Contacts of the helix formed by residues 409 - 422 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B ARG* 5.1 2.3 + - - -
270B ALA* 3.7 19.2 - - - +
337B PHE* 2.7 58.2 + - + +
338B VAL* 3.4 12.4 + - - +
340B PRO* 5.4 4.8 - - - +
407B PHE 3.0 1.4 + - - -
408B PRO* 1.3 83.7 - - - +
410B LEU* 1.3 60.1 + - - +
411B LEU 3.6 0.7 - - - -
412B ILE* 4.2 5.8 - - - -
413B GLY* 2.9 30.2 + - - -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LEU* 3.8 24.7 - - + -
338B VAL* 3.9 8.8 - - + +
367B LEU* 3.8 25.6 - - + -
370B LEU* 4.0 17.3 - - + -
371B LEU* 4.3 13.0 - - + -
374B LEU* 4.0 16.4 - - + -
403B PHE* 4.3 18.8 - - + +
404B THR* 4.4 9.2 - - + -
407B PHE* 3.0 24.9 + - + +
408B PRO 3.3 0.8 - - - -
409B ASN* 1.3 74.6 - - - +
411B LEU* 1.3 61.1 + - - +
414B VAL* 2.8 45.3 + - + +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B SER* 5.6 1.1 - - - -
271B GLU* 3.7 18.4 - - - +
297B PRO* 3.5 33.2 - - + -
300B TRP* 4.9 2.2 - - + -
305B LYS* 3.7 33.4 - - + +
308B PHE* 4.0 11.0 - - + -
309B LEU* 3.9 20.0 - - + -
400B TYR* 3.3 27.8 - - + +
404B THR* 5.0 4.7 - - + +
407B PHE 4.9 0.2 + - - -
408B PRO 4.8 2.3 + - - +
410B LEU* 1.3 80.5 - - - +
412B ILE* 1.3 62.6 + - - +
414B VAL* 3.8 0.9 - - - +
415B TYR* 2.8 34.0 + - + +
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Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ALA* 4.1 27.6 - - + +
271B GLU* 4.0 16.9 + - + -
274B ASP* 3.3 40.6 - - + +
296B HIS* 3.8 17.9 - - + -
297B PRO* 4.2 6.1 - - + -
337B PHE* 4.1 16.2 - - + -
408B PRO 4.7 1.9 + - - +
409B ASN* 3.8 11.6 - - - +
411B LEU* 1.3 79.7 - - - +
413B GLY* 1.3 55.8 + - - +
415B TYR* 3.5 24.7 - - + +
416B MET* 2.8 46.8 + - + +
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Residues in contact with GLY 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLY* 6.6 0.2 - - - -
337B PHE* 3.7 10.5 - - - -
338B VAL* 4.3 6.3 - - - -
367B LEU* 5.1 0.4 - - - -
409B ASN 2.9 19.5 + - - -
410B LEU 3.9 0.2 - - - -
412B ILE* 1.3 77.3 - - - +
414B VAL* 1.3 65.2 + - - +
416B MET* 3.4 16.8 + - - +
417B ILE* 3.3 31.0 + - - +
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Residues in contact with VAL 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 4.2 2.2 - - + -
309B LEU* 3.9 24.0 - - + -
312B VAL* 3.7 42.2 - - + -
331B PHE* 4.1 9.6 - - + -
338B VAL* 4.9 0.4 - - - +
367B LEU* 4.2 17.9 - - + -
371B LEU* 4.5 9.0 - - + -
410B LEU* 2.8 38.8 + - + +
411B LEU 4.0 0.2 - - - +
413B GLY* 1.3 72.7 - - - +
415B TYR* 1.3 63.0 + - - +
417B ILE* 3.2 5.3 + - - +
418B VAL* 3.0 21.2 + - + +
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Residues in contact with TYR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP* 5.0 2.7 - - - -
278B GLN* 6.3 0.2 - - - -
292B LYS* 5.6 2.6 + - - +
295B ARG* 4.6 3.8 + - - +
296B HIS* 4.5 13.9 - + - -
297B PRO* 3.4 39.5 - - + +
300B TRP* 4.0 20.6 - + - -
308B PHE* 3.8 16.5 - + + -
411B LEU* 2.8 27.1 + - + +
412B ILE* 3.5 20.6 - - + +
414B VAL* 1.3 73.6 - - - +
416B MET* 1.3 62.2 + - + +
418B VAL* 3.4 0.3 + - - +
419B LYS* 2.9 54.7 + - + +
432B LEU* 3.7 33.1 + - + +
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP* 4.1 23.3 - - - +
337B PHE* 3.3 42.0 - - + -
412B ILE* 2.8 42.9 + - + +
413B GLY* 3.6 6.7 - - - +
414B VAL 3.3 0.4 - - - -
415B TYR* 1.3 77.4 - - + +
417B ILE* 1.3 65.6 + - + +
419B LYS* 4.0 5.3 - - - +
420B GLU* 3.1 27.0 + - - +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B LYS* 3.6 24.2 - - + +
331B PHE* 3.2 45.8 - - + -
334B GLY* 3.8 24.7 - - - -
367B LEU* 4.0 12.1 - - + -
413B GLY 3.3 15.0 + - - +
414B VAL 3.2 8.0 + - - +
416B MET* 1.3 80.5 - - + +
418B VAL* 1.3 55.2 + - - +
420B GLU* 3.4 1.1 + - - -
421B ASN* 2.7 50.1 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.8 19.7 - - + -
312B VAL* 3.6 29.6 - - + -
331B PHE* 4.2 11.2 - - + -
414B VAL* 3.0 22.3 + - + +
415B TYR 3.9 3.1 - - - +
417B ILE* 1.3 73.2 - - - +
419B LYS* 1.3 62.0 + - - +
420B GLU 3.0 1.8 - - - -
422B LEU* 2.7 43.5 + - + -
423B SER 3.3 4.7 + - - -
428B LEU* 4.2 13.7 - - + -
432B LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B GLN* 4.6 8.7 + - - +
292B LYS* 3.7 33.5 - - - +
415B TYR* 2.9 46.2 + - + +
416B MET* 4.1 4.9 - - - +
418B VAL* 1.3 77.1 - - - +
420B GLU* 1.3 63.0 + - + +
423B SER* 3.4 16.6 + - - -
432B LEU* 4.3 16.8 - - + -
433B TYR* 4.7 13.5 - - + +
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B MET 3.1 19.9 + - - +
417B ILE* 4.6 0.7 - - - -
418B VAL 3.0 0.6 - - - -
419B LYS* 1.3 82.8 - - - +
421B ASN* 1.3 80.0 + - - +
423B SER* 5.0 1.8 + - - -
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Residues in contact with ASN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU* 4.0 21.2 - - + +
330B LYS* 2.6 43.4 + - + +
417B ILE* 2.7 40.9 + - + +
420B GLU* 1.3 97.6 - - - +
422B LEU* 1.3 69.5 + - + +
423B SER 3.6 1.6 - - - -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ARG* 3.7 37.5 - - + +
316B LEU* 4.7 2.5 - - + -
327B LEU* 3.7 35.7 - - + -
331B PHE* 4.4 17.9 - - + -
418B VAL* 2.7 30.6 + - + +
421B ASN* 1.3 79.0 - - + +
423B SER* 1.3 58.7 + - - +
424B ASP* 2.9 12.3 + - - +
425B ASP* 3.0 23.6 + - + +
428B LEU* 3.8 28.6 - - + +
432B LEU* 4.6 1.2 - - - +
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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