Contacts of the helix formed by residues 483 - 502 (chain A) in PDB entry 5MJ6
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 LEU 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLU* 4.3 3.6 - - - +
477A MET* 3.7 25.1 - - + -
479A TRP 4.1 0.2 + - - -
480A TRP* 3.1 25.9 + - + +
481A ASN 3.4 1.8 + - - -
482A ASP* 1.3 75.9 - - - +
484A TRP* 1.3 52.7 + - - +
486A ASN* 2.7 32.5 + - + +
487A GLU* 3.1 30.7 + - + -
543A MET* 3.7 37.4 - - + +
544A PHE* 3.7 48.0 - - + -
548A SER* 4.5 3.1 - - - +
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Residues in contact with TRP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ASP* 3.2 14.9 + - - -
483A LEU* 1.3 77.7 - - - +
485A LEU* 1.3 79.5 + - + +
487A GLU 4.2 0.2 - - - +
488A GLY* 2.8 29.1 + - - +
489A PHE* 3.6 1.6 + + - -
530A ILE* 3.7 42.3 - - + +
531A SER* 4.0 8.2 - - - -
543A MET* 5.2 0.8 - - - +
548A SER* 3.6 30.9 + - - +
552A GLY* 3.8 30.1 - - - -
555A LEU* 4.8 5.8 - - + -
556A LEU* 4.3 15.7 - - + -
586A SER* 3.5 22.6 + - - -
589A LEU* 3.9 12.1 - - + -
590A TRP* 3.6 37.5 - + - -
611A THR* 4.1 9.8 - - + +
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 4.5 6.4 - - - +
477A MET* 4.9 1.6 - - + -
482A ASP* 3.1 26.0 + - + +
483A LEU 3.1 0.4 + - - -
484A TRP* 1.3 107.2 - - + +
486A ASN* 1.3 63.0 + - - +
489A PHE* 3.5 24.2 - - + +
575A TYR* 4.2 8.8 + - - +
584A ILE* 4.1 26.1 - - + +
585A GLN* 3.5 34.1 - - - +
586A SER* 3.6 6.3 - - - +
589A LEU* 3.8 31.0 - - + -
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Residues in contact with ASN 486 (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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295A GLU* 4.9 3.4 + - - -
357A TYR* 3.2 16.2 + - - -
431A GLU* 4.5 7.5 + - - -
468A HIS* 3.9 9.3 - - + -
471A PHE 4.0 7.1 - - - +
472A GLY* 3.2 28.7 + - - -
475A VAL 4.1 1.9 - - - +
476A THR* 4.1 0.2 - - - -
477A MET* 3.0 46.5 + - + +
482A ASP 4.2 0.4 + - - -
483A LEU* 2.7 17.7 + - + +
485A LEU* 1.3 75.2 - - - +
487A GLU* 1.3 64.2 + - + +
489A PHE* 3.4 2.4 + - - +
490A ALA* 2.9 30.8 + - - +
584A ILE* 5.3 1.4 - - - +
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 4.1 4.9 - - - +
431A GLU* 4.2 0.2 - - - +
464A HIS* 3.5 0.2 + - - -
468A HIS* 3.4 10.5 - - - -
483A LEU* 3.1 32.0 + - + +
486A ASN* 1.3 77.2 - - + +
488A GLY* 1.3 58.8 + - - +
490A ALA* 4.0 0.7 - - - +
491A THR* 2.7 39.0 + - - -
544A PHE* 4.0 5.9 - - - -
548A SER* 3.8 7.2 - - - +
549A TYR* 3.0 42.0 + - + -
1136A ZN 2.0 31.4 - - - -
1137A 7O2 3.0 24.8 + - - -
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A TRP* 2.8 19.9 + - - -
487A GLU* 1.3 70.6 - - - +
489A PHE* 1.3 60.9 + - - -
491A THR 3.2 1.0 + - - -
492A PHE* 2.9 20.8 + - - +
548A SER 3.1 18.4 + - - -
549A TYR 3.7 9.4 - - - -
552A GLY 3.9 3.8 - - - -
553A SER* 3.3 17.3 - - - -
556A LEU* 4.1 6.7 - - - -
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Residues in contact with PHE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE* 3.1 54.5 - + + -
484A TRP* 3.6 6.4 + + - -
485A LEU* 3.5 25.6 - - + +
486A ASN 3.4 2.0 + - - +
487A GLU 3.4 0.4 - - - -
488A GLY* 1.3 75.7 - - - +
490A ALA* 1.3 63.6 + - - +
492A PHE* 3.2 2.6 + + - +
493A MET* 2.9 37.5 + - + +
556A LEU* 3.3 34.1 - - + -
568A PHE* 4.7 6.3 - + - -
572A VAL* 4.0 19.1 - - + -
575A TYR* 5.3 2.5 - + - -
589A LEU* 3.5 45.5 - - + -
593A PHE* 5.0 2.2 - + - -
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Residues in contact with ALA 490 (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 HIS* 3.4 18.8 + - + +
467A ALA* 4.0 13.6 - - - +
468A HIS* 3.5 40.4 - - + +
471A PHE* 4.6 3.8 - - - +
486A ASN 2.9 18.3 + - - +
487A GLU 4.0 1.1 - - - +
489A PHE* 1.3 76.4 - - - +
491A THR* 1.3 57.6 + - - +
493A MET* 3.4 1.6 + - - +
494A GLU* 3.0 27.5 + - - +
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Residues in contact with THR 491 (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 HIS* 3.5 4.8 - - - -
487A GLU 2.7 22.3 + - - -
488A GLY 3.7 0.7 - - - -
490A ALA* 1.3 73.8 - - - +
492A PHE* 1.3 67.2 + - - +
494A GLU* 3.3 14.7 - - - +
495A TYR* 3.3 32.9 + - + -
511A PHE* 4.7 0.2 - - + -
549A TYR* 3.4 38.6 + - - +
550A PHE* 3.7 30.5 - - + -
553A SER* 3.8 6.5 - - - +
1137A 7O2 4.4 2.2 - - + -
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Residues in contact with PHE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A GLY 2.9 14.2 + - - +
489A PHE* 3.5 7.0 - + - +
491A THR* 1.3 77.8 - - - +
493A MET* 1.3 74.8 + - + +
495A TYR* 3.4 3.4 + - - +
496A PHE* 3.0 49.0 + + + +
511A PHE* 5.0 8.3 - + - -
553A SER* 3.4 27.2 - - - -
556A LEU* 3.9 16.2 - - + -
557A LEU* 3.7 34.3 - - + -
560A LYS* 3.6 28.0 - - + -
568A PHE* 3.6 29.4 - + - -
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Residues in contact with MET 493 (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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403A PHE* 6.4 0.2 - - - -
404A PHE* 4.1 11.4 - - + -
407A TYR* 4.0 16.4 - - + -
408A PHE* 3.9 34.1 - - + -
467A ALA* 3.7 19.7 - - + -
471A PHE* 4.1 20.9 - - + -
489A PHE* 2.9 24.6 + - + +
492A PHE* 1.3 93.0 - - + +
494A GLU* 1.3 67.6 + - - +
496A PHE* 4.1 17.3 - - - -
497A SER* 2.9 30.0 + - - -
568A PHE* 4.2 13.9 - - + -
572A VAL* 4.4 3.6 - - + -
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Residues in contact with GLU 494 (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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460A LYS* 3.4 50.8 - - + +
463A ALA* 4.0 11.6 - - + +
464A HIS* 2.9 32.4 + - - +
467A ALA* 4.8 1.2 - - - +
490A ALA 3.0 12.7 + - - +
491A THR* 3.3 12.1 - - - +
493A MET* 1.3 78.6 - - - +
495A TYR* 1.3 83.4 + - + +
497A SER* 3.2 5.5 + - - -
498A LEU* 3.1 25.5 - - + +
1137A 7O2 3.9 16.4 - - - -
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Residues in contact with TYR 495 (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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460A LYS* 3.0 35.2 + - + -
491A THR* 3.3 24.9 + - + +
492A PHE 4.2 2.2 - - - +
494A GLU* 1.3 97.9 + - - +
496A PHE* 1.3 63.8 + - - +
498A LEU* 4.1 6.6 - - + +
499A GLU* 3.3 22.9 + - - +
507A SER* 3.4 40.8 + - - -
508A TYR* 5.1 1.1 - - - -
510A ASP* 3.8 7.4 - - + +
511A PHE* 3.6 48.0 + + + -
514A ALA* 5.4 0.5 - - - +
550A PHE* 4.0 29.8 - + - -
1140A BR 4.5 1.8 - - - -
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Residues in contact with PHE 496 (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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403A PHE* 4.5 10.1 - + - -
407A TYR* 3.6 41.3 - + - -
492A PHE* 3.0 32.0 + + + +
493A MET* 3.9 19.5 - - - +
495A TYR* 1.3 78.2 - - - +
497A SER* 1.3 65.7 + - - +
499A GLU* 3.1 14.5 + - + +
500A LYS* 3.1 49.9 + - + +
560A LYS* 3.5 34.3 - - + -
565A GLU* 4.1 11.0 - - + -
1140A BR 4.2 16.5 - - + +
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Residues in contact with SER 497 (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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400A LEU* 3.6 15.0 - - - +
403A PHE* 3.5 34.1 - - - -
404A PHE* 3.6 19.5 - - - -
463A ALA* 3.6 4.9 - - - +
493A MET 2.9 22.3 + - - -
494A GLU 3.2 5.9 + - - -
496A PHE* 1.3 76.5 - - - +
498A LEU* 1.3 59.9 + - - +
500A LYS* 3.2 2.9 + - - +
501A ILE* 3.0 32.7 + - - +
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Residues in contact with LEU 498 (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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400A LEU* 5.0 0.4 - - + -
459A THR* 3.4 42.4 - - + +
460A LYS* 3.5 33.4 - - + -
463A ALA* 4.2 8.3 - - + -
494A GLU* 3.1 22.0 + - + +
495A TYR* 4.2 4.5 - - + +
496A PHE 3.3 0.2 - - - -
497A SER* 1.3 80.0 + - - +
499A GLU* 1.3 60.3 + - - +
502A PHE* 2.7 53.3 + - + +
503A LYS* 3.7 0.2 - - - -
505A LEU* 5.0 2.5 - - + -
507A SER* 3.4 29.2 - - - +
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Residues in contact with GLU 499 (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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495A TYR 3.3 15.9 + - - +
496A PHE* 3.1 9.0 + - + +
498A LEU* 1.3 78.9 - - - +
500A LYS* 1.3 67.0 + - + +
503A LYS* 3.0 53.7 + - + +
506A SER* 5.6 0.2 - - - -
507A SER* 4.5 4.5 + - - +
508A TYR* 4.1 33.2 + - - +
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Residues in contact with LYS 500 (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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403A PHE* 3.7 31.6 - - + -
496A PHE* 3.1 37.0 + - + +
497A SER 3.5 6.7 - - - +
498A LEU 3.2 0.2 - - - -
499A GLU* 1.3 88.9 - - + +
501A ILE* 1.3 65.2 + - + +
503A LYS* 3.8 16.3 + - - +
565A GLU* 2.7 31.0 + - - -
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Residues in contact with ILE 501 (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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399A LYS* 4.2 19.6 + - + +
400A LEU* 3.9 23.8 - - + -
403A PHE* 3.9 39.3 - - + -
497A SER 3.0 13.7 + - - +
500A LYS* 1.3 83.5 - - + +
502A PHE* 1.3 84.7 + - + +
503A LYS 3.7 1.6 - - - -
504A GLU* 4.7 3.3 - - - +
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Residues in contact with PHE 502 (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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392A TYR* 4.3 12.6 - + - -
396A THR* 4.0 15.0 - - + -
399A LYS* 4.0 35.0 - - + -
400A LEU* 4.1 19.1 - - + -
459A THR* 3.6 31.0 - - + -
498A LEU* 2.7 33.3 + - + +
501A ILE* 1.3 96.0 - - + +
503A LYS* 1.3 63.3 + - - +
504A GLU* 3.1 23.1 - - - -
505A LEU* 3.0 35.5 + - + +
506A SER 4.4 0.5 + - - -
507A SER* 5.1 1.6 + - - -
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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