Contacts of the strand formed by residues 449 - 454 (chain E) in PDB entry 1Y8R
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 GLU 449 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442E TYR* 4.8 5.2 - - - +
447E LYS 3.6 6.0 + - - +
448E PRO* 1.3 76.2 - - - +
450E VAL* 1.3 73.3 + - - +
516E ARG* 2.9 32.8 + - - -
528E LEU* 3.8 1.1 - - - +
529E LEU* 3.3 25.7 - - + +
531E ASN* 3.0 30.2 + - - +
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Residues in contact with VAL 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442E TYR* 3.8 34.1 - - + -
449E GLU* 1.3 80.8 - - - +
451E THR* 1.3 59.4 + - - +
452E VAL* 4.9 0.9 - - + -
473E PHE* 4.2 17.7 - - + -
528E LEU* 3.9 18.6 - - + -
529E LEU 2.9 15.0 + - - +
530E ILE* 4.2 16.2 - - + -
531E ASN* 2.8 36.5 + - - +
546E VAL* 5.1 8.1 - - + -
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Residues in contact with THR 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 1.3 74.7 - - - +
452E VAL* 1.3 68.7 + - - +
531E ASN* 3.2 32.6 + - + +
533E LEU* 3.7 25.1 - - + -
546E VAL* 3.7 6.8 - - - +
547E VAL* 3.1 50.2 + - + +
548E GLY 4.5 2.4 + - - +
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Residues in contact with VAL 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 4.9 1.3 - - + -
451E THR* 1.3 82.4 - - - +
453E ARG* 1.3 72.5 + - - +
454E LEU* 4.1 13.7 - - + +
468E ILE* 4.6 9.2 - - + -
473E PHE* 3.9 25.1 - - + -
530E ILE* 3.8 25.1 - - + +
531E ASN 2.7 11.0 + - - +
532E ILE* 3.6 5.9 - - + -
533E LEU* 2.8 24.9 + - - +
544E PHE* 4.2 17.7 - - + -
545E GLU 3.2 13.5 - - - +
546E VAL* 4.5 5.8 - - + -
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Residues in contact with ARG 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E VAL* 1.3 73.9 - - - +
454E LEU* 1.3 67.4 + - - +
533E LEU* 3.2 25.5 - - + +
534E HIS 4.8 0.2 - - - -
535E SER* 3.5 31.0 - - - -
538E LEU* 4.0 13.4 - - + +
544E PHE* 3.3 2.4 - - - +
545E GLU* 2.8 61.8 + - + +
547E VAL* 3.7 35.8 - - + +
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Residues in contact with LEU 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E VAL* 4.1 9.4 - - + +
453E ARG* 1.3 79.3 - - - +
455E ASN* 1.3 63.4 + - - +
456E VAL 3.4 3.0 + - - +
459E VAL* 3.7 28.3 - - + -
464E LEU* 5.3 0.9 - - + -
468E ILE* 4.2 19.3 - - + -
506E LEU* 3.9 16.6 - - + -
532E ILE* 3.4 38.4 - - + -
533E LEU 2.7 14.0 + - - +
534E HIS* 3.1 5.9 - - - -
535E SER 3.0 23.2 + - - -
538E LEU* 4.3 7.6 - - - -
543E GLU 3.6 17.7 - - - +
544E PHE* 4.0 2.7 - - + -
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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