Contacts of the strand formed by residues 477 - 483 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.8 38.8 - - + +
50B LYS* 4.3 4.0 + - - +
51B GLY* 2.7 31.4 + - - -
52B ARG* 2.8 25.2 + - + +
53B ASP 4.5 0.4 - - - -
54B PRO* 3.8 27.6 - - + -
57B ALA* 4.4 7.0 - - + -
470B ILE* 3.9 8.5 - - + -
471B VAL 3.9 4.5 - - - -
472B GLN* 4.6 1.3 - - - +
476B LYS* 1.3 71.0 - - - +
478B GLU* 1.3 64.9 + - - +
479B ASN* 3.7 26.7 - - - +
480B PHE* 3.9 26.5 - - + +
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Residues in contact with GLU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 2.8 40.9 + - - +
471B VAL* 2.9 27.2 + - + +
472B GLN 4.4 1.3 - - - -
473B ARG* 4.0 33.6 - - + +
476B LYS* 3.5 9.4 + - - +
477B ILE* 1.3 79.4 - - - +
479B ASN* 1.3 62.4 + - + +
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Residues in contact with ASN 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 5.7 2.2 - - - +
336B PRO 5.0 0.2 - - - -
337B TYR* 3.3 22.8 + - - -
338B LYS* 4.2 1.0 - - - +
339B GLY 3.2 27.1 + - - +
469B TRP 4.3 1.3 - - - -
470B ILE* 3.4 6.6 - - - +
471B VAL* 2.9 45.0 + - + +
477B ILE* 3.6 4.4 - - - +
478B GLU* 1.3 79.9 - - + +
480B PHE* 1.3 65.7 + - - +
481B GLN* 3.4 23.6 - - - +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLU* 3.2 29.1 + - - +
49B LEU* 3.5 28.3 - - + -
57B ALA* 3.6 19.5 - - + -
61B THR* 4.0 3.4 - - + -
76B SER* 3.1 29.2 - - - -
79B ALA* 5.0 1.6 - - + -
80B VAL* 4.7 6.3 - - + -
468B HIS* 3.7 28.0 - - + -
469B TRP 3.2 6.1 - - - -
470B ILE* 3.8 33.2 - - + -
477B ILE* 3.9 24.5 - - + +
479B ASN* 1.3 73.8 + - - +
481B GLN* 1.3 64.2 + - - +
482B LEU* 3.6 18.6 - - + -
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Residues in contact with GLN 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLU* 3.7 13.7 + - - +
321B GLU* 3.9 9.6 + - - +
336B PRO* 3.0 38.8 - - + +
339B GLY* 3.8 21.6 - - - +
340B VAL 4.2 0.9 + - - -
341B THR* 3.5 13.9 + - - -
358B LYS* 3.4 26.3 - - - +
468B HIS* 3.5 2.1 - - - -
469B TRP* 2.7 41.2 + - + +
479B ASN* 3.4 21.4 - - - +
480B PHE* 1.3 78.8 - - - +
482B LEU* 1.3 62.2 + - - +
483B VAL 4.3 0.2 - - - -
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 5.2 3.8 - - + -
46B GLU* 3.4 14.5 + - + +
49B LEU* 4.6 2.9 - - + -
61B THR* 4.0 13.9 - - + -
64B ALA* 4.4 8.1 - - + -
72B HIS* 3.9 16.6 - - + +
321B GLU* 4.0 0.9 - - - +
467B SER 3.7 4.3 - - - -
468B HIS* 3.7 26.0 - - + +
480B PHE* 3.6 33.2 - - + -
481B GLN* 1.3 70.2 - - - +
483B VAL* 1.3 66.2 + - - +
484B VAL* 4.0 5.4 - - + -
536B HIS* 3.1 37.9 + - + +
540B MG 2.2 31.7 - - - -
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ILE* 4.9 5.2 - - + -
321B GLU* 3.3 40.6 - - + +
336B PRO* 3.9 29.2 - - + -
360B PRO* 3.8 22.9 - - + -
465B MET 3.8 3.2 - - - +
466B LEU* 3.7 3.8 - - - +
467B SER* 2.9 41.1 + - - +
469B TRP* 4.1 4.7 - - + +
481B GLN* 5.1 0.2 - - + -
482B LEU* 1.3 75.4 - - - +
484B VAL* 1.3 60.7 + - - +
487B THR* 4.9 0.9 - - - -
488B TRP* 3.8 19.6 + - + +
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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