Contacts of the helix formed by residues 323 - 336 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLY 5.1 2.4 - - - +
89A THR* 4.1 15.6 + - - -
90A SER* 6.1 1.2 - - - -
285A ILE* 4.8 0.2 - - - -
287A LYS* 4.5 16.1 - - - +
320A TRP* 3.5 5.5 - - - -
322A GLY* 1.3 75.4 - - - -
324A CYS* 1.3 61.0 + - - +
325A ASP* 3.3 1.8 - - + +
326A GLN* 3.2 28.6 + - + +
327A GLY 3.0 23.4 + - - -
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Residues in contact with CYS 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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86A GLY* 3.6 22.7 + - - +
87A ILE* 3.8 6.3 - - - -
148A CYS* 4.1 20.9 - - + -
260A MET* 4.0 2.9 - - + -
261A GLY* 3.3 39.5 - - - -
285A ILE* 3.6 20.1 - - + +
286A ASN* 4.9 2.7 - - - -
322A GLY 5.3 0.2 - - - -
323A GLU* 1.3 71.0 + - - +
325A ASP* 1.3 61.7 + - - +
327A GLY* 3.4 0.7 + - - -
328A CYS* 2.9 34.8 + - - -
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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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90A SER* 2.7 31.3 + - - -
146A THR* 3.3 13.0 + - - -
147A ILE* 3.8 30.0 + - + +
148A CYS* 3.2 24.0 + - - +
323A GLU* 3.3 2.1 - - + +
324A CYS* 1.3 77.0 - - - +
326A GLN* 1.3 76.1 + - - +
328A CYS 3.5 0.2 + - - -
329A LEU* 3.0 33.2 + - - +
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Residues in contact with GLN 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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147A ILE* 5.2 2.0 - - - +
320A TRP* 3.7 16.1 - - + -
323A GLU* 3.2 32.0 + - + +
325A ASP* 1.3 86.5 - - - +
327A GLY* 1.3 60.0 - - - +
329A LEU* 3.4 19.2 + - + +
330A ALA* 3.0 29.1 + - - +
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Residues in contact with GLY 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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64A LEU* 4.7 3.3 - - - +
285A ILE* 3.8 16.1 - - - +
320A TRP* 3.4 31.7 - - - -
323A GLU 3.0 10.9 + - - -
324A CYS 3.8 2.7 - - - -
326A GLN* 1.3 77.6 - - - +
328A CYS* 1.3 55.6 + - - +
330A ALA* 3.4 2.9 + - - +
331A LEU* 3.0 28.2 + - - +
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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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147A ILE* 4.4 5.4 - - + -
148A CYS* 3.9 23.3 - - - -
151A PHE* 3.9 32.3 - - + -
260A MET* 3.6 30.7 - - - -
285A ILE* 4.4 5.6 - - - -
324A CYS 2.9 21.4 + - - +
325A ASP 3.9 3.4 - - - +
327A GLY* 1.3 73.5 - - - +
329A LEU* 1.3 60.9 + - - +
331A LEU* 3.5 3.5 + - - -
332A ALA* 2.9 32.3 + - - +
341A LEU* 4.5 2.0 - - - -
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Residues in contact with LEU 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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147A ILE* 3.9 35.7 - - + -
325A ASP 3.0 21.8 + - - +
326A GLN* 3.7 21.1 - - + +
327A GLY 3.3 0.2 - - - -
328A CYS* 1.3 75.5 - - - +
330A ALA* 1.3 57.8 + - - +
332A ALA* 3.8 4.5 - - + +
333A GLU* 3.0 30.4 + - - +
338A LYS* 5.1 9.2 - - + +
341A LEU* 4.2 11.0 - - + -
342A GLU* 3.8 32.5 - - + +
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Residues in contact with ALA 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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64A LEU* 3.9 18.2 - - + -
320A TRP* 4.3 14.4 - - + +
326A GLN 3.0 17.8 + - - +
327A GLY 3.6 5.2 - - - +
328A CYS 3.3 0.2 - - - -
329A LEU* 1.3 76.6 - - - +
331A LEU* 1.3 61.9 + - - +
333A GLU* 3.4 7.8 + - - +
334A LEU* 3.2 26.0 + - - +
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Residues in contact with LEU 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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64A LEU* 4.0 22.6 - - + +
67A VAL* 4.8 2.2 - - + -
68A ALA* 4.0 27.6 - - + +
71A MET* 4.1 18.2 - - - -
151A PHE* 3.7 24.0 - - + -
258A LEU* 4.4 5.6 - - + -
283A LEU* 3.8 23.6 - - + -
285A ILE* 4.6 6.5 - - + -
327A GLY 3.0 16.9 + - - +
328A CYS* 3.9 4.0 - - - +
330A ALA* 1.3 74.1 - - - +
332A ALA* 1.3 64.2 + - - +
334A LEU* 3.2 4.5 + - - +
335A LEU* 3.0 41.2 + - + +
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Residues in contact with ALA 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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151A PHE* 4.1 12.2 - - + -
154A LEU* 5.6 0.2 - - + -
328A CYS 2.9 19.4 + - - +
329A LEU* 3.8 4.0 - - - +
331A LEU* 1.3 76.0 - - - +
333A GLU* 1.3 55.3 + - - +
335A LEU* 3.2 4.3 + - - -
336A GLY 3.0 8.1 + - - -
337A TRP* 2.7 51.8 + - + -
338A LYS* 3.8 4.0 - - - +
341A LEU* 3.7 23.1 - - + -
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Residues in contact with GLU 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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329A LEU 3.0 18.7 + - - +
330A ALA* 3.8 7.1 - - - +
331A LEU 3.2 0.2 - - - -
332A ALA* 1.3 76.3 - - - +
334A LEU* 1.3 61.9 + - + +
336A GLY* 3.1 13.7 + - - -
338A LYS* 3.8 41.0 - - + +
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Residues in contact with LEU 334 (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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64A LEU* 3.8 53.8 - - + +
65A GLU* 3.8 30.3 - - + +
68A ALA* 3.7 14.7 - - + +
72A GLN* 3.7 11.8 + - - +
330A ALA* 3.2 8.9 + - + +
331A LEU* 3.2 7.9 + - - +
333A GLU* 1.3 79.3 - - + +
335A LEU* 1.3 60.0 + - - +
336A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 3.5 29.8 - - + +
71A MET* 3.8 30.3 - - + -
72A GLN* 3.5 26.8 + - + +
151A PHE* 4.1 2.2 - - + -
331A LEU* 3.0 35.7 + - + +
332A ALA 3.2 4.7 + - - +
334A LEU* 1.3 77.7 - - - +
336A GLY* 1.3 58.6 + - - +
337A TRP* 3.4 60.3 + - + +
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Residues in contact with GLY 336 (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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332A ALA 3.0 2.2 + - - -
333A GLU* 3.1 13.7 + - - -
334A LEU 3.3 1.2 + - - -
335A LEU* 1.3 79.3 - - - +
337A TRP* 1.3 62.3 + - - +
338A LYS* 3.6 2.7 - - - -
339A LYS* 5.3 1.4 + - - +
340A GLU* 5.5 0.9 + - - +
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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