Contacts of the helix formed by residues 448 - 468 (chain E) in PDB entry 1R4N
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 TYR 448 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B TYR* 5.3 4.5 + - - -
236B GLN* 5.8 2.7 - - + +
239B LYS* 3.1 52.9 - - + +
240B GLU* 3.7 32.5 - - + -
446E SER* 3.9 15.0 + - - -
447E ASN* 1.3 77.1 - - - +
449E GLN* 1.3 99.4 + - + +
450E VAL* 2.9 12.0 + - - +
451E GLU* 3.7 14.6 + - - +
452E GLU* 4.4 15.4 + - + +
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Residues in contact with GLN 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B TYR* 5.5 4.6 + - - -
441E ARG* 3.4 36.0 + - - +
444E GLY* 3.7 10.8 - - - -
445E VAL* 3.1 25.0 + - - +
446E SER* 3.2 25.4 + - - +
448E TYR* 1.3 109.1 + - + +
450E VAL* 1.3 67.0 + - - +
452E GLU* 3.6 7.5 + - - +
453E ASP* 2.9 36.0 + - - +
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Residues in contact with VAL 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444E GLY* 4.2 7.6 - - - +
446E SER 3.9 7.1 + - - +
447E ASN* 3.2 28.0 - - - +
448E TYR 2.9 1.6 + - - +
449E GLN* 1.3 80.1 - - - +
451E GLU* 1.3 69.6 - - - +
453E ASP* 3.6 1.3 - - - +
454E ILE* 2.9 35.2 + - + +
480E HIS 5.6 0.7 - - - +
483E CYS* 4.5 17.4 - - + +
484E ARG* 5.0 4.3 - - + +
26F ARG* 4.1 25.1 - - + +
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Residues in contact with GLU 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448E TYR 3.7 7.5 + - - +
449E GLN 3.6 0.2 - - - -
450E VAL* 1.3 80.8 - - - +
452E GLU* 1.3 69.7 + - - +
454E ILE* 3.1 28.2 + - - +
455E GLY 4.0 1.6 + - - -
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Residues in contact with GLU 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS* 5.2 7.6 + - - -
441E ARG* 3.8 5.4 + - - -
448E TYR* 4.4 12.4 + - + +
449E GLN* 3.6 15.0 + - - +
451E GLU* 1.3 83.3 - - - +
453E ASP* 1.3 74.0 + - - +
454E ILE 3.4 0.2 + - - -
455E GLY* 3.5 8.3 + - - -
456E LYS* 3.6 42.8 + - - +
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Residues in contact with ASP 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E PHE* 3.1 19.4 - - + -
441E ARG* 2.5 39.5 + - - -
443E PRO* 3.7 0.4 - - + +
444E GLY 3.0 27.5 + - - +
449E GLN* 2.9 29.4 + - - +
450E VAL 3.7 1.6 - - - +
452E GLU* 1.3 79.0 - - - +
454E ILE* 1.3 57.9 + - - +
456E LYS* 3.0 7.4 + - - +
457E LEU* 2.6 35.7 + - - +
483E CYS* 4.1 7.9 - - - -
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Residues in contact with ILE 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 2.9 29.7 + - + +
451E GLU* 3.1 25.7 + - - +
453E ASP* 1.3 75.3 - - - +
455E GLY* 1.3 64.5 + - - +
457E LEU* 3.7 2.1 - - - +
458E LYS* 3.3 16.1 + - - +
479E VAL* 3.7 9.8 - - + +
480E HIS* 3.4 52.7 - - + +
483E CYS* 3.7 22.0 - - + -
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Residues in contact with GLY 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E GLU 4.0 1.6 + - - -
452E GLU 3.5 7.0 + - - -
453E ASP 3.2 0.4 - - - -
454E ILE* 1.3 77.6 - - - +
456E LYS* 1.3 65.9 + - - +
458E LYS* 3.1 16.9 + - - +
459E SER* 3.1 17.2 + - - -
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Residues in contact with LYS 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435E PHE* 3.8 11.7 - - + -
438E GLN* 5.1 1.3 + - - +
439E GLN* 3.8 25.6 + - - +
441E ARG* 4.0 14.6 - - - +
452E GLU* 3.6 45.3 + - - +
453E ASP* 3.0 13.4 + - - +
455E GLY* 1.3 74.3 - - - +
457E LEU* 1.3 63.6 + - - +
459E SER* 3.4 20.1 + - - -
460E CYS* 3.4 13.9 - - - -
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Residues in contact with LEU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E MET* 4.0 15.9 - - + -
431E ALA* 4.4 5.6 - - + -
432E VAL* 4.0 17.3 - - + +
435E PHE* 3.6 23.9 - - + -
443E PRO* 3.5 26.5 - - + -
453E ASP 2.6 20.0 + - - +
454E ILE 3.7 4.3 - - - +
456E LYS* 1.3 69.8 - - - +
458E LYS* 1.3 57.7 + - - +
460E CYS* 2.6 28.4 + - - +
461E LEU* 3.0 9.0 + - + -
479E VAL* 3.4 35.7 - - + +
482E PHE* 4.4 5.6 - - + -
483E CYS* 3.7 14.6 - - - -
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Residues in contact with LYS 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454E ILE 3.3 9.2 + - - +
455E GLY* 3.1 10.1 + - - +
457E LEU* 1.3 78.0 - - - +
459E SER* 1.3 63.1 + - - +
460E CYS 2.9 1.6 + - - -
461E LEU* 2.9 23.8 + - + +
462E THR* 2.9 24.1 + - - +
474E VAL 5.5 2.0 - - - -
476E ASP* 2.6 41.0 + - - +
479E VAL* 3.8 21.7 - - + +
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Residues in contact with SER 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E GLN* 6.0 1.3 - - - -
455E GLY 3.1 14.1 + - - -
456E LYS* 3.4 14.3 - - - -
457E LEU 3.1 0.2 + - - -
458E LYS* 1.3 75.9 - - - +
460E CYS* 1.3 59.9 + - - +
462E THR* 4.2 5.3 - - - +
463E GLY* 3.2 18.7 + - - -
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Residues in contact with CYS 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E ALA* 4.2 7.0 - - - +
434E ARG* 3.2 23.2 - - - +
435E PHE* 3.9 29.6 - - + +
438E GLN* 3.4 38.4 - - - -
456E LYS 3.4 15.0 - - - -
457E LEU 2.6 17.0 + - - +
459E SER* 1.3 73.3 - - - +
461E LEU* 1.3 62.6 + - - -
462E THR 3.1 1.3 - - - -
463E GLY 3.6 0.7 - - - +
464E PHE* 2.8 21.5 + - - +
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Residues in contact with LEU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E LEU* 4.6 9.0 - - + +
428E MET* 4.2 17.3 - - + -
431E ALA* 3.8 27.0 - - + +
457E LEU* 3.0 7.1 + - + +
458E LYS* 2.9 22.2 + - + +
460E CYS* 1.3 76.7 - - - +
462E THR* 1.3 61.2 + - - +
464E PHE* 3.3 9.6 - - + +
465E LEU* 2.9 50.8 + - + +
474E VAL* 3.5 40.6 - - + +
479E VAL* 4.5 12.3 - - + -
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Residues in contact with THR 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E LYS* 2.9 24.7 + - - +
459E SER* 4.2 5.6 - - - +
461E LEU* 1.3 75.5 - - - +
463E GLY* 1.3 69.8 + - - +
464E PHE 2.9 1.3 - - - -
465E LEU* 2.7 23.1 + - + +
466E GLN* 2.9 33.4 + - + +
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Residues in contact with GLY 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E ARG* 3.4 25.2 + - - -
459E SER 3.2 15.9 + - - -
460E CYS 3.3 2.9 + - - -
462E THR* 1.3 80.0 - - - +
464E PHE* 1.3 61.2 + - - +
466E GLN* 3.5 8.1 + - - +
467E GLU* 3.1 17.8 + - - +
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Residues in contact with PHE 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E ILE* 5.7 1.3 - - + -
426E TYR* 5.2 2.9 - + - -
427E LEU* 3.4 37.2 - - + -
430E ARG* 3.6 60.3 - - + -
431E ALA* 4.7 5.2 - - - -
434E ARG* 3.4 23.8 - - + +
460E CYS 2.8 18.6 + - - +
461E LEU* 3.3 9.6 - - + +
462E THR 2.8 0.4 + - - -
463E GLY* 1.3 75.4 - - - +
465E LEU* 1.3 84.6 + - + +
466E GLN 2.9 1.9 + - - -
467E GLU* 3.0 13.7 + - - +
468E TYR* 3.3 31.2 + + - -
470E LEU* 4.4 10.3 - - + -
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Residues in contact with LEU 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E LEU* 3.9 8.3 - - + -
461E LEU* 2.9 38.7 + - + +
462E THR* 2.7 17.0 + - + +
464E PHE* 1.3 94.8 - - + +
466E GLN* 1.3 56.7 + - + +
468E TYR 4.8 0.2 - - - -
469E GLY 3.0 4.7 + - - -
470E LEU* 2.7 63.8 + - + +
472E VAL* 3.9 32.8 - - + +
474E VAL* 4.3 7.2 - - + -
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Residues in contact with GLN 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E THR* 2.9 33.3 + - + +
463E GLY* 3.9 7.1 - - - +
465E LEU* 1.3 76.9 - - + +
467E GLU* 1.3 60.5 + - - +
468E TYR 2.9 1.5 - - - -
469E GLY* 2.6 26.1 + - - +
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Residues in contact with GLU 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E LEU* 3.0 37.4 - - + +
434E ARG* 3.5 25.6 + - - +
463E GLY 3.1 11.0 + - - +
464E PHE 3.0 9.7 + - - +
466E GLN* 1.3 77.1 - - - +
468E TYR* 1.3 78.5 + - + +
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Residues in contact with TYR 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E GLU 4.4 2.0 - - - -
402E TYR* 2.8 26.9 + - - +
403E GLY 3.8 11.4 - - - -
404E LEU* 4.1 15.2 - - + +
407E ILE* 3.5 47.5 - - + +
409E LYS* 3.4 20.1 + - - +
430E ARG* 3.3 28.0 + - - -
434E ARG* 5.9 0.7 - - - -
464E PHE* 3.3 27.8 + + - +
466E GLN 2.7 1.2 + - - -
467E GLU* 1.3 101.3 + - + +
469E GLY* 1.3 65.8 + - - +
470E LEU* 4.0 21.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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