Contacts of the helix formed by residues 448 - 468 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A SER* 4.0 18.6 - - - -
447A ASN* 1.3 76.4 - - - +
449A GLN* 1.3 99.5 + - + +
450A VAL 2.9 11.7 + - - -
451A GLU* 3.7 14.9 + - - +
452A GLU* 4.4 15.6 + - + +
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ARG* 3.4 36.2 + - - +
444A GLY* 3.8 10.8 - - - -
445A VAL* 3.1 25.1 + - - +
446A SER* 3.2 25.7 + - - +
448A TYR* 1.3 107.6 + - + +
450A VAL* 1.3 68.0 + - - +
451A GLU 3.6 0.2 - - - -
452A GLU* 4.2 6.7 - - - +
453A ASP* 2.8 38.3 + - - +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLY* 4.2 7.4 - - - +
446A SER 3.9 6.8 + - - +
447A ASN 3.1 28.5 - - - +
448A TYR 2.9 1.8 + - - +
449A GLN* 1.3 80.1 - - - +
451A GLU* 1.3 69.8 + - - +
453A ASP* 3.6 1.5 - - - +
454A ILE* 3.0 35.9 + - + +
480A HIS 5.6 0.7 - - - +
483A CYS* 4.5 17.2 - - + +
484A ARG* 5.0 4.7 - - + +
26B ARG* 4.0 27.4 - - + +
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Residues in contact with GLU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TYR 3.7 7.7 + - - +
449A GLN 3.6 0.2 - - - -
450A VAL* 1.3 80.7 - - - +
452A GLU* 1.3 70.3 + - - +
454A ILE* 3.1 28.0 + - - +
455A GLY 4.0 1.7 + - - -
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Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.8 5.9 + - - -
448A TYR* 4.4 13.5 + - + +
449A GLN* 3.6 15.1 + - - +
451A GLU* 1.3 83.7 - - - +
453A ASP* 1.3 73.6 + - - +
454A ILE 3.4 0.2 + - - -
455A GLY* 3.5 8.3 + - - -
456A LYS* 3.6 42.8 + - - +
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Residues in contact with ASP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE* 3.1 18.3 - - + -
441A ARG* 2.6 38.3 + - - -
444A GLY* 3.0 28.7 + - - +
449A GLN* 2.8 26.2 + - - +
450A VAL 3.7 1.8 - - - +
452A GLU* 1.3 78.0 - - - +
454A ILE* 1.3 56.5 + - - +
456A LYS* 2.9 8.3 + - - +
457A LEU* 2.6 35.7 + - - +
483A CYS* 4.1 8.1 - - - -
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Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A VAL* 3.0 30.1 + - + +
451A GLU* 3.1 25.3 + - - +
453A ASP* 1.3 74.4 - - - +
455A GLY* 1.3 65.5 + - - +
457A LEU* 3.7 2.3 - - - +
458A LYS* 3.3 15.6 + - - +
479A VAL* 3.7 9.6 - - + +
480A HIS* 3.3 53.8 - - + +
483A CYS* 3.6 23.3 - - + -
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Residues in contact with GLY 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A GLU 4.0 1.8 + - - -
452A GLU 3.5 6.8 + - - -
453A ASP 3.1 0.4 - - - -
454A ILE* 1.3 76.5 - - - +
456A LYS* 1.3 65.4 - - - +
458A LYS* 3.1 17.5 + - - +
459A SER* 3.1 17.2 + - - -
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A PHE* 3.7 11.7 - - + -
438A GLN* 5.2 1.7 + - - +
439A GLN* 3.8 26.5 + - - +
441A ARG* 4.1 15.5 - - - +
452A GLU* 3.6 45.8 + - - +
453A ASP* 2.9 13.2 + - - +
455A GLY* 1.3 75.3 - - - +
457A LEU* 1.3 63.9 - - - +
459A SER* 3.4 20.0 + - - -
460A CYS* 3.5 13.2 - - - -
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Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A MET* 4.0 16.4 - - + -
431A ALA* 4.5 6.1 - - + -
432A VAL* 4.1 16.6 - - + +
435A PHE* 3.5 23.5 - - + -
443A PRO* 3.5 27.1 - - + -
453A ASP 2.6 19.6 + - - +
454A ILE 3.7 4.0 - - - +
456A LYS* 1.3 70.0 - - - +
458A LYS* 1.3 57.5 + - - +
460A CYS* 2.6 28.8 + - - +
461A LEU* 2.9 9.1 + - + -
479A VAL* 3.4 36.3 - - + +
482A PHE* 4.4 5.2 - - + -
483A CYS* 3.6 14.6 - - - -
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Residues in contact with LYS 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ILE 3.3 9.4 + - - +
455A GLY* 3.1 10.1 + - - +
457A LEU* 1.3 78.2 - - - +
459A SER* 1.3 63.1 + - - +
460A CYS 2.9 1.4 + - - -
461A LEU* 2.9 23.6 + - + -
462A THR* 2.9 24.6 + - - +
474A VAL 5.5 2.2 - - - -
476A ASP* 2.6 41.7 + - + +
479A VAL* 3.8 22.8 - - + +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A GLN* 6.0 1.3 - - - -
455A GLY 3.1 14.3 + - - -
456A LYS* 3.4 13.7 - - - -
458A LYS* 1.3 77.6 - - - +
460A CYS* 1.3 59.2 + - - +
462A THR* 4.2 4.8 - - - -
463A GLY* 3.2 19.6 + - - -
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Residues in contact with CYS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ALA* 4.3 7.3 - - - +
434A ARG* 3.2 22.2 - - - +
435A PHE* 3.8 31.4 - - + +
438A GLN* 3.4 38.6 - - - -
456A LYS 3.5 13.9 - - - -
457A LEU 2.6 16.6 + - - +
459A SER* 1.3 73.9 - - - +
461A LEU* 1.3 63.9 + - - +
462A THR 3.1 1.3 - - - -
463A GLY 4.1 0.2 - - - +
464A PHE* 2.8 22.0 + - - +
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 4.6 11.9 - - + +
428A MET* 4.2 16.6 - - + -
431A ALA* 3.7 27.5 - - + +
457A LEU* 2.9 6.5 + - + +
458A LYS* 2.9 23.2 + - + +
460A CYS* 1.3 76.8 - - - +
462A THR* 1.3 60.0 + - - +
464A PHE* 3.3 6.9 - - + +
465A LEU* 2.9 51.0 + - + +
474A VAL* 3.5 41.7 - - + +
479A VAL* 4.4 12.3 - - + -
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Residues in contact with THR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A LYS* 2.9 26.4 + - - +
459A SER* 4.2 5.4 - - - +
461A LEU* 1.3 75.4 - - - +
463A GLY* 1.3 69.1 + - - +
464A PHE 2.9 1.1 - - - -
465A LEU* 2.8 22.7 + - + +
466A GLN* 2.9 33.9 + - + +
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Residues in contact with GLY 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ARG* 3.3 26.1 + - - -
459A SER 3.2 16.7 + - - -
460A CYS 3.3 2.9 + - - -
462A THR* 1.3 79.8 - - - +
464A PHE* 1.3 61.8 + - - +
466A GLN* 3.5 8.3 + - - +
467A GLU* 3.1 17.2 + - - +
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Residues in contact with PHE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 5.7 1.6 - - + -
426A TYR* 5.2 2.7 - + - -
427A LEU* 3.4 38.4 - - + -
430A ARG* 3.7 60.6 - - + -
431A ALA* 4.8 4.9 - - - -
434A ARG* 3.4 24.3 - - + +
460A CYS 2.8 18.4 + - - +
461A LEU* 3.3 9.9 - - + +
462A THR 2.8 0.4 + - - -
463A GLY* 1.3 72.8 - - - +
465A LEU* 1.3 86.5 + - + +
466A GLN 2.9 1.9 + - - -
467A GLU* 3.0 14.0 + - - +
468A TYR* 3.3 30.7 + + - -
470A LEU* 4.3 9.9 - - + -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LEU* 4.0 7.9 - - + -
461A LEU* 2.9 36.8 + - + +
462A THR* 2.8 17.2 + - + +
464A PHE* 1.3 95.2 - - + +
466A GLN* 1.3 57.1 + - + +
468A TYR 4.1 0.2 - - - -
469A GLY 3.0 4.3 + - - -
470A LEU* 2.7 62.4 + - + +
472A VAL* 3.9 33.2 - - + +
474A VAL* 4.3 7.6 - - + -
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Residues in contact with GLN 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A THR* 2.9 32.7 + - + +
463A GLY* 3.9 7.3 - - - +
465A LEU* 1.3 76.7 - - + +
467A GLU* 1.3 61.5 + - - +
468A TYR 2.9 2.0 - - - -
469A GLY* 2.6 24.9 + - - +
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Residues in contact with GLU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 3.0 37.4 - - + +
434A ARG* 3.5 27.0 + - - +
463A GLY 3.1 11.4 + - - +
464A PHE 3.0 9.7 + - - +
466A GLN* 1.3 77.3 - - - +
468A TYR* 1.3 78.6 + - + +
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Residues in contact with TYR 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A GLU 4.4 2.2 - - - -
402A TYR* 2.8 26.7 + - - +
403A GLY 3.8 11.4 - - - -
404A LEU* 4.1 15.4 - - + +
407A ILE* 3.5 47.1 - - + +
409A LYS* 3.5 20.6 + - - +
430A ARG* 3.3 22.0 + - - -
434A ARG* 5.9 0.4 - - - -
464A PHE* 3.3 35.5 + + - +
466A GLN 2.9 0.6 - - - -
467A GLU* 1.3 102.3 + - + +
469A GLY* 1.3 66.1 + - - +
470A LEU* 4.0 21.1 - - + -
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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
------------------------------------------------------------
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