Contacts of the strand formed by residues 448 - 453 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446C PRO* 3.9 8.9 + - + +
447C GLN* 1.3 81.7 - - - +
449C LYS* 1.3 62.3 + - - +
477C GLU 4.4 1.0 + - - -
478C PRO* 3.1 27.6 + - - +
479C ASN* 4.0 9.6 - - - -
480C HIS* 2.9 37.2 + - - +
481C ILE* 3.9 10.8 - - + -
571C TYR* 3.2 5.4 - - - +
572C GLY 2.8 40.8 + - - +
573C THR* 4.2 6.4 - - - +
574C ALA* 3.8 22.7 - - - +
276D ARG* 4.4 0.9 - - - +
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Residues in contact with LYS 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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448C ARG* 1.3 77.8 - - - +
450C CYS* 1.3 60.6 + - - +
451C ILE* 4.1 18.3 + - + +
479C ASN* 2.9 23.0 + - - +
569C VAL* 3.8 18.6 - - + -
570C LEU 3.2 3.1 - - - -
571C TYR* 3.4 31.9 - - + -
603C FMT 2.9 21.2 + - - +
269D LEU* 4.1 11.5 + - - +
272D GLU* 2.6 38.6 + - - +
273D ALA* 5.1 0.4 - - - +
276D ARG* 3.9 28.0 - - - +
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Residues in contact with CYS 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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449C LYS* 1.3 73.0 - - - +
451C ILE* 1.3 62.1 + - - +
452C ILE* 4.0 16.7 + - - +
473C ALA* 3.4 10.8 - - - +
474C CYS* 2.0 55.9 - - - -
479C ASN* 3.4 13.9 - - - +
481C ILE* 4.1 7.5 - - + +
568C LEU 3.7 1.4 - - - +
569C VAL* 3.6 1.9 - - - -
570C LEU* 2.8 48.5 + - + +
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Residues in contact with ILE 451 (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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449C LYS* 4.1 28.8 + - + +
450C CYS* 1.3 75.2 - - - +
452C ILE* 1.3 68.8 + - - +
474C CYS* 4.5 3.5 - - - -
479C ASN* 4.5 1.2 - - - +
567C THR* 3.8 21.5 - - + -
568C LEU 3.8 2.9 - - - -
569C VAL* 4.5 8.5 - - + +
234D ALA* 4.0 15.5 - - + -
237D ALA* 3.7 30.7 - - + +
238D ARG* 3.6 37.2 + - + +
269D LEU* 4.0 20.9 - - + +
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Residues in contact with ILE 452 (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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450C CYS* 4.0 16.4 - - - -
451C ILE* 1.3 80.7 - - - +
453C ASP* 1.3 66.2 + - - +
454C ILE* 3.4 18.5 + - + +
469C LYS* 4.7 8.5 - - - -
471C VAL* 3.8 34.5 - - + -
472C THR 5.5 0.2 - - - +
473C ALA* 4.5 3.4 - - - +
474C CYS 5.4 0.4 - - - +
567C THR* 4.1 2.2 - - - -
568C LEU* 2.8 48.2 + - + +
570C LEU* 3.8 28.9 - - + -
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Residues in contact with ASP 453 (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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451C ILE* 4.2 2.4 + - - +
452C ILE* 1.3 75.2 - - - +
454C ILE* 1.3 63.4 + - - +
455C LEU 4.8 10.5 + - - +
469C LYS* 5.1 4.0 + - - -
565C LYS* 4.0 12.8 - - - +
566C PHE 3.4 11.4 + - - +
567C THR* 2.7 29.6 + - - +
232D THR* 4.1 24.8 + - - +
234D ALA* 3.9 18.9 - - + +
238D ARG* 5.9 1.6 - - - +
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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