Contacts of the strand formed by residues 464 - 473 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370J GLY* 3.5 21.0 - - - -
460J ASN* 3.4 13.0 - - - -
461J ALA* 2.8 38.9 + - - +
462J PRO 3.4 1.2 + - - -
463J ARG* 1.3 80.8 - - - +
465J MET* 1.3 62.7 + - - -
466J LEU 3.3 1.4 + - - -
485J PRO* 3.5 6.3 - - - +
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Residues in contact with MET 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281J LEU* 4.0 26.7 + - + -
282J THR* 4.6 1.3 - - - -
283J CYS* 3.0 32.5 - - + +
314J PHE* 3.8 19.5 - - + -
319J ILE* 5.0 7.0 - - + -
369J VAL* 4.0 10.0 - - + +
458J PHE* 3.0 43.7 - - + -
459J VAL 3.7 1.8 - - - -
460J ASN* 3.3 8.5 - - - +
464J GLY* 1.3 68.0 - - - -
466J LEU* 1.3 64.9 + - - +
467J SER* 3.5 18.6 - - - +
483J VAL 3.8 5.4 - - - +
484J VAL 3.9 0.7 - - - -
485J PRO* 3.5 21.8 - - - +
488J TRP* 4.0 14.9 + - - -
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Residues in contact with LEU 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J VAL* 3.6 37.0 - - + +
72J HIS* 3.7 26.5 - - + +
75J ALA* 4.1 11.9 - - + -
457J GLY 3.7 0.2 - - - +
458J PHE* 3.4 3.3 - - - -
459J VAL* 2.6 50.2 + - + +
461J ALA* 4.4 1.8 - - + -
464J GLY 3.3 3.8 + - - +
465J MET* 1.3 77.1 - - - +
467J SER* 1.3 67.6 + - - +
468J HIS* 3.7 12.6 - - + +
483J VAL 3.7 9.9 - - - +
484J VAL* 3.9 10.5 - - + -
485J PRO* 4.0 3.1 - - + -
537J FCO 3.3 24.2 - - - +
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Residues in contact with SER 467 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J ILE* 5.3 1.9 - - - +
456J VAL* 4.2 0.7 - - - -
457J GLY 3.0 10.3 - - - -
458J PHE* 3.6 10.1 - - - -
465J MET* 3.5 21.7 - - - +
466J LEU* 1.3 75.9 - - - +
468J HIS* 1.3 64.5 + - - +
469J TRP* 2.7 32.9 + - - -
482J LEU* 3.7 0.9 - - - -
483J VAL* 2.9 41.3 + - - +
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Residues in contact with HIS 468 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J THR* 3.8 9.2 - - - -
72J HIS* 2.9 56.8 + - + -
75J ALA* 3.5 24.8 - - + +
76J SER* 2.8 24.9 + - - -
79J ALA* 3.3 5.0 - - + +
456J VAL* 3.3 6.1 - - - +
457J GLY 3.0 28.4 + - - -
466J LEU* 3.7 11.0 - - + +
467J SER* 1.3 80.3 - - - +
469J TRP* 1.3 62.2 + - - +
480J PHE* 3.7 19.4 - + + -
481J GLN 3.5 2.9 - - - -
482J LEU* 3.7 15.0 - - + +
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Residues in contact with TRP 469 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316J PRO* 3.9 19.5 - - + -
317J ASP* 5.8 1.1 - - - -
319J ILE* 4.2 14.8 - - + -
335J HIS* 3.0 35.4 - + - -
336J PRO* 3.5 41.9 - - + +
337J TYR* 3.6 41.7 - + + -
455J GLY 3.6 3.6 - - - -
456J VAL* 3.8 24.2 - - + -
458J PHE* 4.3 3.8 - + - -
467J SER* 2.7 34.2 + - - -
468J HIS* 1.3 78.3 - - - +
470J ILE* 1.3 61.3 + - - +
471J VAL* 5.7 0.2 - - - -
479J ASN 3.9 0.9 - - - +
480J PHE* 3.2 8.2 - - - -
481J GLN* 2.7 42.7 + - + +
483J VAL* 4.1 4.9 - - + +
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Residues in contact with ILE 470 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J PRO* 3.7 35.7 - - + -
79J ALA* 3.5 31.2 - - + +
80J VAL* 4.2 9.2 - - + +
83J CYS* 4.0 11.2 - - + -
337J TYR* 3.5 1.2 - - - -
454J GLN* 3.0 7.1 - - - +
455J GLY 2.8 44.2 + - - +
468J HIS 4.2 0.2 - - - -
469J TRP* 1.3 75.2 - - - +
471J VAL* 1.3 72.7 + - - +
472J GLN* 4.3 9.4 - - + -
477J ILE* 3.9 11.2 - - + -
479J ASN 3.4 11.2 - - - +
480J PHE* 3.8 21.3 - - + -
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Residues in contact with VAL 471 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337J TYR* 3.8 36.6 - - + +
453J SER 3.5 9.0 - - - +
454J GLN* 4.0 14.8 - - + +
470J ILE* 1.3 80.1 - - - +
472J GLN* 1.3 64.4 + - - +
477J ILE* 3.8 1.6 - - - -
478J GLU* 2.9 41.8 + - + +
479J ASN* 2.9 23.1 + - + +
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Residues in contact with GLN 472 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J PRO* 4.3 16.2 - - + -
83J CYS* 3.7 14.8 - - - -
449J TYR* 3.9 11.8 - - + -
450J PRO* 2.8 31.2 + - - +
452J GLU* 3.2 4.9 - - - +
453J SER* 2.7 71.3 + - - +
470J ILE* 4.1 7.5 - - + +
471J VAL* 1.3 77.1 - - - +
473J ARG* 1.3 63.1 + - - +
474J GLY 3.4 1.9 + - - -
475J GLY* 2.8 32.6 + - - -
476J LYS 3.5 11.9 - - - +
478J GLU* 4.4 2.7 - - - -
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Residues in contact with ARG 473 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451J THR* 3.3 38.7 + - - +
452J GLU* 3.6 28.3 + - + +
472J GLN* 1.3 75.7 - - - +
474J GLY* 1.3 67.0 + - - +
475J GLY 3.4 0.2 - - - -
476J LYS* 3.1 23.4 + - - +
478J 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