Contacts of the strand formed by residues 477 - 483 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49H LEU* 3.8 37.9 - - + +
50H LYS* 4.3 4.1 + - - +
51H GLY* 2.7 30.5 + - - -
52H ARG* 2.8 27.8 + - + +
53H ASP 4.5 0.9 - - - +
54H PRO* 3.8 26.5 - - + -
57H ALA* 4.4 6.1 - - + -
470H ILE* 3.9 8.7 - - + -
471H VAL 3.9 4.3 - - - -
472H GLN* 4.6 1.3 - - - +
476H LYS* 1.3 70.0 - - - +
478H GLU* 1.3 65.0 + - - +
479H ASN* 3.7 27.6 - - - +
480H PHE* 3.9 26.2 - - + +
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Residues in contact with GLU 478 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS* 2.8 41.2 + - - +
471H VAL* 2.9 27.5 + - + +
472H GLN 4.4 1.8 - - - -
473H ARG* 4.0 33.5 - - + +
476H LYS* 3.5 9.7 + - - +
477H ILE* 1.3 79.2 - - - +
479H ASN* 1.3 61.7 + - + +
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Residues in contact with ASN 479 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS* 5.7 2.6 - - - +
336H PRO 5.0 0.2 - - - -
337H TYR 3.3 23.4 + - - +
338H LYS* 4.2 1.0 - - - +
339H GLY 3.2 27.3 + - - +
469H TRP 4.3 1.8 - - - -
470H ILE* 3.4 7.3 - - - +
471H VAL* 2.9 45.5 + - + +
477H ILE* 3.6 4.5 - - - +
478H GLU* 1.3 80.2 - - + +
480H PHE* 1.3 65.1 + - - +
481H GLN* 3.4 23.0 - - - +
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Residues in contact with PHE 480 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H GLU* 3.2 29.3 + - - +
49H LEU* 3.5 26.0 - - + -
57H ALA* 3.6 19.1 - - + -
61H THR* 4.0 3.1 - - + -
76H SER* 3.1 29.6 - - - -
79H ALA* 5.0 1.3 - - + -
80H VAL* 4.7 6.1 - - + -
468H HIS* 3.7 28.0 - - + -
469H TRP 3.2 5.4 - - - -
470H ILE* 3.8 33.2 - - + -
477H ILE* 3.9 25.0 - - + +
479H ASN* 1.3 75.2 + - - +
481H GLN* 1.3 63.4 - - - +
482H LEU* 3.6 19.3 - - + -
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Residues in contact with GLN 481 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H GLU* 3.7 13.1 + - - +
321H GLU* 3.9 10.5 + - - +
336H PRO* 3.0 39.9 - - + +
339H GLY* 3.8 21.8 - - - -
340H VAL 4.5 0.9 - - - -
341H THR* 3.5 14.2 + - - -
358H LYS* 3.4 24.9 - - - +
468H HIS* 3.5 1.7 - - - -
469H TRP* 2.7 41.5 + - + +
479H ASN* 3.4 21.0 - - - +
480H PHE* 1.3 79.1 - - - +
482H LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 482 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 5.2 3.8 - - + -
46H GLU* 3.4 15.2 + - + +
49H LEU* 4.6 2.9 - - + -
61H THR* 4.0 14.1 - - + -
64H ALA* 4.4 7.4 - - + -
72H HIS* 3.9 17.0 - - + +
321H GLU* 4.0 0.9 - - - +
467H SER 3.7 3.6 - - - -
468H HIS* 3.7 26.0 - - + +
480H PHE* 3.6 33.2 - - + -
481H GLN* 1.3 70.9 - - - +
483H VAL* 1.3 67.5 + - - +
484H VAL* 4.0 5.6 - - + -
536H HIS* 3.1 37.2 + - + +
540H MG 2.2 31.2 - - - -
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Residues in contact with VAL 483 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319H ILE* 4.9 4.7 - - + -
321H GLU* 3.3 40.6 - - + +
336H PRO* 3.9 28.3 - - + -
360H PRO* 3.8 22.9 - - + -
465H MET 3.8 2.8 - - - +
466H LEU* 3.7 4.0 - - - +
467H SER* 2.9 40.7 + - - +
469H TRP* 4.1 5.2 - - + +
481H GLN* 5.1 0.2 - - + -
482H LEU* 1.3 76.0 - - - +
484H VAL* 1.3 60.7 + - - +
487H THR* 4.9 0.2 - - - -
488H 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