Contacts of the strand formed by residues 448 - 453 (chain E) in PDB entry 4RYD
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 ARG 448 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446E PRO* 4.0 8.3 + - + +
447E GLN* 1.3 81.6 - - - +
449E LYS* 1.3 61.9 + - - +
477E GLU 4.4 1.0 + - - -
478E PRO* 3.3 28.3 + - - +
479E ASN* 3.8 8.3 - - - -
480E HIS* 2.6 47.0 + - - +
481E ILE* 3.9 11.2 - - + -
571E TYR* 3.2 5.7 - - - -
572E GLY 2.8 40.6 + - - +
573E THR* 4.5 5.1 - - - +
574E ALA* 3.3 25.2 - - - +
276F ARG* 4.3 1.3 - - - +
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Residues in contact with LYS 449 (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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448E ARG* 1.3 76.7 - - - +
450E CYS* 1.3 61.4 + - - +
451E ILE* 4.0 25.0 + - + +
479E ASN* 2.9 22.8 - - - +
481E ILE* 4.4 0.2 - - - -
569E VAL* 3.7 20.6 - - + -
570E LEU 3.2 4.0 - - - +
571E TYR* 3.5 26.2 - - + -
603E FMT 2.7 24.7 + - - +
269F LEU* 4.2 6.0 + - - +
272F GLU* 2.7 38.1 + - - +
276F ARG* 3.8 27.0 - - - +
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Residues in contact with CYS 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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449E LYS* 1.3 72.3 - - - +
451E ILE* 1.3 61.5 + - - +
452E ILE* 3.9 16.7 + - - +
473E ALA* 3.4 10.5 - - - -
474E CYS* 2.1 58.6 - - - -
479E ASN* 3.8 11.4 - - - +
481E ILE* 3.9 10.5 - - + +
568E LEU 3.7 1.6 - - - +
569E VAL* 3.6 2.1 - - - -
570E LEU* 2.8 45.7 + - + +
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Residues in contact with ILE 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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449E LYS* 4.0 34.4 + - + +
450E CYS* 1.3 76.8 - - - +
452E ILE* 1.3 69.5 + - - +
474E CYS* 4.4 3.1 - - - -
479E ASN* 4.7 1.2 + - - -
567E THR* 3.8 23.6 - - + -
568E LEU 3.8 3.1 - - - +
569E VAL* 4.5 8.5 - - + -
234F ALA* 4.0 14.8 - - + -
237F ALA* 3.9 28.7 - - + -
238F ARG* 3.7 37.2 + - + +
269F LEU* 4.0 13.9 - - + +
273F ALA* 6.4 0.2 - - + -
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Residues in contact with ILE 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 CYS* 3.9 17.0 - - - -
451E ILE* 1.3 81.1 - - - +
453E ASP* 1.3 64.6 + - - +
454E ILE* 3.4 19.9 + - + +
469E LYS* 4.7 8.1 - - - -
471E VAL* 3.9 33.2 - - + -
473E ALA* 4.5 2.7 - - - +
474E CYS 5.7 0.2 - - - +
567E THR* 4.1 2.5 - - - -
568E LEU* 2.8 48.3 + - + +
570E LEU* 3.8 30.7 - - + -
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Residues in contact with ASP 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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451E ILE* 4.2 2.4 + - - +
452E ILE* 1.3 76.3 - - - +
454E ILE* 1.3 62.5 + - - +
455E LEU* 4.7 10.6 + - - +
469E LYS* 5.2 4.5 + - - -
565E LYS* 4.0 12.7 - - - +
566E PHE 3.4 11.8 + - - +
567E THR* 2.9 25.4 + - - +
232F THR* 3.8 18.9 + - - +
234F ALA* 3.7 25.6 - - + +
238F ARG* 6.0 1.2 - - - +
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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