Contacts of the helix formed by residues 458 - 476 (chain A) in PDB entry 3RTR
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 ASP 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A PRO* 4.7 7.8 - - + +
456A ILE* 3.6 14.9 - - + +
457A GLU* 1.3 78.0 - - - +
459A LYS* 1.3 66.8 + - - +
460A ASP* 3.4 4.3 - - - +
461A VAL* 3.2 34.5 + - + +
462A PHE 3.8 2.1 + - - -
707A ARG* 3.6 19.4 + - - -
741A ARG 4.1 4.3 - - - -
742A PHE* 4.1 8.1 - - - +
743A LYS 5.0 1.7 + - - -
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Residues in contact with LYS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE 4.2 15.3 - - - +
454A LYS* 4.9 9.4 + - - +
456A ILE* 2.9 28.9 - - + +
457A GLU 3.0 14.1 + - - +
458A ASP* 1.3 69.2 - - - +
460A ASP* 1.3 66.3 + - - +
461A VAL 2.8 2.4 + - - -
462A PHE* 2.9 19.4 + - + +
463A GLN* 3.1 13.3 + - + +
496A CYS* 6.3 2.9 - - - -
740A SER 4.6 14.8 + - - +
741A ARG* 3.7 12.3 + - + +
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Residues in contact with ASP 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ASP* 3.6 6.2 - - - +
459A LYS* 1.3 75.2 - - - +
461A VAL* 1.3 84.6 + - - +
463A GLN* 3.2 20.1 + - - +
464A LYS* 2.9 33.1 + - - +
703A ILE* 3.9 11.7 - - + -
706A ASP* 6.3 2.9 - - + -
707A ARG* 2.7 45.1 + - + +
710A LEU* 5.4 6.2 - - + +
741A ARG* 4.4 7.0 + - + +
742A PHE* 3.6 12.8 - - + -
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Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PRO* 4.3 16.8 - - + -
420A GLU* 4.6 3.8 - - + +
458A ASP* 3.4 27.4 - - + +
459A LYS 2.8 4.4 + - - -
460A ASP* 1.3 95.1 + - - +
462A PHE* 1.3 62.0 + - - +
464A LYS 3.4 0.2 + - - -
465A PHE* 3.1 43.3 + - + -
700A HIS* 4.6 10.1 - - + +
703A ILE* 3.5 30.9 - - + +
707A ARG* 5.0 3.8 - - - +
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Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PRO* 3.4 34.5 - - + +
422A LEU* 3.6 18.2 - - + -
423A ALA* 3.4 28.5 - - + -
426A CYS* 4.4 11.9 - - - -
449A VAL* 6.1 2.2 - - + -
453A PHE* 5.1 17.7 - - + -
456A ILE* 5.4 5.4 - - + -
458A ASP 3.8 2.2 + - - +
459A LYS* 2.9 10.7 + - + +
461A VAL* 1.3 77.9 - - - +
463A GLN* 1.3 73.3 + - - +
465A PHE* 4.1 4.2 - - - +
466A TYR* 3.0 30.9 + + + +
488A MET* 6.2 1.6 - - - -
492A LEU* 4.9 23.3 - - + -
496A CYS* 6.1 4.7 - - - -
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Residues in contact with GLN 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LYS* 3.1 12.1 + - - +
460A ASP* 3.3 22.4 + - - +
462A PHE* 1.3 81.9 - - + +
464A LYS* 1.3 60.9 + - - +
466A TYR* 2.9 9.3 + - - +
467A ALA* 2.8 36.0 + - + +
496A CYS* 6.3 3.1 - - - -
500A TYR* 4.7 25.0 + - - +
503A LYS* 3.9 26.3 - - - +
504A LEU* 5.8 6.6 - - + +
706A ASP* 5.4 3.0 + - - -
741A ARG* 5.4 5.4 + - - -
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Residues in contact with LYS 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ASP 2.9 19.5 + - - +
461A VAL 3.9 1.1 - - - +
463A GLN* 1.3 80.4 - - + +
465A PHE* 1.3 57.3 + - - +
467A ALA* 3.2 8.3 + - + +
468A LYS* 2.9 29.1 + - + +
503A LYS* 4.4 12.2 - - - +
546A PRO* 4.6 26.4 - - + +
699A THR* 3.6 24.9 - - + +
702A ASN* 4.3 18.2 + - + +
703A ILE* 3.6 19.5 - - + +
706A ASP* 3.2 34.4 + - - -
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Residues in contact with PHE 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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420A GLU* 3.7 44.0 - - + -
423A ALA* 4.0 9.6 - - + -
424A ARG* 5.7 0.2 - - + -
461A VAL* 3.1 33.0 + - + +
462A PHE* 4.1 2.0 - - - +
464A LYS* 1.3 78.5 - - - +
466A TYR* 1.3 58.8 + - - +
468A LYS* 3.0 8.5 + - + +
469A MET* 2.7 51.3 + - + +
695A GLU 5.8 0.2 - - - -
696A GLN* 4.3 10.1 - - + -
699A THR* 3.6 35.4 - - + -
700A HIS* 3.2 39.5 - + - -
703A ILE* 4.1 2.0 - - + -
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Residues in contact with TYR 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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423A ALA* 3.8 14.5 - - + +
426A CYS* 4.7 17.7 - - + -
427A ASP 5.5 0.4 - - - -
430A LEU* 3.5 23.2 - - + +
462A PHE* 3.0 28.7 + + + +
463A GLN* 2.9 6.2 + - - +
465A PHE* 1.3 75.6 - - - +
467A ALA* 1.3 62.9 + - - +
469A MET* 3.8 5.2 - - + -
470A LEU* 3.0 29.7 + - + +
473A ARG* 3.0 26.9 - - - -
485A GLU* 3.6 9.4 + - - -
488A MET* 4.4 13.0 - - - +
489A ILE* 4.7 9.8 - - + +
492A LEU* 3.4 34.1 - - + -
504A LEU* 4.4 19.1 - - + -
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Residues in contact with ALA 467 (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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463A GLN* 2.8 14.4 + - + +
464A LYS* 3.3 16.2 - - + +
466A TYR* 1.3 77.0 - - - +
468A LYS* 1.3 65.0 - - - +
470A LEU* 2.9 5.5 + - - +
471A ALA* 2.9 23.7 + - - +
503A LYS* 6.5 1.3 - - - -
504A LEU* 3.5 30.5 - - + +
507A MET* 4.5 4.6 - - + +
546A PRO* 4.8 12.6 - - + -
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Residues in contact with LYS 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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464A LYS* 2.9 15.0 + - + +
465A PHE* 3.5 11.9 - - + +
467A ALA* 1.3 77.4 - - - +
469A MET* 1.3 63.6 + - - +
471A ALA* 3.4 8.8 + - + +
472A LYS* 3.1 51.5 + - - +
546A PRO* 3.8 35.4 + - + +
547A PHE* 4.8 7.1 - - + +
548A GLN* 5.4 5.8 - - - +
695A GLU* 4.4 24.1 - - - +
698A THR* 4.7 6.1 + - - -
699A THR* 2.9 29.2 - - + +
702A ASN* 5.9 2.7 - - - +
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Residues in contact with MET 469 (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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423A ALA* 3.7 25.6 - - + +
424A ARG* 3.9 25.4 - - + +
427A ASP* 3.1 41.6 - - + +
465A PHE* 2.7 40.6 + - + +
466A TYR* 3.8 8.5 - - + +
468A LYS* 1.3 74.8 - - - +
470A LEU* 1.3 63.3 + - - +
472A LYS* 3.2 15.5 + - + +
473A ARG* 3.1 30.5 + - - +
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Residues in contact with LEU 470 (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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466A TYR* 3.0 33.8 + - + +
467A ALA* 2.9 4.8 + - - +
469A MET* 1.3 72.6 - - - +
471A ALA* 1.3 67.1 + - - +
473A ARG* 3.2 36.3 + - + +
474A LEU* 2.9 38.4 + - + +
479A SER* 6.3 0.2 - - - -
485A GLU* 3.6 11.7 - - - +
489A ILE* 4.8 3.4 - - + -
504A LEU* 4.5 14.8 - - + -
507A MET* 3.7 22.7 - - + -
508A PHE* 3.8 22.4 - - + -
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Residues in contact with ALA 471 (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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467A ALA 2.9 11.8 + - - +
468A LYS* 3.5 10.5 - - - +
470A LEU* 1.3 78.0 - - - +
472A LYS* 1.3 62.7 + - - +
474A LEU* 3.2 1.2 + - - +
475A VAL* 2.9 29.9 + - - +
507A MET* 4.1 7.6 - - - +
545A TRP* 3.6 32.1 - - + -
546A PRO* 4.3 9.4 - - + -
547A PHE* 3.7 15.5 - - + -
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Residues in contact with LYS 472 (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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468A LYS* 3.1 52.1 + - + +
469A MET* 3.2 16.1 + - + +
471A ALA* 1.3 81.0 - - - +
473A ARG* 1.3 63.9 + - + +
475A VAL* 3.4 7.8 + - - -
476A HIS* 3.1 34.7 + - + +
478A ASN* 5.0 0.2 - - - +
547A PHE* 4.7 13.6 - - + -
585A LEU* 5.4 8.4 - - + +
691A GLU* 5.9 0.4 - - - -
695A GLU* 3.6 29.6 + - - -
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Residues in contact with ARG 473 (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 ASP* 3.4 28.6 + - - +
430A LEU* 3.5 30.7 - - - +
431A LYS* 4.3 3.4 - - + +
466A TYR* 3.0 35.6 - - - -
469A MET* 3.1 14.5 + - - +
470A LEU* 3.2 38.6 - - + +
472A LYS* 1.3 78.9 - - + +
474A LEU* 1.3 62.2 + - - +
477A GLN 3.4 1.6 + - - -
478A ASN* 3.0 59.2 + - - +
479A SER* 4.2 5.2 + - - +
485A GLU* 2.7 42.5 + - - -
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Residues in contact with LEU 474 (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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470A LEU* 2.9 41.6 + - + +
471A ALA 3.2 3.6 + - - +
473A ARG* 1.3 77.9 - - + +
475A VAL* 1.3 63.0 + - - +
476A HIS 3.3 1.0 + - - -
477A GLN* 3.4 11.7 + - - +
479A SER* 5.6 9.6 - - - -
482A ASP* 5.9 2.9 - - - +
485A GLU* 6.1 1.1 - - + -
507A MET* 4.4 2.5 - - + +
508A PHE* 4.0 39.9 - - + +
511A ILE* 4.2 31.8 - - + +
538A GLN* 4.6 0.7 - - - +
545A TRP* 3.9 28.0 - - + -
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Residues in contact with VAL 475 (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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471A ALA 2.9 20.3 + - - +
472A LYS* 4.1 4.3 - - - +
473A ARG 3.3 0.2 - - - -
474A LEU* 1.3 76.3 - - - +
476A HIS* 1.3 71.5 + - + +
477A GLN* 3.5 2.2 + - - +
511A ILE* 4.9 1.6 - - - -
538A GLN* 3.1 32.4 + - + +
540A LEU* 4.2 13.2 - - + -
545A TRP* 4.3 6.7 - - + -
547A PHE* 3.7 26.7 - - + -
585A LEU* 5.2 2.9 - - + +
587A LYS* 4.8 1.4 + - - -
30B VAL* 3.3 39.5 - - + -
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Residues in contact with HIS 476 (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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472A LYS* 3.1 29.1 + - + +
473A ARG 3.4 2.2 + - - -
474A LEU 3.2 0.6 - - - -
475A VAL* 1.3 87.1 - - + +
477A GLN* 1.3 65.1 + - - +
478A ASN* 2.8 23.1 + - + +
585A LEU* 3.6 46.5 + - + +
587A LYS* 3.3 45.3 + - + +
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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