Contacts of the helix formed by residues 323 - 335 (chain B) in PDB entry 4Y6O
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 GLU 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLY 5.1 2.4 - - - +
89B THR* 4.1 15.9 + - - -
90B SER* 5.8 2.8 + - - -
285B ILE* 4.7 0.2 - - - -
287B LYS* 4.7 11.8 - - - +
320B TRP* 3.5 5.0 - - - -
322B GLY* 1.3 76.6 - - - +
324B CYS* 1.3 67.0 + - - +
325B ASP* 3.3 2.5 - - + +
326B GLN* 3.2 27.2 + - + +
327B GLY 3.1 18.4 + - - -
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Residues in contact with CYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLY* 3.7 20.3 + - - +
87B ILE* 3.9 7.9 - - - -
148B CYS* 4.1 21.8 - - + -
260B MET* 4.0 3.4 - - - -
261B GLY* 3.3 38.6 - - - -
285B ILE* 3.7 20.9 - - + +
286B ASN* 5.0 2.9 - - - -
287B LYS 6.0 0.2 - - - -
322B GLY 3.7 0.8 + - - -
323B GLU* 1.3 74.8 + - - +
325B ASP* 1.3 63.0 + - - +
327B GLY* 3.3 1.6 + - - -
328B CYS* 3.0 28.6 + - - +
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Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ILE 5.2 0.3 - - - +
90B SER* 2.7 30.6 + - - -
146B THR* 3.4 13.0 + - - -
147B ILE* 3.8 28.9 + - + +
148B CYS* 3.2 24.2 + - - +
323B GLU* 3.3 1.5 - - + +
324B CYS* 1.3 77.1 - - - +
326B GLN* 1.3 76.7 + - - +
328B CYS* 3.4 2.3 + - - +
329B LEU* 3.0 32.5 + - - +
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 5.3 2.4 - - - +
320B TRP* 3.7 15.9 - - + -
323B GLU* 3.2 31.4 + - + +
325B ASP* 1.3 84.4 - - - +
327B GLY* 1.3 60.5 + - - +
329B LEU* 3.4 24.1 + - + +
330B ALA* 3.0 29.3 + - - +
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.8 2.6 - - - +
285B ILE* 3.9 15.6 - - - +
320B TRP* 3.3 33.4 - - - -
323B GLU 3.1 10.9 + - - -
324B CYS 3.3 3.1 + - - -
326B GLN* 1.3 74.0 - - - +
328B CYS* 1.3 57.9 + - - +
330B ALA* 3.4 2.8 + - - +
331B LEU* 3.0 29.5 + - - +
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Residues in contact with CYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.5 4.7 - - + -
148B CYS* 3.9 23.1 - - - -
151B PHE* 3.9 30.3 - - + -
260B MET* 3.6 31.6 - - - -
285B ILE* 4.3 5.4 - - - -
324B CYS 3.0 21.2 + - - +
325B ASP 3.8 3.1 - - - +
327B GLY* 1.3 74.0 - - - +
329B LEU* 1.3 59.5 + - - +
331B LEU* 3.5 5.1 + - - +
332B ALA* 2.8 32.3 + - - +
341B LEU* 4.6 2.2 - - - -
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 3.9 34.5 - - + -
325B ASP 3.0 22.2 + - - +
326B GLN* 3.7 26.9 - - + +
327B GLY 3.4 0.2 - - - -
328B CYS* 1.3 74.8 - - - +
330B ALA* 1.3 57.9 + - - +
332B ALA* 3.4 4.3 + - - +
333B GLU* 2.9 31.8 + - - +
338B LYS* 3.9 21.8 - - + +
341B LEU* 4.3 9.2 - - + -
342B GLU* 3.9 27.1 - - + +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.9 18.8 - - + -
320B TRP* 4.3 12.8 - - + +
326B GLN 3.0 17.7 + - - +
327B GLY 3.6 6.1 - - - +
329B LEU* 1.3 76.7 - - - +
331B LEU* 1.3 61.3 + - - +
333B GLU* 3.5 7.6 + - - +
334B LEU* 3.3 26.0 + - - +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.1 22.4 - - + +
67B VAL* 4.9 0.4 - - + -
68B ALA* 4.1 24.7 - - + +
71B MET* 4.0 26.2 - - - -
151B PHE* 3.7 29.6 - - + -
258B LEU* 4.7 4.9 - - + -
283B LEU* 3.9 24.7 - - + -
285B ILE* 4.7 7.6 - - + -
327B GLY 3.0 17.3 + - - +
328B CYS* 3.9 4.0 - - - +
330B ALA* 1.3 73.1 - - - +
332B ALA* 1.3 64.9 + - - +
334B LEU* 3.2 5.2 + - - +
335B LEU* 3.1 29.9 + - + +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PHE* 4.0 14.7 - - + -
328B CYS 2.8 22.8 + - - +
329B LEU* 3.7 4.3 - - - +
331B LEU* 1.3 72.1 - - - +
333B GLU* 1.3 60.3 + - - +
335B LEU* 3.1 5.2 + - - -
336B GLY 3.0 4.7 + - - -
337B TRP* 2.8 49.0 + - + -
338B LYS* 3.9 4.0 - - - +
341B LEU* 3.7 23.1 - - + -
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU 2.9 17.6 + - - +
330B ALA* 3.7 8.0 - - - +
331B LEU 3.2 0.2 - - - -
332B ALA* 1.3 76.1 - - - +
334B LEU* 1.3 63.2 + - + +
336B GLY* 3.1 14.0 + - - -
338B LYS* 3.3 47.6 + - + +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.8 47.8 - - + +
65B GLU* 4.0 34.3 - - + +
68B ALA* 3.7 14.3 - - + +
72B GLN* 3.7 13.9 + - - +
330B ALA 3.3 8.2 + - - +
331B LEU* 3.2 8.4 + - - +
333B GLU* 1.3 80.7 - - + +
335B LEU* 1.3 59.7 + - - +
336B GLY 3.3 1.4 + - - -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 3.5 30.7 - - - +
71B MET* 3.8 31.9 - - + -
72B GLN* 3.7 28.1 + - + +
151B PHE* 4.2 2.5 - - + -
331B LEU* 3.1 26.9 + - + +
332B ALA 3.1 7.9 + - - +
334B LEU* 1.3 75.1 - - - +
336B GLY* 1.3 61.4 + - - +
337B TRP* 3.4 55.2 + - + -
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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