Contacts of the helix formed by residues 325 - 333 (chain A) in PDB entry 2RIO
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 SER 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A GLU* 2.5 36.0 + - - +
320A ASN* 3.1 20.3 + - - -
323A PRO 3.7 1.7 + - - -
324A PRO* 1.3 77.9 - - - +
326A ALA* 1.3 59.5 + - - +
327A LEU* 3.6 2.6 + - - -
328A LEU* 3.2 16.9 + - - +
329A MET* 2.9 24.9 + - - +
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Residues in contact with ALA 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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325A SER* 1.3 71.6 - - - +
327A LEU* 1.3 57.1 + - - +
329A MET* 3.2 12.9 + - - +
330A LYS* 2.9 38.9 + - + +
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Residues in contact with LEU 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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315A ARG* 3.6 28.0 - - - +
316A LEU* 3.1 35.2 - - + -
319A GLU* 3.7 18.8 - - + +
325A SER* 3.2 9.7 - - - +
326A ALA* 1.3 79.4 - - - +
328A LEU* 1.3 59.8 + - - +
330A LYS* 3.4 14.2 + - - +
331A PHE* 3.3 28.8 - - + -
421A ASN* 5.4 7.4 - - + +
422A LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 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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316A LEU* 3.8 27.1 - - + +
319A GLU* 3.6 29.4 - - + +
320A ASN 3.5 20.2 - - - +
321A ARG* 4.2 17.0 - - - +
324A PRO* 4.2 12.8 - - + -
325A SER* 3.2 15.4 + - - +
327A LEU* 1.3 72.9 - - - +
329A MET* 1.3 66.7 + - - +
331A PHE* 3.0 6.8 + - + +
332A ASP* 3.0 22.4 + - - +
368A MET* 3.8 37.0 - - + +
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Residues in contact with MET 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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324A PRO* 3.8 37.5 - - + +
325A SER 2.9 14.1 + - - +
326A ALA* 3.2 11.9 + - - +
328A LEU* 1.3 76.2 - - - +
330A LYS* 1.3 62.8 + - - +
332A ASP* 3.2 7.7 + - + +
333A ALA* 3.1 23.9 + - - +
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Residues in contact with LYS 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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326A ALA* 2.9 28.4 + - + +
327A LEU* 3.6 10.8 - - - +
328A LEU 3.2 0.4 - - - -
329A MET* 1.3 75.9 - - - +
331A PHE* 1.3 61.7 + - + +
333A ALA* 3.7 19.1 - - - +
334A GLY 3.9 0.3 + - - -
417A ILE* 3.8 18.2 - - + +
420A GLU* 6.1 1.8 - - - +
421A ASN* 3.2 41.2 + - + +
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Residues in contact with PHE 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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312A VAL* 4.0 21.8 - - + -
316A LEU* 3.9 34.5 - - + -
327A LEU* 3.3 26.0 - - + -
328A LEU* 3.0 12.3 + - + +
330A LYS* 1.3 79.1 - - + +
332A ASP* 1.3 60.6 - - - +
334A GLY* 3.1 14.6 + - - -
335A SER 3.7 0.9 + - - -
367A LEU* 3.5 32.3 - - + +
368A MET* 5.3 11.0 - - + -
371A LEU* 5.1 2.9 - - + -
414A VAL* 4.3 14.6 - - + -
417A ILE* 3.4 39.0 - - + -
418A VAL* 3.9 22.4 - - + -
421A ASN* 5.4 2.9 - - + -
422A LEU* 4.4 7.6 - - + -
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Residues in contact with ASP 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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328A LEU 3.0 14.1 + - - +
329A MET* 3.2 8.0 + - + +
331A PHE* 1.3 72.6 - - - +
333A ALA* 1.3 63.1 + - - +
334A GLY 3.0 5.5 + - - -
335A SER* 2.8 42.6 + - - -
336A ASP* 4.7 1.7 + - - +
365A SER* 4.8 1.0 - - - +
366A LYS* 3.4 37.2 - - + +
367A LEU* 4.4 1.2 + - - +
368A MET* 6.1 2.7 - - + +
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Residues in contact with ALA 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 MET 3.1 16.4 + - - +
330A LYS* 3.7 15.0 - - - +
332A ASP* 1.3 76.9 - - - +
334A GLY* 1.3 55.9 + - - +
335A SER 3.5 0.6 + - - -
336A ASP* 4.5 12.6 + - - +
337A PHE* 5.1 1.0 + - - +
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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