Contacts of the helix formed by residues 324 - 328 (chain O) in PDB entry 6CNC
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 PRO 324 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285O ASP* 5.7 0.5 - - - +
286O ARG* 4.5 5.9 + - - +
322O LYS 3.1 6.0 - - - +
323O SER* 1.3 86.6 - - - +
325O LYS* 1.3 60.2 + - - +
326O ILE 3.3 0.2 + - - -
327O ARG* 2.8 63.7 + - - +
328O ASP* 3.5 27.1 - - + +
353O GLU* 3.2 40.6 - - + +
481O SER* 5.0 4.7 - - - +
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Residues in contact with LYS 325 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285O ASP 6.0 0.4 - - - +
289O LYS* 3.2 49.6 - - + +
292O ARG* 3.1 23.8 - - + +
293O SER* 4.0 2.6 + - - -
296O LEU* 3.6 10.0 - - - +
323O SER* 3.3 12.4 + - - +
324O PRO* 1.3 81.4 - - - +
326O ILE* 1.3 78.9 + - + +
328O ASP* 2.8 43.0 + - - +
329O PRO* 3.3 0.2 - - - +
484O MET* 3.5 33.8 - - + +
488O LYS* 3.5 25.4 - - - +
654O ALA* 5.9 1.3 - - - -
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Residues in contact with ILE 326 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O GLU* 5.7 0.2 - - - +
288O MET* 3.5 54.7 - - + +
291O ARG* 4.2 4.5 - - - +
292O ARG* 3.2 36.8 - - - +
324O PRO 3.3 0.2 + - - -
325O LYS* 1.3 87.6 - - + +
327O ARG* 1.3 56.4 + - - +
329O PRO* 3.0 20.5 - - - +
330O LEU 5.0 0.2 + - - -
653O MET* 3.5 39.1 - - + +
654O ALA* 3.6 15.0 - - + +
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Residues in contact with ARG 327 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253O ILE* 3.3 32.9 - - + +
254O ASN* 4.4 2.6 + - - -
257O ASN* 4.7 14.3 - - - +
285O ASP* 4.7 28.0 - - + +
286O ARG* 4.2 13.7 - - - +
322O LYS* 4.5 14.3 + - - +
324O PRO* 2.8 49.4 + - - +
326O ILE* 1.3 77.4 - - - +
328O ASP* 1.3 64.6 + - - +
329O PRO* 3.2 1.3 - - - -
330O LEU* 3.2 36.7 + - + +
353O GLU* 4.7 3.4 + - - +
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Residues in contact with ASP 328 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324O PRO* 3.5 25.3 + - + +
325O LYS* 2.8 31.7 + - - +
327O ARG* 1.3 80.9 - - - +
329O PRO* 1.4 85.6 - - - +
330O LEU* 3.7 5.7 - - - +
345O PHE* 4.7 9.2 - - - -
349O ALA* 5.6 12.2 - - + +
481O SER 5.8 0.2 - - - +
484O MET* 5.2 8.8 - - - +
485O PRO* 5.7 4.0 - - - +
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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