Contacts of the helix formed by residues 366 - 380 (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 LYS 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ARG* 3.0 26.8 - - - +
324A PRO* 6.5 0.7 - - - -
332A ASP* 3.4 27.6 - - + +
335A SER* 3.7 2.9 - - - -
339A ILE* 3.9 2.2 - - - -
344A TRP* 3.2 22.7 + - - -
363A HIS* 3.6 34.3 + - + +
364A SER 3.3 3.0 - - - +
365A SER* 1.4 86.5 + - - +
367A LEU* 1.3 64.3 + - - +
368A MET* 4.3 6.3 - - + +
369A ASP* 3.4 19.7 - - - +
370A LEU* 3.3 5.5 + - - +
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PHE* 3.5 34.8 - - + +
332A ASP* 4.4 0.8 + - - +
334A GLY 3.9 17.0 - - - +
335A SER* 2.9 20.9 + - - +
338A VAL* 4.1 25.6 - - + -
339A ILE* 4.1 6.1 - - - -
366A LYS* 1.3 72.7 - - - +
368A MET* 1.3 58.0 + - - +
369A ASP 3.2 0.3 + - - -
370A LEU* 3.2 7.1 + - + +
371A LEU* 2.9 30.1 + - + +
410A LEU* 3.8 30.3 - - + -
414A VAL* 4.3 12.8 - - + +
417A ILE* 4.1 15.0 - - + -
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Residues in contact with MET 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A SER* 5.3 0.7 + - - -
316A LEU* 3.2 51.4 - - + +
317A GLU* 4.1 5.8 - - - +
319A GLU 5.2 1.8 - - - +
321A ARG* 3.2 39.3 - - - +
328A LEU* 3.8 27.4 - - + +
331A PHE* 5.3 9.1 - - + +
332A ASP* 6.1 2.2 - - + +
361A LYS* 3.6 22.0 - - - +
366A LYS* 3.4 4.2 - - + +
367A LEU* 1.3 78.5 - - - +
369A ASP* 1.3 53.8 + - - +
371A LEU* 3.3 12.2 + - - +
372A ARG* 2.8 30.5 + - - +
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG* 2.9 26.1 + - - -
344A TRP* 3.8 10.5 - - + +
361A LYS* 3.0 18.8 - - - +
362A TYR* 3.5 8.8 - - + -
363A HIS* 3.0 51.6 + - - +
366A LYS* 3.4 16.0 + - + +
367A LEU 3.2 0.2 - - - -
368A MET* 1.3 72.3 - - - +
370A LEU* 1.3 66.1 + - - +
371A LEU 3.1 1.1 - - - -
372A ARG* 4.1 4.3 - - - +
373A ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A VAL* 4.4 10.3 - - + -
339A ILE* 4.2 16.6 - - + -
344A TRP* 3.6 26.6 - - + +
348A PHE* 4.0 17.9 - - + -
366A LYS 3.3 11.4 + - - +
367A LEU* 3.2 10.4 + - + +
369A ASP* 1.3 78.4 - - - +
371A LEU* 1.3 63.0 + - - +
373A ALA* 3.4 2.2 + - + +
374A LEU* 3.1 20.1 + - + +
403A PHE* 4.5 11.4 - - + -
407A PHE* 3.9 47.3 - - + -
410A LEU* 4.6 15.9 - - + -
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 4.1 43.0 - - + +
312A VAL* 3.7 29.8 - - + -
313A SER* 4.0 13.6 - - - +
316A LEU* 4.4 11.7 - - + -
331A PHE* 5.1 2.7 - - + -
367A LEU* 2.9 16.1 + - + +
368A MET* 3.4 11.2 - - - +
369A ASP 3.1 0.2 - - - -
370A LEU* 1.3 78.7 - - - +
372A ARG* 1.3 55.6 + - - +
374A LEU* 3.3 13.8 + - + +
375A ARG* 3.1 27.5 + - - +
410A LEU* 4.1 18.6 - - + -
414A VAL* 4.2 11.9 - - + -
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Residues in contact with ARG 372 (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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313A SER* 2.8 32.2 + - - +
314A ASP* 3.0 24.0 + - - +
317A GLU* 3.1 40.0 + - - +
360A ARG* 3.2 38.7 - - - +
361A LYS* 3.6 34.1 - - + +
362A TYR* 3.9 1.1 - - - +
368A MET* 2.8 17.0 + - + +
369A ASP 3.3 4.4 + - - +
371A LEU* 1.3 75.4 - - - +
373A ALA* 1.3 59.1 + - - +
375A ARG* 3.4 23.6 + - - +
376A ASN* 2.8 38.1 + - - +
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Residues in contact with ALA 373 (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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344A TRP* 4.0 20.2 - - + -
352A PHE* 4.9 11.7 - - + -
362A TYR* 3.5 19.1 - - + -
369A ASP 2.9 17.2 + - - +
370A LEU* 3.6 6.7 - - + +
372A ARG* 1.3 71.5 - - - +
374A LEU* 1.4 60.7 + - - +
376A ASN* 4.1 1.5 - - - +
377A LYS* 2.9 37.6 + - - +
403A PHE* 4.7 1.6 - - + -
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Residues in contact with LEU 374 (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 19.3 - - + -
309A LEU* 4.0 35.0 - - + -
310A LEU* 3.6 25.4 - - + +
370A LEU* 3.1 14.0 + - + +
371A LEU* 3.3 14.1 + - + +
373A ALA* 1.4 74.9 - - - +
375A ARG* 1.3 57.6 + - + +
377A LYS 3.5 0.3 + - - -
378A TYR* 3.0 22.9 + - - +
399A PHE* 3.5 13.2 - - + -
400A TYR* 6.0 2.0 - - + -
403A PHE* 3.7 47.3 - - + -
410A LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.6 25.7 - - + +
313A SER* 3.4 30.1 - - - +
314A ASP* 2.9 26.3 + - - +
360A ARG* 4.5 1.4 - - - +
371A LEU 3.1 9.6 + - - +
372A ARG* 3.4 28.2 - - - +
374A LEU* 1.3 75.4 - - + +
376A ASN* 1.3 81.5 + - - +
378A TYR* 3.4 3.8 + - - +
379A HIS* 2.9 63.5 + - - +
380A HIS* 5.4 0.4 - - - -
375B ARG* 4.7 1.8 - - - +
379B HIS* 4.0 21.0 + - - -
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Residues in contact with ASN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ARG* 2.9 28.7 + - - +
362A TYR* 2.8 26.3 + - - +
372A ARG* 2.8 20.1 + - - +
373A ALA* 4.1 2.9 - - - +
375A ARG* 1.3 105.6 - - - +
377A LYS* 1.3 58.3 + - - +
379A HIS* 4.3 1.3 - - - -
380A HIS* 3.0 51.1 + - + +
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Residues in contact with LYS 377 (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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351A THR 5.0 2.4 + - - -
352A PHE* 3.5 69.2 + - + +
353A MET 5.6 0.8 + - - -
373A ALA* 2.9 25.0 + - + +
374A LEU 3.6 4.9 - - - +
376A ASN* 1.3 69.1 - - - +
378A TYR* 1.3 64.7 + - - +
380A HIS* 3.7 1.3 - - - -
381A PHE* 3.0 27.3 + - - +
384A LEU* 4.0 28.9 - - + +
388A ILE* 5.4 2.8 - - - +
392A MET* 4.0 12.9 - - + -
399A PHE* 3.9 12.8 - - + -
403A PHE* 4.2 3.1 - - + -
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Residues in contact with TYR 378 (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* 4.1 10.3 - - + -
307A GLU* 4.4 0.7 + - - -
310A LEU* 3.6 37.2 - - + -
374A LEU 3.0 10.1 + - - +
375A ARG 3.5 9.0 - - - +
376A ASN 3.3 0.2 - - - -
377A LYS* 1.3 75.0 - - - +
379A HIS* 1.3 75.4 + - + +
381A PHE* 3.2 18.2 + - - +
395A VAL* 3.7 29.4 - - + -
396A PRO* 5.9 0.2 - - + -
399A PHE* 3.4 28.8 - + + -
311B LYS* 2.7 33.2 + - + +
427B ILE* 3.6 28.9 - - + +
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Residues in contact with HIS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ARG* 2.9 53.6 + - - +
376A ASN* 3.2 6.0 + - - +
378A TYR* 1.3 89.8 - - + +
380A HIS* 1.3 81.1 + + - +
381A PHE 3.9 0.3 + - - -
382A MET* 5.1 1.4 + - - +
314B ASP* 4.0 27.5 + - + -
318B ILE* 4.9 13.0 - - - +
372B ARG* 6.1 0.2 + - - -
375B ARG* 4.2 11.9 + - - -
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Residues in contact with HIS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ARG* 5.4 0.7 - - - -
376A ASN* 3.0 38.6 + - + +
377A LYS* 3.7 2.7 - - - -
379A HIS* 1.3 102.9 - + + +
381A PHE* 1.3 64.0 + - - +
382A MET* 2.9 5.1 + - - +
383A ASP* 3.0 35.5 + - + +
384A LEU* 3.4 13.1 + - + +
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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