Contacts of the strand formed by residues 464 - 473 (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 GLY 464 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL 4.2 0.2 - - - -
370B GLY* 3.5 22.1 - - - -
460B ASN* 3.4 13.7 - - - -
461B ALA* 2.8 39.4 + - - +
462B PRO 3.4 0.8 - - - -
463B ARG* 1.3 79.3 - - - +
465B MET* 1.3 61.7 + - - -
466B LEU 3.3 1.2 + - - -
485B PRO* 3.5 7.2 - - - +
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Residues in contact with MET 465 (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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281B LEU* 4.0 27.8 - - + -
282B THR* 4.6 1.1 - - - -
283B CYS* 3.0 32.3 - - + +
314B PHE* 3.8 19.7 - - + -
319B ILE* 5.0 6.1 - - + -
369B VAL* 4.0 9.5 - - + +
458B PHE* 3.0 43.7 - - + -
459B VAL 3.7 2.0 - - - -
460B ASN* 3.3 8.5 - - - +
464B GLY* 1.3 68.8 - - - -
466B LEU* 1.3 62.0 - - - +
467B SER* 3.5 19.1 - - - +
483B VAL 3.8 6.2 - - - +
484B VAL 3.9 0.7 - - - -
485B PRO* 3.5 22.7 - - - +
488B TRP* 4.0 15.6 + - - -
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Residues in contact with LEU 466 (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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71B VAL* 3.6 38.1 - - + +
72B HIS* 3.7 26.5 - - + +
75B ALA* 4.1 11.4 - - + -
457B GLY 3.7 0.6 - - - +
458B PHE* 3.4 3.3 - - - -
459B VAL* 2.6 49.9 + - + +
461B ALA* 4.4 1.6 - - + -
464B GLY 3.3 3.5 + - - +
465B MET* 1.3 75.9 - - - +
467B SER* 1.3 68.1 + - - +
468B HIS* 3.7 12.3 - - + +
483B VAL 3.7 10.3 - - - +
484B VAL* 3.9 10.1 - - + -
485B PRO* 4.0 2.2 - - + -
537B FCO 3.3 24.2 - - - +
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Residues in contact with SER 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE* 5.3 1.9 - - - +
456B VAL* 4.2 0.7 - - - -
457B GLY 3.0 10.8 - - - -
458B PHE* 3.6 10.3 - - - -
465B MET* 3.5 21.1 - - - +
466B LEU* 1.3 75.7 - - - +
468B HIS* 1.3 63.7 + - - +
469B TRP* 2.7 33.3 + - - -
482B LEU* 3.7 1.0 - - - -
483B VAL* 2.9 41.2 + - - +
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Residues in contact with HIS 468 (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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61B THR* 3.8 9.6 - - - -
72B HIS* 2.9 56.2 + - + -
75B ALA* 3.5 26.3 - - + +
76B SER* 2.8 24.5 + - - -
79B ALA* 3.3 4.9 - - + +
456B VAL* 3.3 5.5 - - - +
457B GLY 3.0 29.1 + - - -
466B LEU* 3.7 10.3 - - + +
467B SER* 1.3 80.3 - - - +
469B TRP* 1.3 61.2 + - - +
480B PHE* 3.7 20.0 - + + -
481B GLN 3.5 2.7 - - - -
482B LEU* 3.7 14.8 - - + +
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Residues in contact with TRP 469 (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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316B PRO* 3.9 19.5 - - + -
317B ASP* 5.8 0.9 - - - -
319B ILE* 4.2 15.3 - - + -
335B HIS* 3.0 35.2 - + - -
336B PRO* 3.5 42.8 - - + +
337B TYR* 3.6 42.2 - + + -
455B GLY 3.6 4.0 - - - -
456B VAL* 3.8 23.8 - - + -
458B PHE* 4.3 4.5 - + - -
467B SER* 2.7 33.4 + - - -
468B HIS* 1.3 78.5 - - - +
470B ILE* 1.3 62.1 + - - +
471B VAL* 5.7 0.2 - - - -
479B ASN 3.9 0.9 - - - +
480B PHE* 3.2 8.1 - - - -
481B GLN* 2.7 41.8 + - + +
483B VAL* 4.1 4.5 - - + +
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Residues in contact with ILE 470 (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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54B PRO* 3.7 36.3 - - + -
79B ALA* 3.5 31.4 - - + +
80B VAL* 4.2 8.7 - - + +
83B CYS* 4.0 11.9 - - + -
337B TYR* 3.5 1.6 - - - -
454B GLN* 3.0 8.0 - - - +
455B GLY 2.8 43.7 + - - +
468B HIS 4.2 0.4 - - - -
469B TRP* 1.3 75.8 - - - +
471B VAL* 1.3 72.3 + - - +
472B GLN* 4.3 9.0 - - + +
477B ILE* 3.9 11.0 - - + -
479B ASN 3.4 9.9 - - - +
480B PHE* 3.8 21.1 - - + -
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Residues in contact with VAL 471 (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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337B TYR* 3.8 36.1 - - + +
453B SER 3.5 9.0 - - - +
454B GLN* 4.0 14.8 - - + +
469B TRP 5.7 0.4 - - - -
470B ILE* 1.3 80.9 - - - +
472B GLN* 1.3 64.1 + - - +
477B ILE* 3.8 1.9 - - - -
478B GLU* 2.9 41.3 + - + +
479B ASN* 2.9 24.1 + - + +
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Residues in contact with GLN 472 (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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54B PRO* 4.3 15.7 - - + -
83B CYS* 3.7 14.4 - - - -
449B TYR* 3.9 11.8 - - + -
450B PRO* 2.8 31.2 + - - +
452B GLU* 3.2 5.3 - - - +
453B SER* 2.7 72.1 + - - +
470B ILE* 4.1 7.4 - - + +
471B VAL* 1.3 77.8 - - - +
473B ARG* 1.3 63.6 + - - +
474B GLY 3.4 1.9 + - - -
475B GLY* 2.8 32.4 + - - -
476B LYS 3.5 11.2 - - - +
478B GLU* 4.4 2.5 - - - +
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Residues in contact with ARG 473 (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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451B THR* 3.3 38.7 + - - +
452B GLU* 3.6 29.0 + - + +
472B GLN* 1.3 74.9 - - - +
474B GLY* 1.3 66.4 + - - +
475B GLY 3.4 0.2 - - - -
476B LYS* 3.1 22.9 + - - +
478B GLU* 4.0 23.6 - - + +
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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