Contacts of the strand formed by residues 452 - 461 (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 GLU 452 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450L PRO* 3.9 6.5 - - - +
451L THR* 1.3 79.0 + - + +
453L SER* 1.3 62.5 + - - +
472L GLN* 3.2 9.9 - - - +
473L ARG* 3.6 36.6 + - + +
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Residues in contact with SER 453 (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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83L CYS* 2.6 36.7 + - - -
450L PRO* 3.1 12.2 - - - +
452L GLU* 1.3 72.9 - - - +
454L GLN* 1.3 59.1 + - - +
471L VAL* 3.5 3.9 - - - +
472L GLN* 2.7 58.3 + - - +
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Residues in contact with GLN 454 (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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82L ASN* 4.4 3.1 + - - +
83L CYS* 3.2 14.8 - - - +
337L TYR* 3.6 43.1 + - + +
453L SER* 1.3 75.8 - - - +
455L GLY* 1.3 57.8 + - - +
470L ILE 3.0 15.7 - - - +
471L VAL* 4.0 17.7 - - + +
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Residues in contact with GLY 455 (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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79L ALA* 3.7 9.9 - - - -
82L ASN* 3.3 13.7 - - - -
83L CYS* 3.3 15.4 - - - +
337L TYR* 3.1 14.0 + - - -
454L GLN* 1.3 75.9 - - - +
456L VAL* 1.3 58.6 + - - +
468L HIS 4.0 0.2 - - - +
469L TRP* 3.6 0.3 - - - -
470L ILE* 2.8 32.2 + - - +
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Residues in contact with VAL 456 (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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78L ARG 4.0 1.2 - - - +
79L ALA* 3.7 5.2 - - - -
82L ASN* 3.0 29.6 + - - +
316L PRO* 5.9 1.3 - - + -
337L TYR* 3.8 12.1 - - + +
455L GLY* 1.3 75.1 - - - +
457L GLY* 1.3 65.1 + - - +
458L PHE* 3.5 48.6 + - + -
467L SER* 4.2 0.9 - - - -
468L HIS 3.3 11.4 - - - +
469L TRP* 3.8 26.9 - - + -
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Residues in contact with GLY 457 (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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75L ALA* 3.6 25.6 - - - +
78L ARG* 3.8 10.3 - - - -
79L ALA* 3.6 8.5 - - - +
456L VAL* 1.3 71.0 - - - +
458L PHE* 1.3 60.6 - - - -
466L LEU 3.7 0.3 - - - +
467L SER* 3.0 9.2 - - - -
468L HIS 3.0 31.6 + - - -
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Residues in contact with PHE 458 (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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78L ARG* 3.0 15.3 + - - +
283L CYS* 3.7 19.1 - - + -
293L LEU* 4.3 20.2 - - + -
296L ARG* 2.9 27.3 + - - +
314L PHE* 4.0 11.0 - + - -
316L PRO* 3.6 34.5 - - + -
319L ILE* 5.2 0.2 - - + -
456L VAL* 3.5 36.6 - - + -
457L GLY* 1.3 69.9 - - - -
459L VAL* 1.3 64.7 - - - +
465L MET* 3.0 34.8 - - + -
466L LEU 3.4 1.1 - - - -
467L SER* 3.6 15.3 - - - -
469L TRP* 4.3 4.5 - + - -
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Residues in contact with VAL 459 (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* 4.0 12.3 - - + +
74L LEU* 3.8 7.0 - - + -
75L ALA* 3.5 36.8 - - - +
78L ARG* 3.6 14.8 - - - +
100L MET* 3.3 34.1 - - + -
283L CYS* 3.5 7.1 - - - -
285L GLU* 3.4 5.6 - - - +
458L PHE* 1.3 79.4 - - - +
460L ASN* 1.3 60.1 + - - +
461L ALA* 3.5 7.4 - - - +
466L LEU* 2.6 50.7 + - + +
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Residues in contact with ASN 460 (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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100L MET* 4.5 0.5 - - - +
104L TYR* 2.6 36.7 + - - -
281L LEU 5.0 0.6 + - - -
282L THR* 3.1 25.9 + - - +
283L CYS* 4.0 2.5 - - - +
284L GLY* 3.5 24.2 - - - +
285L GLU* 2.7 20.8 + - + +
298L THR* 5.7 0.9 + - - -
370L GLY 5.4 0.2 - - - +
374L SER* 3.1 21.4 + - - -
417L GLN* 4.2 3.8 - - - +
459L VAL* 1.3 73.8 - - - +
461L ALA* 1.3 63.5 + - - +
464L GLY* 3.4 6.7 - - - -
465L MET* 3.3 30.9 - - - +
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Residues in contact with ALA 461 (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* 3.9 17.0 - - + -
100L MET* 4.8 0.2 - - - -
104L TYR* 4.1 2.7 + - - -
417L GLN* 4.5 1.4 + - - -
459L VAL* 3.5 4.4 - - + -
460L ASN* 1.3 84.7 - - - +
462L PRO* 1.3 79.9 - - + +
463L ARG 3.0 0.7 - - - +
464L GLY* 2.8 26.0 + - - +
466L LEU* 4.4 5.8 - - + -
485L PRO* 4.6 0.4 - - + -
537L FCO 3.5 33.9 - - - +
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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