Contacts of the helix formed by residues 448 - 469 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446G SER* 4.0 19.5 - - - -
447G ASN* 1.3 75.6 - - - +
449G GLN* 1.3 98.9 + - + +
450G VAL* 2.9 11.9 + - - +
451G GLU* 3.7 14.4 + - - +
452G GLU* 4.4 15.8 + - + +
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Residues in contact with GLN 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441G ARG* 3.4 36.8 + - - +
444G GLY* 3.8 9.9 - - - -
445G VAL* 3.1 24.8 + - - +
446G SER* 3.2 26.4 + - - +
448G TYR* 1.3 110.1 + - + +
450G VAL* 1.3 64.4 + - - +
451G GLU 3.6 0.2 - - - -
452G GLU* 4.2 6.1 - - - +
453G ASP* 2.9 39.1 + - - +
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Residues in contact with VAL 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444G GLY* 4.5 7.2 - - - -
446G SER 3.9 6.6 + - - +
447G ASN 3.1 28.3 - - - +
448G TYR 2.9 2.0 + - - +
449G GLN* 1.3 80.0 - - - +
451G GLU* 1.3 69.5 + - - +
453G ASP* 3.7 1.3 - - - +
454G ILE* 2.9 35.5 + - + +
480G HIS 5.6 0.4 - - - +
483G CYS* 4.5 16.9 - - + +
484G ARG* 5.0 4.5 - - + +
26H ARG* 4.1 27.1 - - + +
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Residues in contact with GLU 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448G TYR 3.7 6.8 + - - +
449G GLN 3.6 0.2 - - - -
450G VAL* 1.3 80.7 - - - +
452G GLU* 1.3 69.6 + - - +
454G ILE* 3.1 28.1 + - - +
455G GLY 4.0 1.6 + - - -
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Residues in contact with GLU 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441G ARG* 3.8 5.7 + - - -
448G TYR* 4.4 12.8 + - + +
449G GLN* 3.9 15.2 - - - +
450G VAL 3.4 0.2 - - - -
451G GLU* 1.3 84.6 - - - +
453G ASP* 1.3 74.7 + - - +
454G ILE 3.4 0.2 + - - -
455G GLY* 3.6 8.1 + - - -
456G LYS* 3.6 41.3 + - - +
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Residues in contact with ASP 453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G PHE* 3.1 18.8 - - + -
441G ARG* 2.5 38.8 + - - -
443G PRO* 3.6 0.4 - - + +
444G GLY 3.0 28.1 + - - +
449G GLN* 2.9 25.3 + - - +
450G VAL 3.7 1.8 - - - +
452G GLU* 1.3 77.9 - - - +
454G ILE* 1.3 58.2 + - - +
456G LYS* 2.9 8.0 + - - -
457G LEU* 2.6 36.0 + - - +
483G CYS* 4.1 8.1 - - - -
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Residues in contact with ILE 454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450G VAL* 2.9 30.1 + - + +
451G GLU* 3.1 26.4 + - - +
453G ASP* 1.3 74.3 - - - +
455G GLY* 1.3 65.1 + - - +
457G LEU* 3.7 2.1 - - - +
458G LYS* 3.2 16.1 + - - +
479G VAL* 3.7 10.5 - - + +
480G HIS* 3.3 52.5 - - + +
483G CYS* 3.6 22.1 - - + -
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Residues in contact with GLY 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G GLU 4.0 1.8 + - - -
452G GLU 3.6 6.8 + - - -
453G ASP 3.2 0.2 - - - -
454G ILE* 1.3 77.9 - - - +
456G LYS* 1.3 63.9 + - - +
458G LYS* 3.0 17.8 + - - +
459G SER* 3.1 15.9 + - - -
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Residues in contact with LYS 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G PHE* 3.7 12.3 - - + -
438G GLN* 5.1 1.5 + - - +
439G GLN* 3.8 24.7 + - - +
441G ARG* 4.0 15.9 - - - +
452G GLU* 3.6 46.0 + - - +
453G ASP* 2.9 12.7 + - - +
455G GLY* 1.3 74.7 - - - +
457G LEU* 1.3 63.9 + - - +
459G SER* 3.4 18.7 + - - -
460G CYS* 3.5 13.9 - - - -
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Residues in contact with LEU 457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G MET* 4.0 16.2 - - + -
431G ALA* 4.4 5.6 - - + -
432G VAL* 4.1 17.3 - - + +
435G PHE* 3.5 24.1 - - + -
443G PRO* 3.5 26.9 - - + -
453G ASP 2.6 19.8 + - - +
454G ILE 3.7 3.4 - - - +
456G LYS* 1.3 69.8 - - - +
458G LYS* 1.3 57.7 + - - +
460G CYS* 2.6 28.1 + - - +
461G LEU* 2.9 9.1 + - + -
479G VAL* 3.4 35.7 - - + +
482G PHE* 4.4 6.3 - - + -
483G CYS* 3.7 14.4 - - - -
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Residues in contact with LYS 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G ILE 3.2 8.7 + - - +
455G GLY* 3.0 10.7 + - - +
457G LEU* 1.3 78.0 - - - +
459G SER* 1.3 63.1 + - - +
460G CYS 2.9 1.4 + - - -
461G LEU* 2.9 23.4 + - + +
462G THR* 3.0 24.4 + - - +
474G VAL 5.5 2.0 - - - -
476G ASP* 2.6 41.1 + - - +
479G VAL* 3.8 23.7 - - + +
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Residues in contact with SER 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438G GLN* 6.0 1.6 - - - -
455G GLY 3.1 13.2 + - - -
456G LYS* 3.4 14.3 - - - -
457G LEU 3.1 0.8 + - - -
458G LYS* 1.3 75.7 - - - +
460G CYS* 1.3 60.3 + - - +
462G THR* 4.2 4.6 - - - -
463G GLY* 3.2 19.7 + - - -
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Residues in contact with CYS 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431G ALA* 4.3 6.7 - - - +
434G ARG* 3.2 22.6 - - - +
435G PHE* 3.9 29.2 - - + +
438G GLN* 3.4 40.2 - - - -
456G LYS 3.5 13.9 - - - -
457G LEU 2.6 17.5 + - - +
459G SER* 1.3 73.7 - - - +
461G LEU* 1.3 63.4 + - - +
462G THR 3.1 1.6 - - - -
463G GLY 4.1 0.2 - - - +
464G PHE* 2.8 21.8 + - - +
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Residues in contact with LEU 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G LEU* 4.6 12.1 - - + +
428G MET* 4.2 16.8 - - + -
431G ALA* 3.8 27.0 - - + +
457G LEU* 2.9 7.0 + - + +
458G LYS* 2.9 21.7 + - + +
460G CYS* 1.3 77.2 - - - +
462G THR* 1.3 61.3 + - - +
464G PHE* 3.3 6.7 - - + +
465G LEU* 2.9 50.2 + - + +
474G VAL* 3.5 42.2 - - + +
479G VAL* 4.5 12.6 - - + -
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Residues in contact with THR 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458G LYS* 3.0 24.4 + - - +
459G SER* 4.2 5.8 - - - +
461G LEU* 1.3 75.5 - - - +
463G GLY* 1.3 68.5 + - - +
464G PHE 2.9 1.3 - - - -
465G LEU* 2.7 23.0 + - + +
466G GLN* 2.9 33.9 + - + +
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Residues in contact with GLY 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G ARG* 3.4 25.1 + - - -
459G SER 3.2 15.9 + - - -
460G CYS 3.3 3.1 + - - -
462G THR* 1.3 80.5 - - - +
464G PHE* 1.3 61.1 + - - +
466G GLN* 3.5 8.5 + - - +
467G GLU* 3.1 17.0 + - - +
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Residues in contact with PHE 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G ILE* 5.7 1.3 - - + -
426G TYR* 5.2 2.7 - + - -
427G LEU* 3.4 37.5 - - + -
430G ARG* 3.7 62.4 - - + -
431G ALA* 4.8 4.9 - - - -
434G ARG* 3.4 22.9 - - + +
460G CYS 2.8 18.2 + - - +
461G LEU* 3.3 10.3 - - + +
462G THR 2.8 0.2 + - - -
463G GLY* 1.3 74.3 - - - +
465G LEU* 1.3 86.4 + - + +
466G GLN 2.9 1.6 + - - -
467G GLU* 3.0 13.7 + - - +
468G TYR* 3.3 31.3 + + - +
470G LEU* 4.3 10.5 - - + -
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Residues in contact with LEU 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G LEU* 4.0 7.4 - - + -
461G LEU* 2.9 37.0 + - + +
462G THR* 2.7 16.5 + - + +
464G PHE* 1.3 96.1 - - + +
466G GLN* 1.3 57.0 + - + +
468G TYR 3.9 0.4 + - - -
469G GLY 2.9 4.3 + - - -
470G LEU* 2.7 64.0 + - + +
472G VAL* 3.9 33.4 - - + +
474G VAL* 4.3 7.2 - - + -
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Residues in contact with GLN 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462G THR* 2.9 31.8 + - + +
463G GLY* 3.9 7.5 - - - +
465G LEU* 1.3 76.1 - - + +
467G GLU* 1.3 61.4 + - - +
468G TYR 2.9 2.0 - - - -
469G GLY* 2.6 24.8 + - - +
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Residues in contact with GLU 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404G LEU* 3.0 38.4 - - + +
434G ARG* 3.5 26.6 + - - +
463G GLY 3.1 10.8 + - - +
464G PHE 3.0 9.3 + - - +
466G GLN* 1.3 77.2 - - - +
468G TYR* 1.3 79.3 + - + +
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Residues in contact with TYR 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401G GLU 4.4 1.8 - - - -
402G TYR* 2.8 27.2 + - - +
403G GLY 3.8 11.2 - - - -
404G LEU* 4.1 15.4 - - + +
407G ILE* 3.4 47.7 - - + +
409G LYS* 3.5 20.4 + - - +
430G ARG* 3.3 22.1 + - - -
434G ARG* 5.8 0.7 - - - -
464G PHE* 3.3 35.5 + + - +
466G GLN 2.7 1.4 + - - -
467G GLU* 1.3 102.1 + - + +
469G GLY* 1.3 65.7 + - - +
470G LEU* 4.0 20.6 - - + -
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Residues in contact with GLY 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409G LYS* 3.7 15.4 + - - +
413G ILE* 5.2 2.4 - - - +
465G LEU 2.9 5.5 + - - -
466G GLN* 2.6 22.3 + - - -
468G TYR* 1.3 78.1 - - - +
470G LEU* 1.3 61.7 + - - +
471G SER 4.0 1.8 + - - -
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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