Contacts of the strand formed by residues 475 - 482 (chain C) in PDB entry 4YFI
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 GLY 475 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472C GLY 3.1 25.1 + - - +
473C SER 3.3 3.0 + - - -
474C PHE* 1.3 88.6 - - - +
476C LYS* 1.3 69.6 + - - +
491C ARG 3.4 12.3 - - - -
493C ARG* 4.1 9.6 - - - -
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Residues in contact with LYS 476 (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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468C ILE* 4.2 24.3 - - + +
470C GLY 4.0 9.0 - - - +
471C SER* 4.0 21.1 - - - +
474C PHE* 4.2 1.8 - - - -
475C GLY* 1.3 80.2 - - - +
477C VAL* 1.3 66.2 + - - +
478C TYR* 3.6 33.5 - - + +
489C ILE 3.5 1.9 - - - +
490C LYS* 3.5 0.9 - - - +
491C ARG* 2.9 31.9 + - + +
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Residues in contact with VAL 477 (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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468C ILE* 3.6 5.0 - - - +
469C ILE* 2.9 37.5 + - + -
470C GLY* 3.2 24.7 + - - +
471C SER 4.9 0.2 - - - +
474C PHE* 4.4 9.0 - - + -
476C LYS* 1.3 79.5 - - - +
478C TYR* 1.3 63.3 + - - +
488C ALA* 4.7 0.9 - - + -
489C ILE 3.3 13.5 - - - +
490C LYS* 4.1 18.4 - - + -
801C 4CW 3.5 56.3 - - + -
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Residues in contact with TYR 478 (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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465C PHE* 3.8 34.3 - + + -
466C HIS 3.5 19.7 - - - +
467C GLU 3.3 4.5 - - - +
468C ILE* 3.7 24.4 - - + +
469C ILE* 3.8 6.0 - - - +
476C LYS* 3.6 40.0 - - + +
477C VAL* 1.3 76.0 - - - +
479C LYS* 1.3 70.1 + - - +
488C ALA* 3.3 7.1 - - - +
489C ILE* 2.8 48.3 + - + +
491C ARG* 3.8 17.6 - - + +
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Residues in contact with LYS 479 (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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465C PHE 3.8 0.2 - - - -
466C HIS* 2.7 40.2 + - + +
467C GLU* 2.9 42.9 + - - +
469C ILE* 3.9 11.7 - - + +
478C TYR* 1.3 79.1 - - - +
480C GLY* 1.3 61.1 + - - +
486C ILE* 3.8 32.2 - - + +
487C VAL 3.7 5.2 - - - +
541C TYR* 3.7 43.1 + - + +
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Residues in contact with GLY 480 (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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464C GLU 3.1 13.5 - - - -
466C HIS* 4.1 14.4 - - - -
479C LYS* 1.3 79.5 - - - +
481C ARG* 1.3 62.0 + - - +
486C ILE* 3.5 10.7 - - - +
487C VAL* 2.9 32.9 + - - +
489C ILE* 3.6 7.1 - - - +
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Residues in contact with ARG 481 (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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462C GLU 3.9 0.6 - - - +
463C ILE* 3.5 4.7 - - - +
464C GLU* 2.8 53.1 + - + +
466C HIS* 4.5 17.2 - - + -
480C GLY* 1.3 75.0 + - - +
482C CYS* 1.3 66.0 + - - +
484C ASN* 3.5 44.6 + - - +
485C LYS 3.3 15.5 - - - +
486C ILE* 3.4 32.0 - - - +
487C VAL* 3.8 2.8 - - - +
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Residues in contact with CYS 482 (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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458C LEU* 3.9 39.9 - - - -
462C GLU* 3.5 15.7 - - - +
463C ILE* 4.3 9.9 - - + -
481C ARG* 1.3 77.1 - - - +
483C ARG* 1.3 86.7 + - - +
484C ASN 3.1 0.7 - - - +
485C LYS* 2.9 24.6 + - - +
487C VAL* 3.9 19.6 - - + +
525C VAL* 5.2 4.9 - - + -
538C VAL* 4.5 4.5 - - + -
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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