Contacts of the helix formed by residues 327 - 332 (chain A) in PDB entry 3U7U
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 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A ILE* 4.4 4.8 - - - +
317A LEU* 3.7 31.2 - - + +
320A ALA* 4.1 10.1 - - - +
322A THR 3.3 17.5 + - - -
323A VAL* 3.3 10.4 - - - +
324A ASP* 2.8 38.2 + - - -
326A SER* 1.3 83.2 + - - +
328A ILE* 1.3 59.3 + - - +
329A ASP 3.1 3.1 - - - -
330A LYS* 2.9 34.7 + - + +
331A PHE* 3.5 10.4 - - + -
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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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323A VAL* 3.8 5.6 - - + -
324A ASP 2.8 24.1 + - - +
325A SER* 3.6 20.4 - - - +
327A ASN* 1.3 72.8 + - - +
329A ASP* 1.3 65.8 + - - +
331A PHE* 3.4 23.6 + - - +
359A ILE* 3.8 22.2 - - + -
363A LYS* 3.7 55.9 - - + +
364A LEU* 4.0 6.7 - - + -
366A VAL* 3.7 11.4 - - + +
367A PHE* 3.6 31.0 - - + -
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Residues in contact with ASP 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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325A SER 5.0 1.7 + - - +
326A SER 5.5 0.8 - - - -
327A ASN* 3.1 1.8 - - - +
328A ILE* 1.3 75.9 - - - +
330A LYS* 1.3 57.3 + - - +
331A PHE 3.0 6.2 + - - -
332A ILE* 3.0 43.5 - - + +
363A LYS* 3.1 39.4 + - - +
366A VAL* 4.7 2.6 - - - +
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Residues in contact with LYS 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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307A LYS* 5.3 1.9 + - - -
309A CYS* 4.5 5.9 - - - +
316A SER* 5.3 10.5 - - - +
317A LEU* 3.8 35.7 - - + -
326A SER 4.1 20.2 + - - -
327A ASN* 2.9 19.8 + - + +
329A ASP* 1.3 75.3 - - - +
331A PHE* 1.3 62.2 + - + +
332A ILE 3.6 1.4 - - - +
334A CYS* 3.9 9.2 - - - -
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Residues in contact with PHE 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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309A CYS* 4.6 0.9 - - + -
310A ASP 3.5 24.7 - - - -
311A GLY* 4.9 0.7 - - - -
312A ILE* 3.9 24.5 - - + -
317A LEU* 4.0 9.9 - - + -
323A VAL* 4.2 16.2 - - + -
327A ASN* 3.5 24.2 - - - -
328A ILE* 3.4 13.0 + - - +
329A ASP 3.0 1.8 - - - -
330A LYS* 1.3 82.9 - - - +
332A ILE* 1.4 64.3 + - - +
333A ASN 3.3 3.1 + - - -
334A CYS* 3.4 20.5 + - + +
337A ILE* 3.6 29.8 - - + -
341A LEU* 4.0 14.4 - - + -
366A VAL* 3.9 19.7 - - + +
367A PHE* 3.8 27.6 - + + -
370A VAL* 5.5 0.7 - - + +
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Residues in contact with ILE 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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307A LYS* 2.8 31.7 + - - -
329A ASP* 3.0 48.4 + - + +
330A LYS 3.6 1.0 - - - -
331A PHE* 1.4 74.9 - - - +
333A ASN* 1.4 74.1 + - - +
334A CYS 3.4 0.5 + - - -
366A VAL* 3.5 24.5 - - + -
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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