Contacts of the strand formed by residues 444 - 450 (chain C) in PDB entry 1YA8
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 THR 444 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C TYR* 3.4 9.9 - - + +
348C VAL* 5.4 1.1 - - + -
434C ALA* 3.5 40.8 - - + +
437C HIS* 2.8 25.7 - - + -
438C ARG* 3.2 10.8 + - - -
442C ALA 3.0 7.5 + - - -
443C PRO* 1.3 72.1 - - - +
445C TYR* 1.3 70.2 + - - +
519C GLU* 3.3 14.2 + - - +
520C TYR* 2.8 43.9 + - + -
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Residues in contact with TYR 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C TYR 3.1 5.9 + - - +
347C MET* 3.2 19.8 - - + -
348C VAL* 2.7 32.4 + - - +
443C PRO* 4.4 12.0 - - + +
444C THR* 1.3 83.3 - - - +
446C MET* 1.3 59.5 + - - +
503C PHE* 4.1 13.0 - + - -
507C GLY 3.7 18.7 + - - -
508C ASN* 3.0 28.2 + - - +
509C PRO* 3.5 35.7 - - + -
510C ASN* 4.5 2.0 + - - -
517C TRP* 3.9 17.9 - + + +
518C PRO 3.5 23.3 - - - -
519C GLU* 3.8 24.2 + - + +
520C TYR* 4.1 4.0 - - - +
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Residues in contact with MET 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C VAL* 2.9 22.7 - - + +
349C GLY* 5.0 2.7 - - - -
350C ILE* 5.5 1.8 - - + -
430C SER* 3.9 11.9 - - - +
431C VAL* 3.4 41.3 - - + +
434C ALA* 3.5 26.0 - - + -
445C TYR* 1.3 75.4 - - - +
447C TYR* 1.3 63.7 + - - +
517C TRP* 2.9 25.6 + - - +
518C PRO 5.6 0.2 + - - -
520C TYR* 3.5 36.3 - - + +
525C GLY 4.9 2.2 + - - -
526C TYR* 3.8 16.5 - - + -
527C LEU 3.3 7.1 + - - -
539C LEU* 3.9 14.4 - - + -
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Residues in contact with TYR 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 5.1 0.7 - - + -
245C SER 4.9 1.1 - - - -
246C GLU* 3.2 36.8 - - + +
247C SER* 4.9 0.3 + - - -
347C MET* 3.9 19.1 - - + -
348C VAL 3.3 5.7 + - - -
349C GLY* 3.4 22.3 - - - -
350C ILE* 3.0 42.4 + - - +
351C ASN* 4.3 7.2 + - - -
446C MET* 1.3 78.9 - - - +
448C GLU* 1.3 66.0 + - - +
449C PHE* 3.9 10.1 - + + -
471C GLU* 4.3 8.1 - - + +
500C TRP* 3.4 34.2 - + - -
517C TRP* 3.7 12.3 - + + -
526C TYR* 4.3 4.9 - - - +
527C LEU 3.1 16.2 - - - +
529C ILE* 4.1 15.5 - - + -
539C LEU* 4.2 4.4 - - - +
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Residues in contact with GLU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE* 3.3 25.5 - - + +
352C LYS* 3.9 27.5 - - - +
447C TYR* 1.3 76.1 - - - +
449C PHE* 1.3 64.4 + - - +
450C GLN* 2.7 36.4 + - - +
526C TYR* 4.0 26.9 + - + -
527C LEU 3.0 7.3 + - - -
528C GLN* 3.8 1.8 + - + -
529C ILE* 3.1 22.6 + - - +
539C LEU* 3.9 17.4 - - + +
540C LYS* 4.2 10.7 + - - -
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Residues in contact with PHE 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE 2.9 9.9 + - - +
351C ASN* 3.1 24.9 - - - +
352C LYS 3.0 21.3 + - - -
447C TYR* 3.9 7.9 - + + -
448C GLU* 1.3 69.9 - - - +
450C GLN* 1.3 61.2 + - - +
451C TYR* 3.7 36.6 - + + -
453C PRO* 5.0 0.7 - - + -
466C GLY* 3.7 5.5 - - - -
470C ASP* 3.7 13.9 - - + -
471C GLU* 3.5 42.8 - - + -
474C SER* 3.7 28.0 - - - -
492C LEU* 3.9 8.1 - - + -
496C VAL* 4.5 3.6 - - + -
500C TRP* 6.6 0.2 - + - -
529C ILE* 3.6 34.3 - - + -
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Residues in contact with GLN 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LYS* 3.6 40.1 - - + +
448C GLU* 2.7 37.8 + - + +
449C PHE* 1.3 78.9 - - - +
451C TYR* 1.3 62.8 + - - +
465C ILE* 3.9 9.7 - - + +
466C GLY* 4.5 1.3 - - - -
528C GLN* 3.3 33.4 - - - +
529C ILE 2.8 13.9 + - - +
530C GLY* 3.6 12.8 - - - -
531C ALA 4.4 2.4 + - - -
532C ASN 5.7 0.7 - - - +
534C GLN* 5.7 0.2 + - - -
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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