Contacts of the helix formed by residues 451 - 469 (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 SER 451 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A TYR* 4.2 2.5 - - - -
450A SER* 1.3 77.3 - - - +
452A MET* 1.3 63.9 + - - +
453A ALA* 3.5 11.8 + - - +
454A ASP* 3.0 37.6 + - - +
455A ARG* 3.2 12.3 + - - +
817A ARG* 4.7 0.4 - - - -
857A THR* 3.4 32.7 - - - -
858A ASP* 4.2 3.8 - - - -
892A LYS* 3.6 14.3 - - - +
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Residues in contact with MET 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TYR* 5.8 1.1 - - - +
451A SER* 1.3 73.1 - - - +
453A ALA* 1.3 62.4 + - - +
455A ARG* 3.1 23.6 + - - +
456A LYS* 3.0 27.9 + - + +
505A LEU* 4.1 16.2 - - + -
814A PRO* 3.7 53.2 - - + +
817A ARG* 3.7 45.8 - - + +
818A GLU* 5.4 3.6 - - + -
858A ASP* 3.8 8.5 + - - +
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Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A SER* 3.6 10.7 - - - +
452A MET* 1.3 79.0 - - - +
454A ASP* 1.3 59.3 + - - +
456A LYS* 3.4 13.6 + - - +
457A LEU* 3.0 28.1 + - - +
818A GLU* 4.8 15.6 - - + +
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLU 5.4 2.8 - - - +
445A TYR* 4.4 2.2 - - + -
450A SER* 3.7 11.4 - - - -
451A SER* 3.0 37.8 + - - +
453A ALA* 1.3 78.2 - - - +
455A ARG* 1.3 61.5 + - - +
457A LEU* 3.4 16.9 + - + +
458A VAL* 3.1 28.9 + - + +
888A ALA* 3.5 20.3 - - + +
892A LYS* 3.1 19.4 + - - +
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Residues in contact with ARG 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 3.3 43.5 + - + +
445A TYR* 3.0 53.6 + - + +
447A SER* 5.5 2.2 + - - -
451A SER 3.2 7.0 + - - +
452A MET* 3.1 33.2 + - - +
454A ASP* 1.3 73.9 - - - +
456A LYS* 1.3 63.5 + - - +
458A VAL* 3.4 4.1 + - - +
459A THR* 2.8 28.7 + - - +
505A LEU* 4.4 11.2 - - + +
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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
----------------------------------------------------------
452A MET* 3.0 25.9 + - + +
453A ALA* 3.6 10.3 - - - +
455A ARG* 1.3 75.7 - - - +
457A LEU* 1.3 53.2 + - - +
459A THR* 3.1 4.9 + - - -
460A LYS* 2.8 46.2 + - + +
505A LEU* 3.5 50.4 + - + +
506A SER 3.9 8.9 + - - -
507A SER* 4.5 6.5 - - - +
509A GLU* 4.2 0.8 + - - +
510A ASP* 3.0 28.6 + - - -
814A PRO* 5.2 1.1 - - + -
818A GLU* 2.6 43.2 + - - +
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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
----------------------------------------------------------
441A GLU* 3.6 26.9 - - + +
442A THR* 4.1 23.3 - - + -
453A ALA 3.0 13.9 + - - +
454A ASP* 3.5 20.9 - - - +
455A ARG 3.3 0.4 - - - -
456A LYS* 1.3 74.3 - - - +
458A VAL* 1.3 57.2 + - + +
460A LYS* 3.5 8.7 + - - +
461A ILE* 3.0 27.4 + - - +
1137A 7O2 3.3 37.0 - - + -
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 4.0 22.2 - - + -
393A ALA* 4.7 1.3 - - + -
441A GLU 4.9 2.7 - - - +
442A THR* 3.7 25.4 - - - +
443A LEU 3.8 15.3 - - - +
444A LEU 3.7 22.2 - - - +
445A TYR* 4.4 7.6 - - + -
454A ASP* 3.1 15.9 + - + +
455A ARG* 3.8 6.7 - - - +
457A LEU* 1.3 73.1 - - + +
459A THR* 1.3 65.1 + - - +
461A ILE* 3.7 0.5 - - - +
462A ILE* 3.3 43.2 + - + +
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Residues in contact with THR 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 2.6 25.4 + - - +
396A THR* 4.1 12.1 - - + -
400A LEU* 4.1 1.6 - - + +
455A ARG 2.8 14.9 + - - -
456A LYS 3.7 3.1 - - - -
458A VAL* 1.3 77.3 - - - +
460A LYS* 1.3 64.0 + - - +
462A ILE* 3.4 1.9 + - - +
463A ALA* 3.1 22.2 + - - +
498A LEU* 3.4 23.8 - - + -
502A PHE* 3.6 33.9 - - + -
505A LEU* 3.8 14.2 - - + +
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Residues in contact with LYS 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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456A LYS* 2.8 33.1 + - + +
457A LEU* 3.9 5.4 - - - +
459A THR* 1.3 74.1 - - - +
461A ILE* 1.3 57.4 + - - +
463A ALA* 3.3 1.2 + - - +
464A HIS* 2.9 23.7 + - - +
494A GLU* 3.4 23.6 - - - +
495A TYR* 3.0 32.7 + - + -
498A LEU* 3.5 29.6 - - + -
505A LEU* 6.2 0.7 - - + -
507A SER* 4.7 3.6 - - - -
510A ASP* 3.7 29.7 + - - +
1137A 7O2 4.1 16.9 - - + -
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Residues in contact with ILE 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY* 3.7 32.5 - - - +
429A ALA* 3.8 15.3 - - + -
438A PHE* 3.9 11.4 - - + -
442A THR* 3.3 35.2 - - + +
457A LEU 3.0 18.1 + - - +
458A VAL 3.7 4.3 - - - +
460A LYS* 1.3 74.9 - - - +
462A ILE* 1.3 63.7 + - + +
464A HIS* 3.4 2.0 + - - +
465A GLU* 3.0 35.9 + - - +
1137A 7O2 3.5 47.1 - - + -
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA* 3.9 21.8 - - + +
396A THR* 4.2 10.1 - - + -
397A THR* 3.7 23.8 - - - +
400A LEU* 3.9 15.5 - - + -
419A LEU* 4.5 4.9 - - + -
436A LEU* 6.5 0.2 - - + -
438A PHE* 4.3 12.3 - - + -
443A LEU* 3.8 25.4 - - + -
458A VAL* 3.3 36.2 + - + +
459A THR 3.9 2.7 - - - +
460A LYS 3.2 0.4 - - - -
461A ILE* 1.3 77.1 - - + +
463A ALA* 1.3 65.5 + - - +
465A GLU* 4.0 0.9 - - - +
466A LEU* 3.0 30.9 + - + +
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Residues in contact with ALA 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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400A LEU* 3.6 17.2 - - + +
404A PHE* 3.6 8.8 - - + -
459A THR 3.1 14.1 + - - +
460A LYS 3.5 8.3 - - - +
462A ILE* 1.3 78.7 - - - +
464A HIS* 1.3 56.6 + - - +
467A ALA* 2.9 31.2 + - - +
494A GLU* 4.0 15.3 - - - +
497A SER* 3.6 24.0 - - - +
498A LEU* 4.2 5.8 - - + -
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Residues in contact with HIS 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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460A LYS 2.9 17.7 + - - +
461A ILE* 3.6 8.7 - - - +
462A ILE 3.2 0.2 - - - -
463A ALA* 1.3 78.8 - - - +
465A GLU* 1.3 81.3 + - - +
467A ALA* 3.3 2.9 + - - +
468A HIS* 3.2 21.3 + + - -
487A GLU* 3.9 2.0 - - - -
490A ALA* 3.4 22.8 + - + +
491A THR* 3.5 22.9 - - - -
494A GLU* 2.9 29.1 + - - +
549A TYR* 4.1 1.0 - + - -
1136A ZN 2.1 36.3 - - - -
1137A 7O2 3.3 24.3 + + + -
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Residues in contact with GLU 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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429A ALA* 3.3 25.1 - - + +
430A MET 4.0 2.7 - - - +
431A GLU* 3.1 24.3 + - - +
436A LEU* 3.6 22.4 - - + -
438A PHE* 3.7 13.5 - - + -
461A ILE 3.0 21.6 + - - +
462A ILE 3.4 1.8 + - - +
463A ALA 3.4 0.2 - - - -
464A HIS* 1.3 83.1 - - - +
466A LEU* 1.3 62.6 + - - +
468A HIS* 3.3 18.0 - - - +
469A GLN* 3.4 13.7 + - - -
1137A 7O2 2.8 44.9 + - - +
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Residues in contact with LEU 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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397A THR* 3.7 22.9 - - + +
400A LEU* 3.5 31.4 - - + -
401A LEU* 3.8 14.8 - - + +
404A PHE* 3.8 10.5 - - + -
417A LEU* 3.9 27.4 - - + -
419A LEU* 5.2 0.7 - - + -
436A LEU* 3.9 17.0 - - + -
462A ILE* 3.0 29.3 + - + +
463A ALA 3.8 3.4 - - - +
465A GLU* 1.3 76.4 - - - +
467A ALA* 1.3 63.5 + - - +
469A GLN* 2.9 29.2 + - + +
470A TRP* 3.3 11.5 - - + -
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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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404A PHE* 3.9 10.6 - - + -
408A PHE* 4.9 2.9 - - + -
463A ALA 2.9 18.0 + - - +
464A HIS 3.7 4.9 - - - +
465A GLU 3.3 0.2 - - - -
466A LEU* 1.3 74.6 - - - +
468A HIS* 1.3 57.2 + - - +
470A TRP* 2.9 26.2 + - - +
471A PHE* 3.0 14.9 + - + -
490A ALA* 4.0 16.6 - - - +
493A MET* 3.7 32.1 - - + -
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Residues in contact with HIS 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLU* 3.4 35.1 + - + -
464A HIS* 3.2 20.4 + - - -
465A GLU* 3.3 11.2 - - - +
467A ALA* 1.3 78.4 - - - +
469A GLN* 1.3 62.5 + - - +
470A TRP 3.0 1.1 + - - -
471A PHE 3.0 25.8 + - - +
472A GLY* 3.6 2.5 - - - -
473A ASN* 3.0 25.9 + - - -
486A ASN* 3.9 11.2 - - + -
487A GLU* 3.3 19.6 + - - -
490A ALA* 3.5 13.8 - - + +
1136A ZN 2.0 37.0 - - - -
1137A 7O2 3.3 14.5 + - - -
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Residues in contact with GLN 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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412A TYR* 3.6 29.6 - - + -
413A PRO* 5.9 0.2 - - - +
417A LEU* 5.0 0.2 - - + -
431A GLU* 3.1 25.5 + - - +
433A TRP* 3.5 26.7 - - + -
434A GLY 3.6 6.6 + - - -
436A LEU* 3.5 19.6 - - + +
465A GLU 3.4 17.9 + - - +
466A LEU* 2.9 31.7 + - + +
468A HIS* 1.3 76.8 - - - +
470A TRP* 1.3 70.0 + - + +
473A ASN* 3.2 20.8 + - - +
474A LEU* 3.4 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
------------------------------------------------------------
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