Contacts of the strand formed by residues 477 - 483 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49F LEU* 3.8 36.3 - - + +
50F LYS* 4.3 3.9 + - - +
51F GLY* 2.7 31.0 + - - -
52F ARG* 2.8 28.3 + - + +
53F ASP 4.5 0.7 - - - +
54F PRO* 3.8 26.9 - - + -
57F ALA* 4.4 6.5 - - + -
470F ILE* 3.9 8.7 - - + -
471F VAL 3.9 4.3 - - - -
472F GLN* 4.6 1.3 - - - +
476F LYS* 1.3 70.6 - - - +
478F GLU* 1.3 65.1 + - - +
479F ASN* 3.7 26.9 - - - +
480F PHE* 3.9 27.4 - - + +
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Residues in contact with GLU 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 2.8 40.4 + - - +
471F VAL* 2.9 28.1 + - + +
472F GLN 4.4 1.6 - - - -
473F ARG* 4.0 33.1 - - + +
476F LYS* 3.5 9.0 + - - +
477F ILE* 1.3 79.9 - - - +
479F ASN* 1.3 62.4 + - + +
307J ASP* 5.7 1.4 - - - +
309J SER* 6.6 0.2 - - - -
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Residues in contact with ASN 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 5.7 2.5 - - - +
337F TYR 3.3 23.2 + - - +
338F LYS 4.2 1.0 - - - -
339F GLY 3.2 27.6 + - - +
469F TRP 4.3 1.6 - - - -
470F ILE* 3.4 7.1 - - - +
471F VAL* 2.9 45.0 + - + +
477F ILE* 3.7 3.9 - - - +
478F GLU* 1.3 80.9 - - + +
480F PHE* 1.3 65.6 + - - +
481F GLN* 3.4 23.9 - - - +
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Residues in contact with PHE 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLU* 3.2 29.5 + - - +
49F LEU* 3.5 28.0 - - + -
57F ALA* 3.6 20.0 - - + -
61F THR* 4.0 3.4 - - + -
76F SER* 3.1 28.9 - - - -
79F ALA* 5.0 1.8 - - + -
80F VAL* 4.7 5.4 - - + -
468F HIS* 3.7 27.4 - - + -
469F TRP 3.2 5.6 - - - -
470F ILE* 3.8 33.2 - - + -
477F ILE* 3.9 24.7 - - + +
479F ASN* 1.3 73.3 + - - +
481F GLN* 1.3 64.5 + - - +
482F LEU* 3.6 18.8 - - + -
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Residues in contact with GLN 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLU* 3.7 13.3 + - - +
321F GLU* 3.9 9.8 + - - +
336F PRO* 3.0 40.1 - - + +
339F GLY* 3.8 22.3 - - - +
340F VAL* 4.5 1.0 - - - -
341F THR* 3.5 14.2 + - - -
358F LYS* 3.4 25.5 - - - +
468F HIS* 3.5 1.9 - - - -
469F TRP* 2.7 42.7 + - + +
479F ASN* 3.4 21.2 - - - +
480F PHE* 1.3 78.7 - - - +
482F LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 5.2 4.3 - - + -
46F GLU* 3.4 14.1 + - + +
49F LEU* 4.6 2.9 - - + -
61F THR* 4.0 14.4 - - + -
64F ALA* 4.4 7.0 - - + -
72F HIS* 3.9 17.3 - - + +
321F GLU* 4.0 0.7 - - - +
467F SER 3.7 4.0 - - - -
468F HIS* 3.7 26.5 - - + +
480F PHE* 3.6 32.1 - - + -
481F GLN* 1.3 70.4 - - - +
483F VAL* 1.3 68.8 + - - +
484F VAL* 4.0 4.9 - - + -
536F HIS* 3.1 36.9 + - + +
540F MG 2.2 31.2 - - - -
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Residues in contact with VAL 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F ILE* 4.9 5.4 - - + -
321F GLU* 3.3 40.6 - - + +
336F PRO* 3.9 28.3 - - + -
360F PRO* 3.8 23.1 - - + -
465F MET 3.8 3.3 - - - +
466F LEU* 3.7 3.3 - - - -
467F SER* 2.9 40.9 + - - +
469F TRP* 4.1 4.3 - - + +
481F GLN* 5.1 0.7 - - + -
482F LEU* 1.3 76.1 - - - +
484F VAL* 1.3 59.6 + - - +
487F THR* 4.9 0.9 - - - -
488F TRP* 3.8 18.3 + - + +
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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