Contacts of the strand formed by residues 444 - 449 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A TYR* 3.4 10.3 - - + +
348A VAL* 5.9 2.2 - - + +
434A ALA* 3.6 33.7 - - + +
437A HIS* 2.8 17.4 - - + -
438A ARG* 3.3 11.2 + - - -
442A ALA 2.7 21.0 + - - -
443A PRO* 1.3 70.3 - - - +
445A TYR* 1.3 69.9 + - - +
519A GLU* 3.1 14.8 + - - +
520A TYR* 2.8 48.1 + - + -
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Residues in contact with TYR 445 (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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346A TYR 3.0 8.4 + - - +
347A MET* 3.3 18.5 - - + -
348A VAL* 2.9 25.8 + - - +
443A PRO* 4.8 7.0 - - + -
444A THR* 1.3 86.5 - - - +
446A MET* 1.3 67.2 + - - +
503A PHE* 3.9 13.9 - + - -
507A GLY 3.7 16.5 + - - -
508A ASN* 3.0 28.2 + - - +
509A PRO* 3.5 31.9 - - + -
510A ASN* 4.3 1.5 + - - -
517A TRP* 3.7 26.5 - + + +
518A PRO 3.6 15.9 - - - -
519A GLU* 3.8 29.9 + - + +
520A TYR* 4.1 3.1 - - - +
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Residues in contact with MET 446 (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 VAL* 3.1 28.0 - - + +
349A GLY* 4.8 1.6 - - - +
350A ILE* 5.5 0.7 - - + -
430A SER* 3.8 31.9 - - - +
431A VAL* 4.0 16.8 - - + +
434A ALA* 3.2 27.4 - - + -
444A THR* 4.9 0.2 - - + -
445A TYR* 1.3 79.0 - - - +
447A TYR* 1.3 62.0 + - - +
517A TRP* 3.0 24.2 + - - +
518A PRO 5.5 0.2 + - - -
520A TYR* 3.5 41.1 - - + +
525A GLY 5.0 1.0 + - - -
526A TYR* 3.5 13.1 - - + +
527A LEU 3.2 9.5 + - - -
539A LEU* 4.2 14.6 - - + -
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Residues in contact with TYR 447 (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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244A ILE* 4.9 0.7 - - + -
245A SER 4.5 3.6 - - - -
246A GLU* 3.3 35.1 - - + +
347A MET* 4.1 20.2 - - + -
348A VAL 3.4 3.4 + - - -
349A GLY* 3.4 28.9 - - - -
350A ILE 3.3 30.8 + - - -
351A ASN* 4.4 3.5 + - - -
446A MET* 1.3 78.0 - - - +
448A GLU* 1.3 67.1 + - - +
449A PHE* 3.7 19.3 - + + -
471A GLU* 3.9 10.4 - - + +
500A TRP* 3.7 29.8 - + - -
517A TRP* 3.6 12.3 - - + -
526A TYR* 4.5 3.8 - - - -
527A LEU 3.2 13.7 - - - +
529A ILE* 3.8 18.6 - - + -
539A LEU* 4.0 7.7 - - - +
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Residues in contact with GLU 448 (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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350A ILE* 3.2 22.7 - - + +
351A ASN 4.3 7.8 - - - +
352A LYS* 3.3 33.9 - - + +
447A TYR* 1.3 76.9 - - - +
449A PHE* 1.3 62.6 + - - +
450A GLN* 3.5 10.3 + - - +
526A TYR* 3.8 23.3 + - + -
527A LEU 3.0 7.6 + - - +
528A GLN* 3.8 10.0 + - + +
529A ILE 3.1 22.7 + - - +
539A LEU* 3.3 26.6 - - + +
540A LYS* 4.8 6.8 + - - -
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Residues in contact with PHE 449 (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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350A ILE 3.0 7.5 + - - -
351A ASN* 3.2 21.2 - - - +
352A LYS 2.9 24.2 + - - -
447A TYR* 3.7 9.9 - + + -
448A GLU* 1.3 70.2 - - - +
450A GLN* 1.3 60.0 + - - +
451A TYR* 3.7 28.9 - + + -
453A PRO* 5.1 1.1 - - + -
466A GLY* 3.7 3.6 - - - -
470A ASP* 3.7 12.8 - - + -
471A GLU* 3.4 42.8 - - + -
474A SER* 3.8 17.9 - - - -
492A LEU* 3.6 33.2 - - + -
496A VAL* 4.6 4.0 - - + -
529A ILE* 3.7 26.5 - - + -
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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