* 1.3 76.9 - - - +
326A SER* 1.3 66.3 + - - +
328A LYS* 3.0 29.9 + - - +
329A ARG 3.7 2.1 + - - -
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Residues in contact with SER 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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264A PRO* 3.8 5.2 - - - -
321A ASN* 3.3 27.6 + - - -
323A THR* 3.0 32.9 + - - -
324A VAL 3.1 0.6 - - - -
325A ASN* 1.3 75.2 - - - +
327A TYR* 1.3 62.7 + - - +
329A ARG* 3.1 25.3 + - - +
330A LEU* 3.5 10.0 + - - +
371A ASP* 2.6 29.0 + - - +
373A SER* 3.2 5.4 + - - -
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Residues in contact with TYR 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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317A LEU* 3.5 13.0 + - + +
321A ASN* 2.9 31.3 + - + -
323A THR 3.2 18.4 - - - -
324A VAL 3.2 8.0 + - - +
325A ASN 3.1 0.8 - - - -
326A SER* 1.3 74.6 - - - +
328A LYS* 1.3 65.0 + - + +
329A ARG 3.2 1.7 + - - -
330A LEU* 3.7 33.3 + - + +
331A VAL* 4.0 10.2 - - - +
420A PRO* 3.5 38.1 - - + -
421A THR 3.3 18.8 - - - +
422A GLN* 3.7 13.0 - - - -
423A LEU* 3.5 22.7 - - + -
426A VAL* 3.3 28.8 - - + +
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Residues in contact with LYS 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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265A LYS* 3.5 27.4 - - + -
324A VAL* 4.0 30.9 - - - +
325A ASN* 3.0 23.1 + - - +
327A TYR* 1.3 78.3 - - + +
329A ARG* 1.3 59.2 + - - +
331A VAL* 3.5 22.8 - - - +
463A VAL* 5.5 4.8 - - - +
468A HIS* 5.5 13.2 - - - -
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Residues in contact with ARG 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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264A PRO* 3.8 28.9 - - + +
265A LYS* 4.0 10.2 + - + +
272A GLY* 4.3 6.1 - - - +
273A SER 3.5 18.6 - - - +
274A GLY* 3.4 19.9 - - - -
276A HIS* 4.2 0.4 + - - -
321A ASN* 3.9 4.9 - - - +
325A ASN 3.7 1.2 + - - -
326A SER 3.1 12.8 + - - +
328A LYS* 1.3 78.9 - - - +
330A LEU* 1.3 60.8 + - - +
331A VAL* 2.7 24.5 + - - +
334A TYR* 5.4 2.6 - - + +
336A ALA* 3.6 25.2 - - + +
337A PRO* 4.4 0.6 - - - +
368A ARG 2.9 22.6 + - - -
369A SER 2.8 26.1 + - - -
370A PRO 3.6 5.7 + - - -
371A ASP* 4.2 2.0 - - - +
505A P3S 2.8 39.6 + - - +
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Residues in contact with LEU 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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317A LEU* 4.0 22.2 - - + -
321A ASN* 3.8 16.4 - - - +
326A SER 3.5 10.4 + - - +
327A TYR* 3.7 28.5 + - + +
328A LYS 3.5 0.6 - - - -
329A ARG* 1.3 97.3 - - - +
331A VAL* 1.3 63.9 + - - +
336A ALA* 4.4 1.6 - - + -
337A PRO* 3.5 41.3 - - + +
338A ILE* 4.1 5.2 - - - +
369A SER* 4.3 6.7 - - - +
419A THR* 4.3 19.5 + - + +
420A PRO 4.9 6.0 - - - +
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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