Contacts of the strand formed by residues 464 - 473 (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 GLY 464 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369F VAL 4.2 0.4 - - - -
370F GLY* 3.5 20.1 - - - -
460F ASN* 3.4 13.9 - - - -
461F ALA* 2.8 38.6 + - - +
462F PRO 3.4 1.4 + - - -
463F ARG* 1.3 79.9 - - - +
465F MET* 1.3 63.4 + - - -
466F LEU 3.3 1.2 + - - -
485F PRO* 3.5 7.0 - - - +
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Residues in contact with MET 465 (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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281F LEU* 4.0 26.9 - - + -
282F THR* 4.6 1.1 - - - -
283F CYS* 3.0 32.8 - - + +
314F PHE* 3.8 19.7 - - + -
319F ILE* 5.0 6.5 - - + -
369F VAL* 4.0 9.7 - - + +
458F PHE* 3.0 44.0 - - + -
459F VAL 3.7 2.0 - - - -
460F ASN* 3.3 8.5 - - - +
464F GLY* 1.3 67.5 - - - -
466F LEU* 1.3 63.5 + - - +
467F SER* 3.5 18.6 - - - +
483F VAL 3.8 6.1 - - - +
484F VAL 3.9 1.0 - - - -
485F PRO* 3.5 21.5 - - - +
488F TRP* 4.0 15.1 + - - -
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Residues in contact with LEU 466 (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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71F VAL* 3.6 37.9 - - + +
72F HIS* 3.7 25.1 - - + +
75F ALA* 4.1 11.9 - - + -
457F GLY 3.7 0.3 - - - +
458F PHE* 3.4 3.5 - - - -
459F VAL* 2.6 49.4 + - + +
461F ALA* 4.4 1.3 - - + -
464F GLY 3.3 3.7 + - - +
465F MET* 1.3 77.4 - - - +
467F SER* 1.3 67.1 + - - +
468F HIS* 3.7 12.8 - - + +
483F VAL 3.7 10.5 - - - +
484F VAL* 3.9 9.6 - - + -
485F PRO* 4.0 2.9 - - + -
537F FCO 3.3 24.9 - - - +
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Residues in contact with SER 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ILE* 5.3 2.1 - - - +
456F VAL* 4.2 0.4 - - - -
457F GLY 3.0 11.0 - - - -
458F PHE* 3.6 9.9 - - - -
465F MET* 3.5 22.5 - - - +
466F LEU* 1.3 76.1 - - - +
468F HIS* 1.3 62.9 - - - +
469F TRP* 2.7 33.4 + - - -
482F LEU* 3.7 0.9 - - - -
483F VAL* 2.9 40.8 + - - +
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Residues in contact with HIS 468 (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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61F THR* 3.8 9.0 - - - -
72F HIS* 2.9 56.2 + - + -
75F ALA* 3.5 23.6 - - + +
76F SER* 2.8 24.3 + - - -
79F ALA* 3.3 5.4 - - + +
456F VAL* 3.3 5.9 - - - +
457F GLY 3.0 28.8 + - - -
466F LEU* 3.7 10.9 - - + +
467F SER* 1.3 82.1 - - - +
469F TRP* 1.3 61.2 + - - +
480F PHE* 3.7 20.5 - + + -
481F GLN 3.5 3.4 - - - -
482F LEU* 3.7 15.2 - - + +
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Residues in contact with TRP 469 (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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316F PRO* 3.9 19.7 - - + -
317F ASP* 5.8 0.7 - - - -
319F ILE* 4.2 15.7 - - + -
335F HIS* 3.0 36.6 - + - -
336F PRO* 3.5 42.3 - - + +
337F TYR* 3.6 43.1 - + + -
455F GLY 3.6 3.4 - - - -
456F VAL* 3.8 24.5 - - + -
458F PHE* 4.3 4.3 - + - -
467F SER* 2.7 34.7 + - - -
468F HIS* 1.3 80.2 - - - +
470F ILE* 1.3 60.2 + - - +
471F VAL* 5.7 0.2 - - - -
479F ASN 3.9 0.9 - - - +
480F PHE* 3.2 7.9 - - - -
481F GLN* 2.7 41.1 + - + +
483F VAL* 4.1 3.9 - - + +
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Residues in contact with ILE 470 (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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54F PRO* 3.7 36.6 - - + -
79F ALA* 3.5 31.4 - - + +
80F VAL* 4.2 8.3 - - + +
83F CYS* 4.0 11.7 - - + -
337F TYR* 3.5 1.6 - - - -
454F GLN* 3.0 7.5 - - - +
455F GLY 2.8 43.6 + - - +
469F TRP* 1.3 74.2 - - - +
471F VAL* 1.3 73.6 + - - +
472F GLN* 4.3 8.1 - - + -
477F ILE* 3.9 11.7 - - + -
479F ASN 3.4 10.1 - - - +
480F PHE* 3.8 22.2 - - + -
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Residues in contact with VAL 471 (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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337F TYR* 3.8 35.9 - - + +
453F SER 3.5 8.7 - - - +
454F GLN* 4.0 13.9 - - + +
469F TRP 5.7 0.2 - - - -
470F ILE* 1.3 78.7 - - - +
472F GLN* 1.3 62.1 + - - +
477F ILE* 3.8 1.6 - - - -
478F GLU* 2.9 41.4 + - + +
479F ASN* 2.9 25.8 + - + +
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Residues in contact with GLN 472 (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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54F PRO* 4.3 15.7 - - + -
83F CYS* 3.7 15.3 - - - -
449F TYR* 3.9 12.0 - - + -
450F PRO* 2.8 31.1 + - - +
452F GLU* 3.2 5.1 - - - +
453F SER* 2.7 70.3 + - - +
470F ILE* 4.1 7.1 - - + -
471F VAL* 1.3 76.9 - - - +
473F ARG* 1.3 65.2 + - - +
474F GLY 3.4 2.3 + - - -
475F GLY* 2.8 32.2 + - - -
476F LYS 3.5 11.4 - - - +
478F GLU* 4.4 2.7 - - - +
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Residues in contact with ARG 473 (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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451F THR* 3.3 38.2 + - - +
452F GLU* 3.6 29.2 + - + +
472F GLN* 1.3 75.2 - - - +
474F GLY* 1.3 67.6 + - - +
475F GLY 3.4 0.2 - - - -
476F LYS* 3.1 22.3 + - - +
478F GLU* 4.0 23.9 - - + +
309J SER* 4.3 35.6 + - - +
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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