Contacts of the strand formed by residues 479 - 484 (chain C) in PDB entry 4JVG
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 ASP 479 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473C LYS* 4.2 14.5 + - - -
474C GLY 3.7 5.7 - - - +
475C LYS* 2.9 25.5 + - - +
476C TRP 4.5 0.2 - - - +
477C HIS 5.0 1.0 - - - +
478C GLY* 1.3 72.1 - - - -
480C VAL* 1.3 68.8 + - - +
517C MET* 4.8 4.5 - - - +
530C GLN* 4.7 2.1 - - - -
531C TRP* 3.5 38.7 + - + +
562D ARG* 3.7 21.4 + - - +
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Residues in contact with VAL 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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457C ILE* 4.6 3.4 - - + -
473C LYS* 3.7 5.4 - - - +
474C GLY* 2.8 49.1 + - - +
475C LYS 3.8 3.1 - - - +
476C TRP* 3.6 30.5 - - + +
479C ASP* 1.3 86.0 - - - +
481C ALA* 1.3 60.6 + - - +
482C VAL* 4.0 11.9 - - + -
517C MET* 4.0 14.8 - - - -
528C VAL* 3.7 23.1 - - + -
529C THR 3.4 8.7 - - - +
531C TRP* 3.8 14.6 - - - +
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Residues in contact with ALA 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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471C VAL* 5.3 2.9 - - + -
472C TYR 3.5 7.6 - - - +
480C VAL* 1.3 72.4 - - - +
482C VAL* 1.3 63.3 + - - +
527C ILE 3.6 0.7 - - - +
528C VAL* 3.4 4.2 - - - +
529C THR* 2.8 40.7 + - - +
530C GLN 4.1 0.6 + - - -
531C TRP* 3.8 13.7 - - + -
801C B96 3.5 43.0 - - + +
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Residues in contact with VAL 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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457C ILE* 4.4 16.8 - - + -
459C VAL* 4.5 15.3 - - + -
470C THR 3.2 1.9 - - - +
471C VAL* 2.9 24.5 - - - -
472C TYR* 3.0 17.9 + - - +
474C GLY* 4.2 10.5 - - - -
480C VAL* 4.0 18.8 - - + -
481C ALA* 1.3 79.8 - - - +
483C LYS* 1.3 60.3 + - - +
484C MET* 4.3 9.2 - - + -
526C ALA* 3.9 24.7 - - + -
527C ILE 3.2 9.0 - - - +
528C VAL* 4.3 12.3 - - + -
801C B96 3.9 2.0 - - - -
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Residues in contact with LYS 483 (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 PHE 5.8 0.4 - - - +
469C GLY* 5.0 1.6 - - - -
470C THR 3.2 8.5 - - - +
471C VAL* 3.6 13.0 - - + -
482C VAL* 1.3 70.8 - - - +
484C MET* 1.3 65.7 + - - +
485C LEU* 4.5 15.1 - - + +
501C GLU* 3.2 40.8 + - - +
526C ALA* 3.1 4.2 - - - -
527C ILE* 2.7 40.2 + - + +
594C ASP 4.2 9.7 + - - -
595C PHE* 5.5 0.8 + - - +
596C GLY 4.2 12.1 + - - -
597C LEU* 3.8 29.2 - - + +
801C B96 3.3 35.5 - - + -
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Residues in contact with MET 484 (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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459C VAL* 4.0 16.4 - - + -
469C GLY* 3.1 23.9 - - - -
470C THR 3.0 9.7 + - - +
472C TYR* 3.1 37.9 - - + +
482C VAL* 4.2 6.7 - - + +
483C LYS* 1.3 82.6 - - - +
485C LEU* 1.3 65.9 + - - +
486C ASN* 3.1 16.0 + - - +
524C GLN* 2.6 55.9 - - + +
525C LEU 3.4 7.4 - - - +
526C ALA* 4.2 14.4 - - + -
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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