Contacts of the helix formed by residues 326 - 333 (chain A) in PDB entry 4ZGY
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 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU* 3.7 29.6 - - + -
288A VAL* 4.6 3.8 - - + -
320A ASP* 4.1 11.4 - - + -
321A GLY* 3.0 33.6 + - - +
322A VAL* 3.3 17.0 - - + +
325A SER* 1.3 78.7 - - - +
327A ASN* 1.3 64.2 + - - +
328A CYS* 3.1 8.3 - - - +
329A ILE* 3.1 25.0 + - + +
336A VAL* 4.2 19.5 - - + -
366A ILE* 3.8 37.5 - - + -
383A PHE* 4.0 24.2 - + - -
386A MET* 3.6 23.8 - - + -
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Residues in contact with ASN 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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322A VAL 2.4 35.3 + - - -
323A TYR* 3.8 13.5 + - - +
324A GLY 4.2 8.3 + - - +
325A SER 3.5 3.6 + - - -
326A PHE* 1.3 77.2 - - - +
328A CYS* 1.3 56.4 + - - +
330A LEU* 2.9 23.1 + - - +
331A TYR* 2.9 38.9 + - + -
389A TYR 4.5 12.4 + - - +
196B GLU* 6.2 0.2 - - - +
197B ILE* 3.9 26.4 + - + +
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Residues in contact with CYS 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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325A SER 4.8 3.4 - - - -
326A PHE* 3.1 17.6 - - - -
327A ASN* 1.3 77.4 - - - +
329A ILE* 1.3 60.7 + - - +
330A LEU 3.3 0.2 - - - -
331A TYR* 4.1 11.1 - - - -
332A ASP* 2.9 32.2 + - - +
334A ALA* 3.3 30.6 + - + +
336A VAL* 4.6 15.7 - - - -
386A MET* 5.3 5.8 - - - -
388A ALA 6.0 2.5 - - - +
389A TYR* 5.2 6.8 + - + +
390A THR* 5.8 3.6 - - - -
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Residues in contact with ILE 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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322A VAL* 3.6 17.5 - - + -
326A PHE* 3.1 25.5 + - + +
327A ASN 3.1 0.4 + - - -
328A CYS* 1.3 80.5 - - - +
330A LEU* 1.3 65.4 + - + +
333A HIS* 3.3 24.6 + - - -
334A ALA* 3.2 31.2 - - + +
336A VAL* 4.3 11.7 - - + -
363A LEU 4.9 4.3 - - - +
365A ARG 3.5 18.2 - - - +
366A ILE* 3.3 27.4 - - - +
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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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322A VAL* 3.8 33.7 - - + +
323A TYR* 3.9 17.5 - - + +
327A ASN 2.9 6.9 + - - +
329A ILE* 1.3 79.0 - - + +
331A TYR* 1.3 64.2 + - - +
333A HIS* 4.9 1.7 - - - -
363A LEU* 4.0 43.7 - - + +
183B ARG* 5.2 7.0 + - - +
184B ALA* 3.3 24.1 - - - +
187B LEU* 3.7 20.8 - - + +
197B ILE* 3.8 25.8 - - + -
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Residues in contact with TYR 331 (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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327A ASN* 2.9 40.8 + - + +
328A CYS* 4.1 4.9 - - - -
330A LEU* 1.3 79.2 - - - +
332A ASP* 1.3 68.7 + - - +
333A HIS 3.6 0.4 - - - -
389A TYR* 5.8 9.9 - + + -
184B ALA* 3.4 4.7 - - - +
187B LEU* 3.6 34.5 - - + -
188B ARG* 2.4 50.4 + - + +
191B SER* 3.7 23.5 + - - -
195B PHE 4.5 2.9 + - - -
196B GLU* 4.7 1.0 - - - -
197B ILE* 3.4 36.0 + - + +
214B MET* 4.0 4.2 - - - +
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Residues in contact with ASP 332 (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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164A CYS* 6.1 0.2 - - - -
200A SER* 5.0 7.5 + - - -
277A ARG* 4.9 12.6 + - - -
328A CYS* 2.9 20.3 + - - +
331A TYR* 1.3 88.5 - - - +
333A HIS* 1.3 76.8 + - - +
334A ALA* 4.1 7.4 - - + +
188B ARG* 3.4 20.2 - - - +
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Residues in contact with HIS 333 (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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328A CYS 3.4 1.8 + - - -
329A ILE* 3.3 18.7 + - - -
330A LEU 4.9 2.0 - - - -
331A TYR 3.6 0.4 - - - -
332A ASP* 1.3 83.6 - - - +
334A ALA* 1.3 65.0 + - - +
335A HIS* 3.2 22.8 + - + -
183B ARG* 5.3 11.4 - - - -
184B ALA* 3.3 33.2 - - + +
188B ARG* 4.8 4.0 + - - -
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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