Contacts of the helix formed by residues 409 - 422 (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 ASN 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ALA* 3.4 23.8 - - - +
337A PHE* 2.9 58.2 - - + +
338A VAL* 3.7 13.1 + - - +
340A PRO* 5.9 0.5 - - - +
407A PHE 3.2 1.4 + - - -
408A PRO* 1.3 82.4 - - - +
410A LEU* 1.3 58.8 + - - +
411A LEU 3.5 1.6 - - - -
412A ILE* 3.9 5.2 - - - -
413A GLY* 2.8 30.8 + - - -
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Residues in contact with LEU 410 (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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309A LEU* 4.2 13.0 - - + -
338A VAL* 3.7 11.9 - - + +
367A LEU* 3.8 28.3 - - + -
370A LEU* 4.6 14.1 - - + -
371A LEU* 4.1 17.5 - - + -
374A LEU* 4.0 27.1 - - + -
403A PHE* 4.3 15.7 - - + +
404A THR* 5.2 4.5 - - - +
407A PHE* 2.9 32.1 + - + +
408A PRO 3.3 0.4 - - - -
409A ASN* 1.3 77.8 - - - +
411A LEU* 1.3 67.6 + - - +
413A GLY* 4.0 0.2 - - - -
414A VAL* 3.0 30.4 + - + +
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Residues in contact with LEU 411 (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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267A SER* 5.7 3.3 - - - -
271A GLU* 3.8 17.7 - - - +
297A PRO* 3.4 37.7 - - + -
300A TRP* 4.9 2.5 - - + -
305A LYS* 3.8 33.2 - - + +
308A PHE* 3.9 12.8 - - + -
309A LEU* 3.8 20.0 - - + -
400A TYR* 3.1 27.6 - - + +
404A THR* 5.2 3.2 + - - +
407A PHE 4.8 0.4 + - - -
408A PRO 5.0 1.8 + - - -
409A ASN 3.5 0.4 - - - -
410A LEU* 1.3 83.3 - - - +
412A ILE* 1.3 60.2 + - - +
414A VAL* 3.8 1.0 - - - +
415A TYR* 3.0 24.6 + - + +
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Residues in contact with ILE 412 (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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270A ALA* 4.0 22.0 - - + +
271A GLU* 3.9 15.1 + - + -
274A ASP* 3.5 41.5 - - + +
296A HIS* 3.8 19.7 - - + +
297A PRO* 4.1 6.5 - - + -
337A PHE* 4.1 12.6 - - + -
408A PRO 4.4 1.5 + - - +
409A ASN* 3.4 22.9 - - - +
411A LEU* 1.3 75.7 - - - +
413A GLY* 1.3 58.7 + - - +
415A TYR* 4.0 18.8 - - + -
416A MET* 2.8 47.7 + - + +
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Residues in contact with GLY 413 (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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337A PHE* 3.9 21.8 - - - -
338A VAL* 4.3 7.0 - - - -
367A LEU* 5.4 0.2 - - - -
409A ASN 2.8 22.6 + - - -
410A LEU 4.0 0.2 - - - -
412A ILE* 1.3 73.8 - - - +
414A VAL* 1.3 61.6 + - - +
416A MET* 3.9 5.8 - - - +
417A ILE* 3.1 34.3 + - - +
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Residues in contact with VAL 414 (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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308A PHE* 4.0 2.7 - - + -
309A LEU* 4.0 17.7 - - + -
312A VAL* 3.7 39.5 - - + -
331A PHE* 4.3 5.2 - - + -
338A VAL* 5.0 0.6 - - - +
367A LEU* 4.3 16.2 - - + -
371A LEU* 4.2 15.0 - - + -
410A LEU* 3.0 36.9 + - + +
411A LEU 3.8 2.5 - - - +
413A GLY* 1.3 71.1 - - - +
415A TYR* 1.3 57.6 + - - +
417A ILE* 3.3 7.0 + - - +
418A VAL* 2.8 41.2 + - + +
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Residues in contact with TYR 415 (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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274A ASP* 4.8 2.2 - - - -
295A ARG 4.5 6.8 + - - -
296A HIS* 4.5 14.7 - + - -
297A PRO* 3.4 42.9 - - + +
300A TRP* 4.0 17.5 - + - -
308A PHE* 3.8 14.8 - + + -
411A LEU* 3.0 20.1 + - + +
412A ILE* 3.4 17.5 + - + +
414A VAL* 1.3 76.5 - - - +
416A MET* 1.3 64.1 + - + +
418A VAL* 3.7 0.5 - - - +
419A LYS* 2.9 68.0 + - + +
432A LEU* 3.6 33.9 + - + -
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Residues in contact with MET 416 (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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274A ASP* 3.6 27.4 - - - +
337A PHE* 3.8 33.9 - - + -
412A ILE* 2.8 36.5 + - + +
413A GLY* 3.9 6.1 - - - +
415A TYR* 1.3 77.7 - - + +
417A ILE* 1.3 65.6 + - + +
419A LYS* 3.4 6.7 + - + +
420A GLU* 3.0 26.4 + - - +
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Residues in contact with ILE 417 (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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330A LYS 3.8 21.8 - - - +
331A PHE* 3.4 45.1 - - + +
334A GLY* 3.9 24.7 - - - -
367A LEU* 4.1 12.8 - - + -
413A GLY* 3.1 20.5 + - - +
414A VAL 3.8 2.7 - - - +
416A MET* 1.3 75.6 - - + +
418A VAL* 1.3 56.9 + - - +
420A GLU* 4.6 0.9 - - - -
421A ASN* 2.8 50.4 + - - +
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Residues in contact with VAL 418 (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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308A PHE* 3.9 13.2 - - + -
312A VAL* 3.5 30.5 - - + -
331A PHE* 3.9 17.5 - - + -
414A VAL* 2.8 27.7 + - + +
415A TYR 3.8 3.1 - - - +
417A ILE* 1.3 71.6 - - - +
419A LYS* 1.3 57.4 + - - +
422A LEU* 2.6 40.1 + - + -
428A LEU* 3.8 28.3 - - + -
432A LEU* 3.9 17.7 - - + -
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Residues in contact with LYS 419 (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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278A GLN* 5.9 4.5 - - - +
292A LYS* 6.3 1.5 - - - +
296A HIS* 6.4 0.4 - - - -
415A TYR* 2.9 59.6 + - + +
416A MET* 3.7 6.7 - - + +
418A VAL* 1.3 69.3 - - - +
420A GLU* 1.3 69.2 + - - +
423A SER* 3.4 16.3 + - - -
432A LEU* 3.8 25.8 + - + +
433A TYR* 4.5 19.6 + - - +
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Residues in contact with GLU 420 (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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330A LYS* 6.1 2.2 - - - +
416A MET 3.0 18.6 + - - +
417A ILE* 4.6 0.7 - - - -
419A LYS* 1.3 82.5 - - - +
421A ASN* 1.3 77.4 + - - +
423A SER* 5.1 1.4 + - - -
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Residues in contact with ASN 421 (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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327A LEU* 5.4 8.1 - - + +
330A LYS* 3.2 41.2 + - + +
331A PHE* 5.4 3.8 - - + -
417A ILE* 2.8 43.4 + - + +
420A GLU* 1.3 94.9 - - - +
422A LEU* 1.3 72.5 + - + +
423A SER 3.7 1.3 - - - -
424A ASP* 4.0 10.7 - - - +
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Residues in contact with LEU 422 (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* 5.8 0.2 - - + -
315A ARG* 4.0 26.5 - - + +
316A LEU* 4.5 2.9 - - + -
327A LEU* 3.7 40.2 - - + -
331A PHE* 4.4 16.4 - - + -
418A VAL* 2.6 33.3 + - + +
421A ASN* 1.3 81.3 - - + +
423A SER* 1.3 57.4 + - - +
424A ASP* 3.1 17.9 - - - +
425A ASP* 3.1 29.6 + - + +
428A LEU* 3.7 25.3 - - + +
429A ARG 5.1 0.3 + - - -
432A LEU* 4.8 0.3 - - - +
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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