Contacts of the helix formed by residues 412 - 423 (chain F) in PDB entry 5YW9
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 MET 412 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411F GLU* 1.3 76.4 - - - +
413F THR* 1.3 63.0 + - + +
415F GLY* 3.4 1.7 + - - +
416F GLN* 2.9 29.5 + - - +
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Residues in contact with THR 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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406F ASN* 3.4 38.4 + - + -
411F GLU 4.1 8.3 + - - -
412F MET* 1.3 79.8 - - + +
414F ALA* 1.3 59.4 + - - +
416F GLN* 3.7 6.5 - - - +
417F ILE* 2.8 41.7 + - - +
1208F VAL* 5.8 1.6 - - - +
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Residues in contact with ALA 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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411F GLU* 3.4 16.0 + - - +
412F MET 3.2 0.4 - - - -
413F THR* 1.3 79.1 + - - +
415F GLY* 1.3 60.5 + - - +
417F ILE* 3.2 5.5 + - - +
418F CYS* 2.9 31.5 + - - +
1205F ALA* 6.5 0.2 - - - -
1208F VAL* 3.6 26.5 - - + +
1209F GLU* 3.6 24.0 - - - +
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Residues in contact with GLY 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 GLU 3.2 11.6 + - - -
412F MET* 3.4 2.7 + - - -
414F ALA* 1.3 78.1 - - - +
416F GLN* 1.3 56.6 + - - +
418F CYS* 3.4 5.0 + - - +
419F ASN* 2.9 37.5 + - - +
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Residues in contact with GLN 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 MET 2.9 18.7 + - - +
413F THR* 3.7 8.3 - - - +
415F GLY* 1.3 75.5 - - - +
417F ILE* 1.3 57.9 + - + +
419F ASN* 3.8 9.6 + - - +
420F LEU* 2.9 31.8 + - + +
609F LYS* 3.3 43.3 - - + +
613F PHE* 6.4 2.5 - - + -
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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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395F ILE* 6.2 0.4 - - + -
399F ILE* 3.6 32.8 - - + -
402F LEU* 4.6 7.4 - - + -
413F THR* 2.8 29.2 + - - +
414F ALA 3.5 5.6 - - - +
416F GLN* 1.3 77.3 - - + +
418F CYS* 1.3 61.7 + - - +
420F LEU* 2.9 28.6 + - + +
421F VAL* 3.1 14.4 + - + +
613F PHE* 3.6 29.8 - - + -
1204F PHE* 4.4 14.8 - - + -
1208F VAL* 4.4 26.7 - - + -
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Residues in contact with CYS 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 ALA 2.9 16.9 + - - +
415F GLY* 4.1 4.9 - - - +
417F ILE* 1.3 76.8 - - - +
419F ASN* 1.3 61.6 + - - +
421F VAL* 3.5 6.1 + - - +
422F ALA* 3.0 28.6 + - - +
1201F LEU* 4.2 16.8 - - + +
1204F PHE* 4.1 13.9 - - - -
1205F ALA* 4.0 35.0 - - - -
1208F VAL* 5.7 1.3 - - - -
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Residues in contact with ASN 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 GLY 2.9 22.4 + - - +
416F GLN* 3.9 11.1 + - - +
418F CYS* 1.3 73.8 - - - +
420F LEU* 1.3 58.0 + - - +
421F VAL 3.0 5.2 - - - -
422F ALA* 4.2 7.1 - - - +
423F ILE* 3.0 53.8 + - + +
424F ASP 3.2 1.2 + - - -
609F LYS* 6.2 1.1 - - - +
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Residues in contact with LEU 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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395F ILE* 3.7 28.3 - - + +
416F GLN* 2.9 19.8 + - + +
417F ILE* 2.9 15.9 + - + +
419F ASN* 1.3 74.8 - - - +
421F VAL* 1.3 58.5 + - - +
424F ASP* 3.5 17.0 - - - +
425F THR* 3.1 15.6 + - - -
609F LYS* 3.8 31.9 - - + +
610F LEU* 3.7 37.3 - - + +
613F PHE* 3.7 37.7 - - + -
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Residues in contact with VAL 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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392F GLN* 3.3 39.4 + - + +
395F ILE* 3.6 20.6 - - + -
417F ILE* 3.1 18.1 + - + +
418F CYS* 3.5 2.4 + - - +
419F ASN 3.0 0.6 - - - -
420F LEU* 1.3 81.0 - - - +
422F ALA* 1.3 60.0 + - - +
423F ILE 3.7 0.4 - - - -
425F THR* 3.6 18.5 - - - +
426F ASN* 4.6 3.3 + - - +
1200F LEU* 6.1 0.4 - - + -
1201F LEU* 4.0 20.7 - - + +
1204F PHE* 3.9 31.4 - - + -
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Residues in contact with ALA 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 CYS 3.0 18.8 + - - +
419F ASN* 3.3 7.2 + - - +
421F VAL* 1.3 78.9 - - - +
423F ILE* 1.3 66.3 + - + +
426F ASN* 3.9 20.9 + - - +
1197F GLN* 5.4 5.8 + - - +
1201F LEU* 3.7 25.8 - - + -
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Residues in contact with ILE 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 ASN* 3.0 37.5 + - + +
422F ALA* 1.3 87.6 - - + +
424F ASP* 1.3 77.5 + - + +
425F THR 3.4 1.1 - - - -
426F ASN* 3.5 4.3 + - - +
427F GLN* 2.9 37.4 + - + +
602F LYS* 4.5 17.9 - - - +
609F LYS* 4.4 16.8 - - - +
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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