Contacts of the helix formed by residues 396 - 407 (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 PRO 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LYS 5.6 0.7 - - - -
303A SER* 3.7 29.6 - - - +
306A LEU* 3.8 19.8 - - + +
378A TYR* 5.9 0.2 - - + -
394A PRO 3.5 2.2 - - - -
395A VAL* 1.4 88.1 - - + +
397A ASP* 1.3 72.0 + - - +
398A GLY 3.4 2.2 - - - -
399A PHE* 3.3 4.0 + - - +
400A TYR* 2.9 30.5 + - - +
426B GLN 3.9 8.1 - - - +
427B ILE* 5.3 1.6 - - + -
430B GLU* 3.5 29.6 - - + +
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Residues in contact with ASP 397 (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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302A LYS* 3.8 34.7 + - + +
303A SER* 4.2 4.5 + - - -
394A PRO* 3.5 4.3 + - + +
396A PRO* 1.3 89.3 - - - +
398A GLY* 1.3 58.3 + - - +
400A TYR* 3.4 6.7 + - - +
401A ASP* 3.0 37.6 + - - +
430B GLU* 5.3 1.5 - - - +
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Residues in contact with GLY 398 (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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391A LEU 5.5 0.3 - - - +
392A MET 4.2 4.5 - - - -
393A GLY 3.8 16.3 - - - +
394A PRO* 2.6 24.7 + - - +
397A ASP* 1.3 73.4 - - - +
399A PHE* 1.3 63.4 + - - +
401A ASP* 3.4 7.6 + - - +
402A TYR* 2.9 24.6 + - - +
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Residues in contact with PHE 399 (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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306A LEU* 3.8 30.5 - - + -
374A LEU* 3.5 16.8 - - + -
377A LYS* 3.9 3.8 - - + -
378A TYR* 3.4 43.1 - + + -
381A PHE* 3.7 16.6 - + - -
392A MET* 3.2 47.4 + - + +
394A PRO 3.0 9.1 + - - +
395A VAL* 4.1 15.3 - - + -
396A PRO* 3.6 6.7 - - + +
398A GLY* 1.3 73.8 - - - +
400A TYR* 1.3 67.4 + - - +
402A TYR* 3.0 18.6 - - - +
403A PHE* 3.4 29.7 + + - -
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Residues in contact with TYR 400 (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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265A ASP* 5.9 0.9 - - - -
267A SER* 5.0 2.8 + - - -
271A GLU* 4.3 2.3 + - - -
302A LYS* 3.8 29.2 - - + +
305A LYS* 3.2 42.1 - - + +
306A LEU* 3.7 29.6 - - + -
309A LEU* 3.9 19.7 - - + -
374A LEU* 6.0 2.0 - - + -
396A PRO 2.9 16.2 + - - +
397A ASP 3.5 4.7 - - - +
399A PHE* 1.3 81.5 - - - +
401A ASP* 1.3 71.8 + - - +
403A PHE* 3.1 8.3 + - - +
404A THR* 3.1 49.7 + - + +
411A LEU* 3.1 28.4 - - - +
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Residues in contact with ASP 401 (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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265A ASP* 4.4 8.9 - - - +
302A LYS* 2.8 42.0 + - - +
397A ASP* 3.0 21.1 + - - +
398A GLY* 3.8 6.7 - - - +
400A TYR* 1.3 79.7 - - - +
402A TYR* 1.3 55.3 + - - +
404A THR* 4.1 7.1 - - - +
405A LYS* 2.7 39.0 + - + +
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Residues in contact with TYR 402 (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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348A PHE* 4.0 18.5 - + - -
349A ASP* 5.4 6.8 + - - -
352A PHE* 4.1 22.2 - + - -
391A LEU* 3.3 32.7 - - + +
392A MET* 3.8 23.8 - - + +
398A GLY 2.9 13.4 + - - +
399A PHE* 3.0 20.0 - - - +
401A ASP* 1.3 76.7 - - - +
403A PHE* 1.3 76.7 - + + +
405A LYS* 4.4 3.6 - - - +
406A ARG* 3.2 72.6 + - - +
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Residues in contact with PHE 403 (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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348A PHE* 3.9 30.7 - + - -
352A PHE* 3.9 22.7 - + - -
370A LEU* 4.5 11.2 - - + -
373A ALA* 4.7 0.7 - - + -
374A LEU* 3.7 56.5 - - + -
377A LYS* 4.2 4.3 - - + -
392A MET* 3.7 17.0 - - + -
399A PHE* 3.4 39.5 - + - -
400A TYR* 3.1 7.7 + - + +
402A TYR* 1.3 83.9 - + - +
404A THR* 1.3 55.1 + - - +
406A ARG* 3.3 4.7 + - - +
407A PHE* 3.0 34.0 + + - +
410A LEU* 4.3 8.7 - - + -
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Residues in contact with THR 404 (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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265A ASP* 4.1 10.7 - - - +
267A SER* 2.9 35.1 + - - +
309A LEU* 5.6 0.5 - - - +
400A TYR* 3.1 46.7 + - + -
401A ASP* 3.8 8.1 - - - +
403A PHE* 1.3 71.3 - - - +
405A LYS* 1.3 62.8 + - - +
406A ARG 3.2 1.6 - - - -
407A PHE 3.8 10.1 + - - -
408A PRO* 3.0 28.9 - - - +
410A LEU* 5.4 5.9 - - - +
411A LEU* 5.2 3.1 + - - +
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Residues in contact with LYS 405 (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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265A ASP* 5.9 0.7 - - - -
266A ARG* 6.1 1.9 - - - +
347A LYS* 4.9 2.8 + - - -
401A ASP* 2.7 23.2 + - + +
402A TYR* 4.4 4.0 - - - +
404A THR* 1.3 75.6 - - - +
406A ARG* 1.3 75.6 + - + +
408A PRO* 4.0 6.8 - - - +
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Residues in contact with ARG 406 (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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347A LYS* 2.6 76.1 + - + +
348A PHE* 3.6 28.6 - - - +
349A ASP* 4.9 1.0 + - - +
402A TYR* 3.2 59.7 + - - +
403A PHE 3.3 3.9 + - - +
404A THR 3.2 0.2 - - - -
405A LYS* 1.3 91.5 - - + +
407A PHE* 1.3 78.1 + - + +
408A PRO* 3.6 4.6 - - - +
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Residues in contact with PHE 407 (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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338A VAL* 3.7 25.8 - - + +
339A ILE* 4.0 20.9 - - + -
344A TRP* 3.3 45.3 - - + -
347A LYS* 3.7 15.5 - - + -
348A PHE* 3.3 30.1 - + - -
370A LEU* 3.9 19.5 - - + -
403A PHE* 3.0 19.0 + - - +
404A THR* 3.3 11.1 + - - +
406A ARG* 1.3 85.9 - - + +
408A PRO* 1.3 58.6 - - - +
409A ASN 3.2 5.4 - - - -
410A LEU* 2.9 38.0 + - + +
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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