Contacts of the strand formed by residues 327 - 331 (chain d) in PDB entry 5M32
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 VAL 327 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220d LYS* 4.7 3.4 - - + -
221d GLY* 3.3 30.2 - - - +
222d VAL 2.9 14.6 - - - +
271d PHE* 4.4 13.5 - - + -
282d VAL* 3.3 24.7 - - + -
284d ILE* 4.9 10.1 - - + -
316d LEU* 4.5 20.6 - - + -
324d ASP* 4.4 16.2 - - - +
326d LYS* 1.3 81.5 + - - +
328d ILE* 1.3 58.9 + - - +
329d MET* 3.8 7.3 + - + +
346d ARG 4.5 16.2 - - - +
347d ILE* 5.1 2.1 - - + +
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Residues in contact with ILE 328 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197d ILE* 3.8 18.4 - - + -
201d VAL* 3.7 31.2 - - + -
221d GLY* 5.1 0.2 - - - -
222d VAL* 3.3 11.2 - - + +
224d LEU* 3.8 26.7 - - + -
237d LYS* 4.1 35.9 - - + -
240d ALA* 4.9 2.7 - - + -
281d ILE* 4.7 2.7 - - + -
282d VAL 3.7 4.9 + - - -
283d PHE* 3.3 24.6 - - + -
284d ILE 3.5 10.6 + - - -
326d LYS* 3.7 20.8 - - + +
327d VAL* 1.3 75.3 - - - +
329d MET* 1.3 62.8 + - - +
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Residues in contact with MET 329 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222d VAL 3.0 6.7 + - - +
223d ILE* 3.2 18.3 - - + +
224d LEU* 2.7 33.1 + - - +
284d ILE* 3.6 39.3 - - + +
287d ILE* 3.7 37.2 - - + -
312d LEU* 5.0 10.3 - - + -
316d LEU* 5.8 4.7 - - - -
327d VAL* 4.3 8.3 - - - +
328d ILE* 1.3 79.8 - - - +
330d ALA* 1.3 60.4 + - - +
337d LEU* 4.6 12.8 - - + -
341d LEU* 4.9 9.0 - - + -
347d ILE* 4.0 22.0 - - - -
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Residues in contact with ALA 330 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224d LEU 3.8 0.2 - - - -
233d THR* 3.3 35.0 - - + -
234d LEU* 3.7 13.7 - - + -
237d LYS* 3.6 25.8 - - - +
283d PHE* 3.8 4.0 - - + -
284d ILE 4.3 0.3 - - - +
286d GLU* 3.2 28.9 + - - +
287d ILE* 4.0 1.7 + - - +
329d MET* 1.3 71.8 - - - +
331d THR* 1.3 68.7 + - - +
501d ADP 5.4 0.2 - - - +
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Residues in contact with THR 331 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223d ILE* 3.4 21.3 - - + +
224d LEU 3.9 4.5 + - - +
225d TYR* 3.2 12.9 - - + -
226d GLY 3.1 25.3 + - - +
233d THR* 4.7 4.0 + - - +
286d GLU* 3.6 8.0 + - - +
287d ILE* 4.0 10.8 - - + +
288d ASP* 3.7 13.2 - - - +
329d MET* 4.3 1.0 - - - +
330d ALA* 1.3 83.6 + - - +
332d ASN* 1.3 66.0 + - - +
333d ARG 3.4 31.6 - - - +
334d ILE* 3.8 7.9 - - - +
337d LEU* 4.3 7.6 - - + -
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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