Contacts of the strand formed by residues 477 - 483 (chain J) in PDB entry 2FRV
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 ILE 477 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49J LEU* 3.8 38.4 - - + +
50J LYS* 4.3 3.9 - - - +
51J GLY* 2.7 31.0 + - - -
52J ARG* 2.8 26.1 + - + +
53J ASP 4.5 0.7 - - - +
54J PRO* 3.8 26.2 - - + -
57J ALA* 4.4 6.5 - - + -
470J ILE* 3.9 8.3 - - + -
471J VAL 3.9 4.3 - - - -
472J GLN* 4.6 1.6 - - - +
476J LYS* 1.3 70.3 - - - +
478J GLU* 1.3 63.9 + - - +
479J ASN* 3.7 26.9 - - - +
480J PHE* 3.9 26.9 - - + +
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Residues in contact with GLU 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LYS* 2.8 41.0 + - - +
471J VAL* 2.9 27.7 + - + +
472J GLN 4.4 1.3 - - - -
473J ARG* 4.0 34.8 - - + +
476J LYS* 4.1 8.8 - - - +
477J ILE* 1.3 81.2 - - - +
479J ASN* 1.3 61.6 + - + +
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Residues in contact with ASN 479 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LYS* 5.7 2.6 - - - +
336J PRO 5.0 0.2 - - - -
337J TYR* 3.3 22.8 + - - +
338J LYS* 4.2 1.0 - - - +
339J GLY 3.2 26.8 + - - +
469J TRP 4.3 1.3 - - - -
470J ILE* 3.4 6.8 - - - +
471J VAL* 2.9 44.2 + - + +
477J ILE* 3.6 4.8 - - - +
478J GLU* 1.3 80.0 - - + +
480J PHE* 1.3 67.1 + - - +
481J GLN* 3.4 23.9 - - - +
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Residues in contact with PHE 480 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J GLU* 3.2 29.1 + - - +
49J LEU* 3.5 27.1 - - + -
50J LYS* 6.2 0.2 - - - +
57J ALA* 3.6 19.3 - - + -
61J THR* 4.0 3.4 - - + -
76J SER* 3.1 28.3 - - - -
79J ALA* 5.0 1.3 - - + -
80J VAL* 4.7 6.1 - - + -
468J HIS* 3.7 28.3 - - + -
469J TRP 3.2 5.8 - - - -
470J ILE* 3.8 33.2 - - + -
477J ILE* 3.9 24.3 - - + +
479J ASN* 1.3 74.3 + - - +
481J GLN* 1.3 63.0 + - - +
482J LEU* 3.6 18.8 - - + -
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Residues in contact with GLN 481 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J GLU* 3.7 13.3 + - - +
321J GLU* 3.9 9.8 + - - +
336J PRO* 3.0 39.9 - - + +
339J GLY* 3.8 21.3 - - - -
340J VAL* 4.2 1.0 + - - -
341J THR* 3.5 14.2 + - - -
358J LYS* 3.4 25.5 - - - +
468J HIS* 3.5 2.1 - - - -
469J TRP* 2.7 41.3 + - + +
479J ASN* 3.4 21.6 - - - +
480J PHE* 1.3 80.3 - - - +
482J LEU* 1.3 61.4 - - - +
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Residues in contact with LEU 482 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J LEU* 5.2 3.6 - - + -
46J GLU* 3.4 15.0 + - + +
49J LEU* 4.6 3.4 - - + -
61J THR* 4.0 13.0 - - + -
64J ALA* 4.4 7.6 - - + -
72J HIS* 3.9 16.8 - - + +
321J GLU* 4.0 0.9 - - - +
467J SER 3.7 4.7 - - - -
468J HIS* 3.7 27.1 - - + +
480J PHE* 3.6 32.3 - - + -
481J GLN* 1.3 71.0 - - - +
483J VAL* 1.3 67.5 + - - +
484J VAL* 4.0 5.4 - - + -
536J HIS* 3.1 38.2 + - + +
540J MG 2.2 30.7 - - - -
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Residues in contact with VAL 483 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319J ILE* 4.9 4.9 - - + -
321J GLU* 3.3 39.7 - - + +
336J PRO* 3.9 29.4 - - + -
360J PRO* 3.8 23.1 - - + -
465J MET 3.8 3.0 - - - +
466J LEU* 3.7 3.9 - - - +
467J SER* 2.9 41.4 + - - +
469J TRP* 4.1 4.3 - - + +
481J GLN* 5.1 0.2 - - + -
482J LEU* 1.3 76.2 - - - +
484J VAL* 1.3 58.9 + - - +
487J THR* 4.9 0.4 - - - -
488J TRP* 3.8 19.2 + - + +
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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