Contacts of the strand formed by residues 464 - 473 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370H GLY* 3.5 20.7 - - - -
460H ASN* 3.4 14.4 - - - -
461H ALA* 2.8 39.9 + - - +
462H PRO 3.4 1.0 - - - -
463H ARG* 1.3 79.8 - - - +
465H MET* 1.3 62.2 + - - -
466H LEU 3.3 1.4 + - - -
485H PRO* 3.5 6.4 - - - +
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Residues in contact with MET 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H LEU* 4.0 26.7 - - + -
282H THR* 4.6 1.1 - - - -
283H CYS* 3.0 32.3 - - + +
314H PHE* 3.8 20.0 - - + -
319H ILE* 5.0 6.7 - - + -
369H VAL* 4.0 10.3 - - + +
458H PHE* 3.0 43.1 - - + -
459H VAL 3.7 1.8 - - - -
460H ASN* 3.3 8.3 - - - +
464H GLY* 1.3 67.8 - - - -
466H LEU* 1.3 63.7 - - - +
467H SER* 3.5 18.8 - - - +
483H VAL 3.8 6.6 - - - +
484H VAL 3.9 0.7 - - - -
485H PRO* 3.5 22.0 - - - +
488H TRP* 4.0 14.7 + - - -
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Residues in contact with LEU 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H VAL* 3.6 37.5 - - + +
72H HIS* 3.7 26.5 - - + +
75H ALA* 4.1 11.7 - - + -
457H GLY 3.7 0.2 - - - +
458H PHE* 3.4 3.3 - - - -
459H VAL* 2.6 50.2 + - + +
461H ALA* 4.4 1.1 - - + -
464H GLY 3.3 3.7 + - - +
465H MET* 1.3 76.7 - - - +
467H SER* 1.3 66.7 + - - +
468H HIS* 3.7 12.8 - - + +
483H VAL 3.7 10.8 - - - +
484H VAL* 3.9 10.1 - - + -
485H PRO* 4.0 2.7 - - + -
537H FCO 3.3 24.0 - - - +
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Residues in contact with SER 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H ILE* 5.3 2.3 - - - +
456H VAL* 4.2 0.7 - - - -
457H GLY 3.0 10.3 - - - -
458H PHE* 3.6 10.1 - - - -
465H MET* 3.5 21.6 - - - +
466H LEU* 1.3 77.1 - - - +
468H HIS* 1.3 63.3 - - - +
469H TRP* 2.7 33.6 + - - -
482H LEU* 3.7 0.7 - - - -
483H VAL* 2.9 41.1 + - - +
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Residues in contact with HIS 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H THR* 3.8 9.4 - - - -
72H HIS* 2.9 56.4 + - + -
75H ALA* 3.5 25.9 - - + +
76H SER* 2.8 24.5 + - - -
79H ALA* 3.3 5.4 - - + +
456H VAL* 3.3 5.4 - - - +
457H GLY 3.0 28.8 + - - -
466H LEU* 3.7 10.8 - - + +
467H SER* 1.3 79.7 - - - +
469H TRP* 1.3 61.8 + - - +
480H PHE* 3.7 19.8 - + + -
481H GLN 3.5 3.4 - - - -
482H LEU* 3.7 14.4 - - + +
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Residues in contact with TRP 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316H PRO* 3.9 18.6 - - + -
317H ASP* 5.8 1.1 - - - -
319H ILE* 4.2 14.6 - - + -
335H HIS* 3.0 36.6 - + - -
336H PRO* 3.5 42.4 - - + +
337H TYR* 3.6 41.1 - + + -
455H GLY 3.6 3.4 - - - -
456H VAL* 3.8 24.5 - - + -
458H PHE* 4.3 4.3 - + - -
467H SER* 2.7 35.4 + - - -
468H HIS* 1.3 80.2 - - - +
470H ILE* 1.3 60.5 + - - +
471H VAL* 5.7 0.2 - - - -
479H ASN 3.9 0.9 - - - +
480H PHE* 3.2 8.1 - - - -
481H GLN* 2.7 41.9 + - + +
483H VAL* 4.1 4.6 - - + +
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Residues in contact with ILE 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H PRO* 3.7 36.1 - - + -
79H ALA* 3.5 31.0 - - + +
80H VAL* 4.2 9.0 - - + +
83H CYS* 4.0 10.8 - - + -
337H TYR* 3.5 0.9 - - - -
454H GLN* 3.0 7.8 - - - +
455H GLY 2.8 43.8 + - - +
469H TRP* 1.3 74.4 - - - +
471H VAL* 1.3 72.1 + - - +
472H GLN* 4.3 8.3 - - + -
477H ILE* 3.9 12.3 - - + -
479H ASN 3.4 10.8 - - - +
480H PHE* 3.8 20.9 - - + -
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Residues in contact with VAL 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337H TYR* 3.8 36.6 - - + +
453H SER 3.5 7.9 - - - +
454H GLN* 4.0 14.1 - - + +
469H TRP 5.7 0.2 - - - -
470H ILE* 1.3 79.4 - - - +
472H GLN* 1.3 63.6 + - - +
477H ILE* 3.8 1.7 - - - -
478H GLU* 2.9 41.3 + - + +
479H ASN* 2.9 25.1 + - + +
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Residues in contact with GLN 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H PRO* 4.3 15.5 - - + -
83H CYS* 3.7 15.3 - - - -
449H TYR* 3.9 12.1 - - + -
450H PRO* 2.8 31.0 + - - +
452H GLU* 3.2 4.6 - - - +
453H SER* 2.7 71.0 + - - +
470H ILE* 4.1 7.1 - - + -
471H VAL* 1.3 77.7 - - - +
473H ARG* 1.3 64.6 + - - +
474H GLY 3.4 1.7 + - - -
475H GLY* 2.8 32.9 + - - -
476H LYS 3.5 11.4 - - - +
478H GLU* 4.4 2.7 - - - +
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Residues in contact with ARG 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451H THR* 3.3 39.5 + - - +
452H GLU* 3.6 28.5 + - + +
472H GLN* 1.3 75.2 - - - +
474H GLY* 1.3 66.8 + - - +
475H GLY 3.4 0.2 - - - -
476H LYS* 3.1 22.4 + - - +
478H GLU* 4.0 23.4 - - + +
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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