Contacts of the helix formed by residues 486 - 495 (chain A) in PDB entry 1YI1
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 GLY 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A VAL* 1.3 83.4 - - - +
487A GLN* 1.3 66.6 + - - -
488A HIS 3.3 2.5 - - - -
489A GLN* 3.1 16.1 + - - +
490A MET* 3.2 16.1 + - - +
570A MET* 3.7 23.1 - - - -
700A P22 3.3 10.5 - - - -
701A FAD 4.6 2.3 - - - +
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Residues in contact with GLN 487 (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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486A GLY* 1.3 71.2 - - - -
488A HIS* 1.3 65.0 + - - +
490A MET* 2.9 4.9 + - - +
491A TRP* 2.9 49.5 + - + -
565A ASN* 3.7 12.5 + - - -
569A GLY* 3.2 24.3 + - - -
570A MET* 3.4 29.3 - - + +
572A MET* 4.6 3.0 - - - +
573A GLN* 3.0 25.9 + - - +
643A HIS 4.7 1.2 + - - +
645A GLU* 2.9 27.5 + - - +
646A HIS* 3.8 3.0 - - - +
647A VAL* 3.8 10.1 - - + +
700A P22 2.9 12.2 + - - +
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE* 4.3 1.7 - - - +
484A GLY* 3.1 34.7 - - - -
485A VAL 3.3 23.1 + - - -
487A GLN* 1.3 75.8 - - - +
489A GLN* 1.3 57.3 + - - +
491A TRP* 3.7 12.3 - - + +
492A ALA* 2.7 37.2 + - - +
535A ILE* 3.0 19.7 + - + +
536A ASP* 3.3 9.7 - - - +
537A GLY* 3.2 22.9 + - - -
540A SER* 3.9 4.0 + - - -
563A LEU* 4.1 24.0 - - + +
700A P22 2.9 41.5 + - - +
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Residues in contact with GLN 489 (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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332A LEU* 4.7 10.2 - - + +
483A THR* 3.3 26.0 - - + -
484A GLY 3.3 14.1 + - - +
485A VAL* 3.2 14.2 - - - +
486A GLY 3.1 24.7 + - - +
487A GLN 3.1 0.2 - - - -
488A HIS* 1.3 83.0 - - - +
490A MET* 1.3 66.2 + - - +
492A ALA* 3.3 1.3 + - - +
493A ALA* 3.1 22.0 + - - +
504A TRP* 3.6 9.0 - - + -
506A SER* 2.7 23.7 + - - +
507A SER 3.2 23.2 + - - +
701A FAD 3.6 19.3 - - - +
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Residues in contact with MET 490 (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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332A LEU* 4.2 11.2 - - - -
348A MET* 3.7 15.9 - - + +
352A HIS* 3.2 43.3 - - + -
486A GLY 3.4 12.3 - - - +
487A GLN 2.9 6.1 + - - +
489A GLN* 1.3 76.2 - - - +
491A TRP* 1.3 63.5 + - - +
493A ALA* 3.1 4.7 + - - +
494A GLN* 2.9 34.7 + - + +
570A MET* 3.9 18.8 - - + -
647A VAL* 3.7 18.6 - - + -
701A FAD 3.4 40.8 - - + +
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Residues in contact with TRP 491 (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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464A PRO* 3.6 27.8 - - + -
465A GLN* 3.7 33.1 - - + +
468A ILE* 3.4 19.3 - - + +
487A GLN* 2.9 52.7 + - + +
488A HIS* 3.9 8.5 - - + +
490A MET* 1.3 72.1 - - - +
492A ALA* 1.3 58.8 + - - +
493A ALA 3.0 4.7 - - - -
494A GLN* 3.5 18.5 + - - -
495A PHE* 2.8 38.2 + + + -
563A LEU* 4.9 1.6 - - + -
565A ASN* 5.9 2.2 - - - -
645A GLU* 3.7 24.2 - - + -
646A HIS 3.8 17.6 + - - -
647A VAL* 3.6 32.8 - - + +
648A LEU 4.9 0.8 - - - +
700A P22 5.0 1.6 - - - -
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Residues in contact with ALA 492 (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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468A ILE* 3.3 13.4 - - - +
481A ILE* 4.8 0.4 - - + -
483A THR* 3.8 20.6 - - - +
488A HIS 2.7 22.3 + - - +
489A GLN 3.7 5.8 - - - +
491A TRP* 1.3 73.3 - - - +
493A ALA* 1.3 54.9 + - - +
495A PHE 4.5 0.4 - - - -
496A TYR* 3.5 12.0 - - - +
498A TYR* 2.7 26.9 + - - +
504A TRP* 4.0 4.3 - - + -
535A ILE* 3.9 26.6 - - + +
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Residues in contact with ALA 493 (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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332A LEU* 5.1 3.4 - - + -
335A LEU* 3.8 29.2 - - + +
340A CSD 5.5 2.4 + - - -
348A MET* 4.8 16.4 - - + +
489A GLN 3.1 13.0 + - - +
490A MET* 3.5 10.1 - - - +
491A TRP 3.0 0.6 - - - -
492A ALA* 1.3 78.9 - - - +
494A GLN* 1.3 64.6 + - + +
496A TYR 3.9 11.3 - - - +
498A TYR* 4.2 2.7 - - - -
504A TRP* 3.7 18.8 - - + -
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Residues in contact with GLN 494 (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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348A MET* 5.6 6.5 - - + -
352A HIS* 3.2 25.5 + - + +
353A GLY 5.2 0.2 - - - -
354A THR* 5.5 0.4 - - - +
453A LEU* 3.3 39.6 - - + +
490A MET* 2.9 19.3 + - + +
491A TRP* 3.5 15.8 + - - -
493A ALA* 1.3 81.0 - - + +
495A PHE* 1.3 86.9 + - + +
496A TYR 3.5 4.2 + - - +
497A ASN* 5.2 2.6 - - - +
647A VAL* 4.2 10.0 - - - +
648A LEU 3.2 26.6 + - - +
649A PRO* 4.4 0.2 - - - +
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Residues in contact with PHE 495 (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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453A LEU* 4.4 28.3 - - + -
454A SER 4.8 6.5 - - - -
455A PHE* 3.8 17.9 - + + -
465A GLN* 3.3 57.0 - - + +
468A ILE* 3.5 15.3 - - + +
469A LYS* 3.8 44.5 - - + +
472A ASP* 4.0 4.6 - - - +
491A TRP* 2.8 28.1 + + - +
494A GLN* 1.3 104.4 - - + +
496A TYR* 1.3 56.5 + - - +
497A ASN* 5.5 2.0 - - - -
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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