Contacts of the strand formed by residues 464 - 473 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370L GLY* 3.5 20.3 - - - -
460L ASN* 3.4 14.1 - - - -
461L ALA* 2.8 38.8 + - - +
462L PRO 3.4 1.0 + - - -
463L ARG* 1.3 81.0 - - - +
465L MET* 1.3 62.6 + - - -
466L LEU 3.3 1.4 + - - -
485L PRO* 3.5 6.2 - - - +
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Residues in contact with MET 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L LEU* 4.0 27.4 - - + -
282L THR* 4.6 0.9 - - - -
283L CYS* 3.0 33.0 - - + +
314L PHE* 3.8 20.2 - - + -
319L ILE* 5.0 6.5 - - + -
369L VAL* 4.0 9.8 - - + +
458L PHE* 3.0 42.6 - - + -
459L VAL 3.7 2.0 - - - -
460L ASN* 3.3 8.5 - - - +
464L GLY* 1.3 68.0 - - - -
466L LEU* 1.3 63.6 + - - +
467L SER* 3.5 19.5 - - - +
483L VAL 3.8 5.7 - - - +
484L VAL 3.9 1.0 - - - -
485L PRO* 3.5 21.5 - - - +
488L TRP* 4.0 15.3 + - - -
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Residues in contact with LEU 466 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L VAL* 3.6 37.9 - - + +
72L HIS* 3.7 25.6 - - + +
75L ALA* 4.1 12.3 - - + -
458L PHE* 3.4 3.1 - - - -
459L VAL* 2.6 49.3 + - + +
461L ALA* 4.4 2.0 - - + -
464L GLY 3.3 3.7 + - - +
465L MET* 1.3 76.4 - - - +
467L SER* 1.3 67.5 + - - +
468L HIS* 3.7 12.6 - - + +
483L VAL 3.7 10.1 - - - +
484L VAL* 3.9 9.9 - - + -
485L PRO* 4.0 2.7 - - + -
537L FCO 3.3 25.1 - - - +
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Residues in contact with SER 467 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L ILE* 5.3 2.4 - - - +
456L VAL* 4.2 0.4 - - - -
457L GLY 3.0 9.6 - - - -
458L PHE* 3.6 10.5 - - - -
465L MET* 3.5 21.4 - - - +
466L LEU* 1.3 76.7 - - - +
468L HIS* 1.3 64.1 - - - +
469L TRP* 2.7 31.5 + - - -
482L LEU* 3.7 1.2 - - - -
483L VAL* 2.9 40.8 + - - +
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Residues in contact with HIS 468 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L THR* 3.8 9.2 - - - -
72L HIS* 2.9 56.4 + - + -
75L ALA* 3.5 25.2 - - + +
76L SER* 2.8 24.5 + - - -
79L ALA* 3.3 5.5 - - + +
456L VAL* 3.3 5.2 - - - +
457L GLY 3.0 29.1 + - - -
466L LEU* 3.7 10.8 - - + +
467L SER* 1.3 79.2 - - - +
469L TRP* 1.3 62.0 + - - +
480L PHE* 3.7 19.6 - + + -
481L GLN 3.5 3.6 - - - -
482L LEU* 3.7 14.4 - - + +
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Residues in contact with TRP 469 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316L PRO* 3.9 20.0 - - + -
317L ASP* 5.8 0.7 - - - -
319L ILE* 4.2 14.8 - - + -
335L HIS* 3.0 35.7 - + - -
336L PRO* 3.5 43.6 - - + +
337L TYR* 3.6 42.6 - + + -
455L GLY 3.6 4.0 - - - -
456L VAL* 3.8 23.8 - - + -
458L PHE* 4.3 4.3 - + - -
467L SER* 2.7 35.1 + - - -
468L HIS* 1.3 78.7 - - - +
470L ILE* 1.3 59.5 - - - +
471L VAL* 5.7 0.2 - - - -
479L ASN 3.9 0.7 - - - +
480L PHE* 3.2 8.4 + - - -
481L GLN* 2.7 40.7 + - - +
483L VAL* 4.1 3.9 - - + +
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Residues in contact with ILE 470 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L PRO* 3.7 35.7 - - + -
79L ALA* 3.5 31.9 - - + +
80L VAL* 4.2 8.7 - - + -
83L CYS* 4.0 11.9 - - + -
337L TYR* 3.5 1.0 - - - -
454L GLN* 3.0 7.4 - - - +
455L GLY 2.8 43.5 + - - +
469L TRP* 1.3 75.8 - - - +
471L VAL* 1.3 73.2 + - - +
472L GLN* 4.3 8.5 - - + +
477L ILE* 3.9 11.9 - - + -
479L ASN 3.4 9.9 - - - +
480L PHE* 3.8 21.3 - - + -
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Residues in contact with VAL 471 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337L TYR* 3.8 37.0 - - + +
453L SER 3.5 8.1 - - - +
454L GLN* 4.0 14.4 - - + +
470L ILE* 1.3 79.7 - - - +
472L GLN* 1.3 64.2 + - - +
477L ILE* 3.8 1.9 - - - -
478L GLU* 2.9 40.3 + - + +
479L ASN* 2.9 24.2 + - + +
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Residues in contact with GLN 472 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L PRO* 4.3 16.4 - - + -
83L CYS* 3.7 15.5 - - - -
449L TYR* 3.9 11.6 - - + -
450L PRO* 2.8 30.4 + - - +
452L GLU* 3.2 4.8 - - - +
453L SER* 2.7 71.3 + - - +
470L ILE* 4.1 6.7 - - + -
471L VAL* 1.3 79.1 - - - +
473L ARG* 1.3 64.1 + - - +
474L GLY 3.4 1.6 + - - -
475L GLY* 2.8 33.4 + - - -
476L LYS 3.5 11.2 - - - +
478L GLU* 4.4 2.9 - - - +
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Residues in contact with ARG 473 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451L THR* 3.3 39.1 + - - +
452L GLU* 3.6 28.2 + - + +
472L GLN* 1.3 75.7 - - - +
474L GLY* 1.3 66.4 + - - +
475L GLY 3.4 0.7 - - - -
476L LYS* 3.1 23.2 + - - +
478L GLU* 4.0 23.0 - - + +
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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