Contacts of the strand formed by residues 464 - 473 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369D VAL 4.2 0.4 - - - -
370D GLY* 3.5 20.1 - - - -
460D ASN* 3.4 14.4 - - - -
461D ALA* 2.8 39.2 + - - +
462D PRO 3.4 1.4 + - - -
463D ARG* 1.3 81.2 - - - +
465D MET* 1.3 62.5 + - - -
466D LEU 3.3 1.0 + - - -
485D PRO* 3.5 6.2 - - - +
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Residues in contact with MET 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D LEU* 4.0 27.4 - - + -
282D THR* 4.6 1.3 - - - -
283D CYS* 3.0 32.3 - - + +
314D PHE* 3.8 20.4 - - + -
319D ILE* 5.0 6.3 - - + -
369D VAL* 4.0 9.6 - - + +
458D PHE* 3.0 42.8 - - + -
459D VAL 3.7 1.8 - - - -
460D ASN* 3.3 8.5 - - - +
464D GLY* 1.3 68.4 - - - -
466D LEU* 1.3 63.9 + - - +
467D SER* 3.5 19.5 - - - +
483D VAL 3.8 5.5 - - - +
484D VAL 3.9 1.0 - - - -
485D PRO* 3.5 22.0 - - - +
488D TRP* 4.0 15.1 + - - -
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Residues in contact with LEU 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D VAL* 3.6 37.9 - - + +
72D HIS* 3.7 26.9 - - + +
75D ALA* 4.1 11.9 - - + -
457D GLY 3.7 0.4 - - - +
458D PHE* 3.4 3.5 - - - -
459D VAL* 2.6 50.4 + - + +
461D ALA* 4.4 1.8 - - + -
464D GLY 3.3 3.5 + - - +
465D MET* 1.3 77.1 - - - +
467D SER* 1.3 68.8 + - - +
468D HIS* 3.7 12.3 - - + +
483D VAL 3.7 10.3 - - - +
484D VAL* 3.9 10.3 - - + -
485D PRO* 4.0 3.1 - - + -
537D FCO 3.3 24.2 - - - +
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Residues in contact with SER 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ILE* 5.3 1.9 - - - +
456D VAL* 4.2 0.4 - - - -
457D GLY 3.0 10.3 - - - -
458D PHE* 3.6 10.3 - - - -
465D MET* 3.5 21.7 - - - +
466D LEU* 1.3 74.9 - - - +
468D HIS* 1.3 64.4 + - - +
469D TRP* 2.7 33.3 + - - -
482D LEU* 3.7 1.2 - - - -
483D VAL* 2.9 41.2 + - - +
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Residues in contact with HIS 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D THR* 3.8 9.0 - - - -
72D HIS* 2.9 57.1 + - + -
75D ALA* 3.5 24.5 - - + +
76D SER* 2.8 24.3 + - - -
79D ALA* 3.3 5.8 - - + +
456D VAL* 3.3 5.4 - - - +
457D GLY 3.0 29.5 + - - -
466D LEU* 3.7 10.5 - - + +
467D SER* 1.3 79.7 - - - +
469D TRP* 1.3 60.7 + - - +
480D PHE* 3.7 19.6 - + + -
481D GLN 3.5 3.1 - - - -
482D LEU* 3.7 15.9 - - + +
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Residues in contact with TRP 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D PRO* 3.9 20.0 - - + -
317D ASP* 5.8 0.9 - - - -
319D ILE* 4.2 15.3 - - + -
335D HIS* 3.0 35.0 - + - -
336D PRO* 3.5 42.6 - - + +
337D TYR* 3.6 42.4 - + + -
455D GLY 3.6 3.4 - - - -
456D VAL* 3.8 24.0 - - + -
458D PHE* 4.3 4.0 - + - -
467D SER* 2.7 34.6 + - - -
468D HIS* 1.3 78.1 - - - +
470D ILE* 1.3 61.3 + - - +
471D VAL* 5.7 0.2 - - - -
479D ASN 3.9 0.7 - - - +
480D PHE* 3.2 7.9 + - - -
481D GLN* 2.7 41.4 + - + +
483D VAL* 4.1 5.1 - - + +
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Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PRO* 3.7 34.8 - - + -
79D ALA* 3.5 31.9 - - + +
80D VAL* 4.2 9.2 - - + +
83D CYS* 4.0 11.2 - - + -
337D TYR* 3.5 1.1 - - - -
454D GLN* 3.0 7.4 - - - +
455D GLY 2.8 44.6 + - - +
468D HIS 4.2 0.4 - - - -
469D TRP* 1.3 75.2 - - - +
471D VAL* 1.3 73.4 + - - +
472D GLN* 4.3 9.0 - - + -
477D ILE* 3.9 12.1 - - + -
479D ASN 3.4 9.2 - - - +
480D PHE* 3.8 21.5 - - + -
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Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D TYR* 3.8 35.7 - - + +
453D SER 3.5 9.0 - - - +
454D GLN* 4.0 14.6 - - + +
469D TRP 5.7 0.2 - - - -
470D ILE* 1.3 80.4 - - - +
472D GLN* 1.3 62.3 + - - +
477D ILE* 3.8 1.7 - - - -
478D GLU* 2.9 41.7 + - + +
479D ASN* 2.9 25.7 + - + +
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Residues in contact with GLN 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PRO* 4.3 15.9 - - + -
83D CYS* 3.7 14.6 - - - -
449D TYR* 3.9 11.6 - - + -
450D PRO* 2.8 30.4 + - - +
452D GLU* 3.2 4.9 - - - +
453D SER* 2.7 71.7 + - - +
470D ILE* 4.1 6.5 - - + -
471D VAL* 1.3 78.9 - - - +
473D ARG* 1.3 64.3 + - - +
474D GLY 3.4 1.6 + - - -
475D GLY* 2.8 32.7 + - - -
476D LYS 3.5 11.7 - - - +
478D GLU* 4.4 2.2 - - - -
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Residues in contact with ARG 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D THR* 3.3 39.8 + - - +
452D GLU* 3.6 29.1 + - + +
472D GLN* 1.3 75.5 - - - +
474D GLY* 1.3 66.9 + - - +
476D LYS* 3.1 23.1 + - - +
478D GLU* 4.0 22.8 - - + +
309L SER* 4.3 36.2 + - - +
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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