Contacts of the helix formed by residues 322 - 327 (chain B) in PDB entry 2WSC
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 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B LEU* 4.2 16.1 - - + +
319B HIS* 3.5 30.4 + - + +
320B LYS 2.4 21.9 + - - +
321B GLY* 1.3 67.2 - - - -
323B TYR* 1.3 54.7 + - - +
325B THR* 3.3 5.3 - - + +
326B ILE* 3.0 33.6 + - - +
332B PHE* 5.1 4.4 - - + -
403B ASN* 4.0 4.9 - - - +
406B ASN* 3.9 20.2 - - - +
407B VAL* 5.2 3.6 - - + -
408B LEU* 3.8 32.3 - - + -
1753B CLA 3.7 42.2 - - + -
1754B CLA 5.8 0.9 - - + -
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Residues in contact with TYR 323 (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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169B LYS 3.7 2.6 + - - -
170B ASN* 2.3 31.9 + - - -
172B GLU* 2.9 26.3 + - - -
301B ILE* 3.5 19.7 - - + +
302B LYS* 4.4 19.7 - - + +
305B LEU* 4.7 7.7 - - + +
321B GLY* 4.0 3.8 - - - +
322B LEU* 1.3 73.0 - - - +
324B ASP* 1.3 56.3 + - - +
325B THR 2.8 4.9 + - - -
326B ILE* 3.1 6.3 - - - +
327B ASN* 2.8 42.3 + - - +
1754B CLA 2.9 47.8 - - + -
47G GLY 4.3 0.9 - - - -
48G ASP* 1.2 72.2 - - - -
49G THR 3.1 2.4 + - - -
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Residues in contact with ASP 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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302B LYS* 5.3 2.5 + - - -
321B GLY* 2.6 36.4 - - - +
323B TYR* 1.3 71.0 - - - +
325B THR* 1.3 53.7 + - - +
327B ASN* 4.1 3.1 - - - -
328B ASN* 2.7 49.5 - - - +
402B GLN* 4.5 22.0 - - - +
47G GLY* 1.2 65.6 + - - +
48G ASP 3.9 0.9 - - - +
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Residues in contact with THR 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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321B GLY 2.9 19.5 - - - +
322B LEU* 3.3 22.4 - - + +
323B TYR 2.8 5.5 + - - -
324B ASP* 1.3 76.7 - - - +
326B ILE* 1.3 51.7 + - - +
327B ASN 3.2 1.1 - - - -
328B ASN* 4.2 2.0 - - - +
329B SER* 2.7 32.7 + - - -
332B PHE* 3.8 7.1 - - - -
393B PHE* 4.1 13.3 - - - -
397B ASP* 4.7 0.7 - - - +
398B TYR* 5.5 1.6 - - - -
402B GLN* 5.4 9.4 - - + +
403B ASN* 3.4 36.6 + - - +
408B LEU* 4.2 1.6 - - + +
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Residues in contact with ILE 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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322B LEU 3.0 27.1 + - - +
323B TYR* 3.1 14.1 - - - +
325B THR* 1.3 74.9 - - - +
327B ASN* 1.3 57.2 + - - +
329B SER* 4.0 6.4 + - - -
332B PHE* 3.9 29.8 - - + -
333B GLN* 3.0 32.2 + - + +
336B LEU* 4.6 12.8 - - + -
1753B CLA 5.9 2.2 - - + -
1754B CLA 3.4 72.5 - - + +
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Residues in contact with ASN 327 (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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43B TYR* 3.3 20.4 + - - -
169B LYS* 2.8 50.1 + - - +
170B ASN 4.1 4.0 + - - -
171B ALA* 5.0 1.6 - - - +
323B TYR* 2.8 34.6 + - + +
324B ASP* 4.1 3.1 - - - -
326B ILE* 1.3 78.1 - - - +
328B ASN* 1.3 63.1 + - - +
329B SER 3.0 8.8 + - - -
330B ILE 4.1 0.7 + - - -
333B GLN* 3.4 17.8 + - - +
1754B CLA 4.1 16.8 - - + +
48G ASP* 4.7 7.1 - - - +
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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