Contacts of the helix formed by residues 323 - 330 (chain A) in PDB entry 3OY3
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 LEU 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A GLY 3.8 0.6 + - - -
322A ASN* 1.3 70.2 - - - +
324A LEU* 1.3 61.2 + - - +
326A TYR* 3.4 3.4 - - + +
327A LEU* 2.8 42.1 + - + +
343A MET* 3.8 31.0 - - + -
347A ILE* 3.9 22.4 - - + -
366A ALA* 3.4 21.5 + - + +
369A CYS* 2.8 33.0 + - + +
371A VAL* 3.7 27.6 - - + -
377A VAL* 4.7 5.4 - - + -
428A LEU* 4.4 1.1 - - + -
432A ILE* 4.4 12.3 - - + -
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Residues in contact with LEU 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 ASN* 3.1 9.7 + - - +
323A LEU* 1.3 79.2 - - - +
325A ASP* 1.3 66.4 + - - +
327A LEU* 3.3 3.9 + - - +
328A ARG* 3.1 69.7 + - - +
366A ALA* 3.4 10.9 + - + -
367A ARG* 3.8 29.8 - - + +
388A MET* 6.3 0.9 - - + -
405A TRP* 6.2 2.2 - - + -
431A GLU* 3.7 21.3 - - - +
436A GLY* 3.6 22.2 - - - +
437A MET 5.1 0.4 - - - +
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Residues in contact with ASP 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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253A TYR* 5.4 1.2 - - - -
320A TYR 6.0 0.4 - - - +
322A ASN* 2.6 38.3 + - - +
324A LEU* 1.3 77.4 - - - +
326A TYR* 1.3 65.6 + - - +
328A ARG* 3.3 18.6 + - - +
329A GLU* 3.0 46.1 + - - +
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Residues in contact with TYR 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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320A TYR* 3.7 51.6 + + + +
322A ASN 3.0 15.8 + - - +
323A LEU* 3.4 19.5 - - + +
325A ASP* 1.3 77.1 - - - +
327A LEU* 1.3 68.8 + - + +
329A GLU* 3.2 3.6 + - - -
330A CYS* 3.0 32.6 + - + +
334A GLU* 3.6 11.1 + - - -
335A VAL* 3.6 27.7 - - + +
343A MET* 4.6 11.4 - - - -
371A VAL* 4.0 27.6 - - + -
375A HIS* 3.5 23.1 - + - -
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Residues in contact with LEU 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 LEU* 2.8 41.6 + - + +
324A LEU* 3.7 6.3 - - - +
326A TYR* 1.3 74.4 - - + +
328A ARG* 1.3 63.6 + - - +
329A GLU 3.3 0.5 + - - -
330A CYS* 3.3 20.7 - - - -
332A ARG* 5.2 1.9 + - - -
335A VAL* 4.6 6.5 - - + -
340A LEU* 3.8 28.5 - - + -
343A MET* 3.9 12.8 - - + -
366A ALA* 4.9 4.0 - - + -
431A GLU 3.9 9.0 - - - +
432A ILE* 3.8 28.9 - - + +
435A TYR* 3.6 35.4 - - + +
436A GLY* 4.0 4.9 - - - +
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Residues in contact with ARG 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 LEU* 3.1 50.2 + - - +
325A ASP* 3.8 16.8 + - - +
326A TYR 3.2 0.2 - - - -
327A LEU* 1.3 77.1 - - - +
329A GLU* 1.3 64.9 + - + +
332A ARG* 6.3 0.2 - - - +
435A TYR 3.9 14.8 - - - +
436A GLY* 2.8 24.2 + - - +
437A MET 4.3 0.2 - - - -
438A SER* 4.0 20.8 - - - +
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Residues in contact with GLU 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 ASP* 3.0 36.2 + - - +
326A TYR* 3.7 2.6 - - - +
327A LEU 3.2 0.2 - - - -
328A ARG* 1.3 86.1 - - + +
330A CYS* 1.3 63.7 + - - +
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Residues in contact with CYS 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 TYR* 3.0 23.1 + - + +
327A LEU* 3.3 20.5 + - - -
328A ARG 3.7 0.4 - - - -
329A GLU* 1.3 82.1 - - - +
331A ASN* 1.3 61.1 + - - +
332A ARG* 3.6 13.2 + - - +
335A VAL* 3.6 28.7 - - + -
435A TYR* 3.5 30.7 - - - -
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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