Contacts of the helix formed by residues 406 - 423 (chain F) in PDB entry 5IJO
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 ASP 406 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405F ALA* 1.3 86.9 - - + +
407F GLU* 1.3 62.6 + - - +
409F GLN* 3.0 22.0 + - - +
410F LEU* 3.2 9.6 + - - +
343G ALA* 5.6 10.1 - - + -
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Residues in contact with GLU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F ILE* 4.4 10.3 - - + +
404F GLN* 4.2 21.2 - - + -
405F ALA 3.0 2.4 - - - +
406F ASP* 1.3 79.7 - - - +
408F GLU* 1.3 57.7 + - - +
410F LEU* 3.2 9.8 + - + +
411F ARG* 2.8 27.8 + - + +
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Residues in contact with GLU 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F GLN* 4.9 7.6 - - + +
405F ALA 3.5 12.9 + - - +
406F ASP 3.3 0.8 + - - -
407F GLU* 1.3 79.0 - - - +
409F GLN* 1.4 42.4 + - - +
411F ARG* 3.1 9.2 + - + +
412F VAL* 2.5 32.1 + - - +
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Residues in contact with GLN 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F ALA 4.4 1.7 + - - +
406F ASP* 3.0 16.2 + - - +
408F GLU* 1.4 70.7 - - - +
410F LEU* 1.3 67.9 + - - +
411F ARG 3.1 0.7 - - - -
412F VAL* 3.9 8.1 - - - +
413F GLN* 3.2 19.9 + - - +
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Residues in contact with LEU 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F ASP 3.2 5.2 + - - +
407F GLU* 3.2 15.3 + - + +
409F GLN* 1.3 81.4 - - - +
411F ARG* 1.3 65.7 + - + +
413F GLN* 3.2 5.7 + - - +
414F LEU* 3.0 22.6 + - - +
343G ALA* 6.2 5.2 - - + -
346G PHE* 5.8 5.4 - - + -
347G ARG* 5.2 19.7 - - + +
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Residues in contact with ARG 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407F GLU* 2.8 17.5 + - + +
408F GLU* 3.1 12.1 + - + +
410F LEU* 1.3 81.9 - - - +
412F VAL* 1.4 53.5 + - - +
414F LEU* 3.3 7.5 + - - +
415F ASP* 3.0 27.5 + - - +
433H THR* 6.1 5.6 - - - -
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Residues in contact with VAL 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408F GLU 2.5 17.5 + - - +
409F GLN* 3.4 9.6 + - - +
410F LEU 3.3 0.6 - - - -
411F ARG* 1.4 69.6 - - - +
413F GLN* 1.4 60.6 + - - +
415F ASP* 3.3 7.2 + - - +
416F THR* 3.2 22.3 + - - -
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Residues in contact with GLN 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F GLN 3.2 9.6 + - - +
410F LEU* 3.2 10.9 + - - +
412F VAL* 1.4 72.8 - - - +
414F LEU* 1.3 66.7 + - - +
416F THR* 3.2 6.9 + - - -
417F ILE* 3.1 22.5 + - - +
350G VAL* 4.7 19.3 - - + -
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Residues in contact with LEU 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410F LEU 3.0 10.5 + - - +
411F ARG* 3.3 10.1 + - - +
413F GLN* 1.3 82.5 - - - +
415F ASP* 1.4 61.3 + - - +
417F ILE* 4.0 4.4 - - - +
418F GLN* 3.0 24.8 + - - +
350G VAL* 5.7 2.9 - - - +
437H ALA* 5.6 12.1 - - + -
440H ILE* 5.8 3.5 - - + +
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Residues in contact with ASP 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411F ARG 3.0 14.1 + - - +
412F VAL* 3.6 10.3 - - - +
413F GLN 3.2 0.4 - - - -
414F LEU* 1.4 71.8 - - - +
416F THR* 1.4 69.5 - - - +
418F GLN* 3.1 11.4 + - - +
419F GLY 3.5 10.2 + - - -
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Residues in contact with THR 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F VAL 3.2 10.5 + - - -
413F GLN* 3.8 7.9 - - - -
414F LEU 3.2 0.2 - - - -
415F ASP* 1.4 82.1 - - - +
417F ILE* 1.4 65.8 + - - +
419F GLY 4.3 0.3 - - - -
420F GLU* 3.3 19.7 + - - +
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Residues in contact with ILE 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413F GLN 3.1 13.8 + - - +
414F LEU* 4.0 4.9 - - - +
416F THR* 1.4 77.4 - - - +
418F GLN* 1.3 65.4 + - - +
420F GLU* 3.1 22.7 + - - +
421F LEU* 3.2 7.6 + - - +
354G GLU* 6.1 4.5 - - - -
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Residues in contact with GLN 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414F LEU 3.0 18.9 + - - +
415F ASP* 3.1 5.1 + - - +
416F THR 3.1 2.2 - - - -
417F ILE* 1.3 74.4 - - - +
419F GLY* 1.3 67.5 + - - +
420F GLU 3.0 1.2 + - - -
421F LEU* 3.2 18.6 - - - +
422F ASN* 3.3 3.5 + - - +
440H ILE* 4.9 17.5 - - + -
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Residues in contact with GLY 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415F ASP 3.5 8.7 + - - -
416F THR 3.9 0.4 + - - -
418F GLN* 1.3 78.9 - - - +
420F GLU* 1.5 64.7 + - - +
421F LEU 2.9 0.4 - - - -
422F ASN* 3.0 18.3 - - - +
423F ALA* 3.1 10.4 + - - +
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Residues in contact with GLU 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416F THR 3.3 14.4 + - - +
417F ILE* 3.1 16.7 + - - +
418F GLN 3.0 2.0 - - - -
419F GLY* 1.5 67.7 - - - +
421F LEU* 1.4 67.6 - - - +
423F ALA 2.7 12.0 + - - -
424F PRO 4.1 2.3 - - - -
425F THR 5.0 0.3 + - - -
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Residues in contact with LEU 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F ILE 3.7 7.0 - - - +
418F GLN* 3.2 13.5 - - - +
420F GLU* 1.4 78.7 - - - +
422F ASN* 1.4 70.1 + - - +
423F ALA* 2.6 0.7 + - - -
424F PRO 3.8 2.3 - - - -
425F THR 4.2 0.5 + - - -
426F GLN* 4.0 16.2 - - - +
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Residues in contact with ASN 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F GLN 3.3 1.5 + - - +
419F GLY* 3.0 23.6 - - - +
420F GLU 2.9 0.2 - - - -
421F LEU* 1.4 86.4 - - - +
423F ALA* 1.3 98.8 + - + +
425F THR 3.8 1.0 + - - -
426F GLN* 4.0 3.3 + - - +
427F PHE* 4.2 7.8 + - - +
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Residues in contact with ALA 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419F GLY 3.1 3.8 + - - +
420F GLU 2.7 8.3 + - - -
421F LEU 2.6 4.8 + - - -
422F ASN* 1.3 113.7 - - + +
424F PRO* 1.3 71.8 - - + +
426F GLN 3.8 0.9 + - - -
427F PHE* 3.8 9.4 + - - +
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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