Contacts of the helix formed by residues 471 - 495 (chain E) in PDB entry 5MG3
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 THR 471 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E ARG* 4.0 20.5 + - - +
470E GLU* 1.3 89.3 + - - +
472E LEU* 1.4 66.3 + - - +
473E HIS* 3.7 21.1 - - + +
474E THR* 3.1 33.2 + - + +
475E THR 3.1 18.2 + - - -
239Y ARG* 3.5 2.0 - - - +
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Residues in contact with LEU 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E ARG* 5.1 1.8 - - - +
470E GLU* 4.7 3.6 - - - +
471E THR* 1.4 71.7 - - - +
473E HIS* 1.4 56.5 + - - +
475E THR* 3.2 14.6 - - + -
476E LEU* 2.8 54.6 + - + +
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Residues in contact with HIS 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471E THR* 3.5 16.6 - - + +
472E LEU* 1.4 77.1 - - - +
474E THR* 1.4 79.4 + - + +
476E LEU* 3.2 16.4 + - + +
477E ILE* 2.9 37.2 + - + +
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Residues in contact with THR 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471E THR* 3.1 21.9 + - + -
473E HIS* 1.4 98.2 - - + +
475E THR* 1.3 59.8 + - - +
477E ILE* 3.6 7.8 + - - +
478E VAL* 3.4 28.9 + - - +
239Y ARG* 3.0 32.0 + - - -
243Y ARG* 4.5 27.7 - - + +
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Residues in contact with THR 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E GLU* 2.5 34.1 + - - +
471E THR 3.1 0.9 + - - -
472E LEU* 3.2 19.7 - - + +
474E THR* 1.3 79.4 + - - +
476E LEU* 1.3 66.5 + - + +
478E VAL* 3.6 8.2 - - - +
479E ALA* 3.1 32.9 + - + +
235Y VAL* 4.7 16.3 - - + +
239Y ARG* 3.1 11.8 + - - +
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Residues in contact with LEU 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E LEU* 2.8 43.6 + - + +
473E HIS* 3.2 15.8 + - + +
475E THR* 1.3 78.4 - - + +
477E ILE* 1.4 52.3 + - + +
479E ALA* 3.4 6.8 + - + +
480E ALA* 2.7 37.1 + - - +
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Residues in contact with ILE 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473E HIS* 2.9 26.4 + - + +
474E THR* 3.6 9.2 + - - +
475E THR 3.4 0.6 - - - -
476E LEU* 1.4 71.8 - - + +
478E VAL* 1.4 60.9 + - + +
480E ALA* 3.3 9.5 + - + +
481E VAL* 3.0 31.2 + - + +
245Y VAL* 5.2 6.3 - - + -
264Y HIS* 3.7 45.5 - - + +
266Y PRO* 4.3 16.6 - - + -
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Residues in contact with VAL 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474E THR 3.4 13.8 + - - +
475E THR* 3.6 15.7 - - - +
477E ILE* 1.4 73.8 - - + +
479E ALA* 1.3 63.6 - - - +
481E VAL* 3.7 4.6 + - - +
482E THR* 2.7 29.1 + - - -
235Y VAL* 4.5 13.0 - - + -
238Y GLU* 3.9 47.9 - - + +
239Y ARG* 4.9 4.5 - - - +
266Y PRO* 3.8 31.6 - - + -
268Y LYS* 4.6 3.4 - - - +
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Residues in contact with ALA 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475E THR* 3.1 24.0 + - + +
476E LEU* 3.8 8.7 - - + +
478E VAL* 1.3 76.4 - - - +
480E ALA* 1.4 59.6 + - - +
482E THR* 3.6 7.4 - - - +
483E ALA* 2.9 30.1 + - - +
235Y VAL* 4.0 18.8 - - + -
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Residues in contact with ALA 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E LEU 2.7 19.6 + - - +
477E ILE* 3.3 15.7 - - + +
478E VAL 3.2 0.2 - - - -
479E ALA* 1.4 74.1 - - - +
481E VAL* 1.4 67.0 + - + +
483E ALA* 3.4 4.1 + - - +
484E VAL* 3.0 32.6 + - + +
264Y HIS* 5.7 3.4 - - - +
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Residues in contact with VAL 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477E ILE 3.0 15.9 + - - +
478E VAL* 4.2 4.5 - - - +
480E ALA* 1.4 72.9 - - - +
482E THR* 1.3 64.5 + - - +
484E VAL* 3.6 5.2 + - - +
485E MET* 3.1 22.9 + - + +
238Y GLU* 6.0 2.5 - - - +
264Y HIS* 3.9 32.1 - - + +
265Y LEU* 4.1 14.6 - - + -
266Y PRO* 6.3 0.7 - - + -
413Y ILE* 5.9 4.5 - - + -
417Y MET* 3.8 39.0 - - + +
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Residues in contact with THR 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478E VAL 2.7 23.8 + - - -
479E ALA* 3.6 8.2 - - - +
481E VAL* 1.3 78.6 - - - +
483E ALA* 1.3 62.6 + - - +
485E MET* 3.4 4.6 + - - +
486E SER* 3.1 25.7 + - - +
199Y LEU* 6.3 2.2 - - + -
231Y THR* 4.7 16.8 - - + -
234Y VAL* 4.0 26.0 - - + +
235Y VAL* 4.7 8.8 - - + +
238Y GLU* 4.4 16.6 + - - +
413Y ILE* 5.7 7.9 - - + +
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Residues in contact with ALA 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479E ALA 2.9 21.2 + - - +
480E ALA* 3.7 6.1 - - - +
482E THR* 1.3 71.9 - - - +
484E VAL* 1.4 63.7 - - + +
486E SER* 3.4 9.0 - - - -
487E LEU* 3.0 30.5 + - + +
231Y THR* 6.2 2.5 - - - -
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Residues in contact with VAL 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480E ALA* 3.0 19.6 + - + +
481E VAL* 4.0 4.7 - - - +
483E ALA* 1.4 79.0 - - + +
485E MET* 1.3 58.8 + - - +
487E LEU* 3.0 19.6 + - + +
488E ILE* 2.7 50.2 + - + +
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Residues in contact with MET 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481E VAL* 3.1 18.6 + - + +
482E THR 3.8 3.6 - - - +
484E VAL* 1.3 77.6 - - - +
486E SER* 1.3 62.9 + - - +
488E ILE* 3.7 8.5 + - - +
489E LEU* 3.4 40.0 + - + +
27Y ILE* 4.8 15.0 - - + -
30Y LEU* 4.6 4.5 - - + -
192Y PHE* 3.6 34.5 - - + -
199Y LEU* 6.4 0.7 - - + -
413Y ILE* 3.9 36.8 - - + +
416Y PHE* 6.3 0.2 - - + -
417Y MET* 4.6 24.0 - - + -
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Residues in contact with SER 486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E THR* 3.1 19.8 + - - +
483E ALA* 3.4 11.7 - - - -
485E MET* 1.3 80.0 - - - +
487E LEU* 1.3 59.2 + - - +
489E LEU* 3.5 12.1 + - - +
490E TRP* 3.3 21.5 + - - +
199Y LEU* 4.0 23.1 - - - +
200Y PRO* 3.7 25.0 - - - +
231Y THR* 5.6 4.0 - - - +
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Residues in contact with LEU 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483E ALA* 3.0 19.7 + - + +
484E VAL* 3.0 22.5 + - + +
486E SER* 1.3 68.6 - - - +
488E ILE* 1.4 62.3 + - + +
490E TRP* 3.7 25.3 - - + +
491E GLY* 2.9 26.6 + - - -
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Residues in contact with ILE 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484E VAL* 2.7 38.1 + - + +
485E MET* 3.9 11.7 - - - +
487E LEU* 1.4 70.3 - - + +
489E LEU* 1.4 66.6 + - - +
491E GLY* 3.6 1.1 + - - -
492E LEU* 3.3 34.6 + - + +
27Y ILE* 4.2 24.0 - - + -
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Residues in contact with LEU 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485E MET* 3.4 36.6 + - + +
486E SER* 3.6 10.8 - - - +
487E LEU 3.4 0.2 - - - -
488E ILE* 1.4 77.0 - - - +
490E TRP* 1.3 55.8 + - + +
492E LEU* 3.0 19.5 + - - +
493E ASP* 3.1 19.7 + - - +
27Y ILE* 4.3 14.1 - - + -
30Y LEU* 4.1 26.7 - - + -
31Y ILE* 3.9 23.4 - - + +
34Y ARG* 4.2 19.5 - - - +
196Y VAL* 3.8 24.2 - - + -
199Y LEU* 5.7 7.9 - - + -
200Y PRO* 5.5 1.3 - - + -
413Y ILE* 6.0 1.6 - - + -
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Residues in contact with TRP 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486E SER 3.3 15.9 + - - +
487E LEU* 3.7 25.8 - - + +
488E ILE 3.3 0.2 - - - -
489E LEU* 1.3 77.1 - - - +
491E GLY* 1.3 67.2 + - - +
493E ASP* 3.1 9.1 - - - +
494E GLY* 3.2 5.7 + - - -
498E ARG* 2.8 56.3 + - - +
34Y ARG* 5.0 0.9 - - - +
200Y PRO* 3.7 27.6 - - + +
201Y PRO* 5.5 1.8 - - - +
205Y HIS* 4.1 6.7 - + - -
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Residues in contact with GLY 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E LEU* 2.9 16.8 + - - -
488E ILE 4.2 1.6 - - - -
490E TRP* 1.3 82.5 - - - +
492E LEU* 1.3 59.3 + - - +
494E GLY* 3.2 15.2 + - - -
495E ILE* 3.6 14.5 + - - +
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Residues in contact with LEU 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488E ILE* 3.3 29.6 + - + +
489E LEU 3.0 10.4 + - - +
491E GLY* 1.3 75.8 - - - +
493E ASP* 1.4 54.5 + - - +
495E ILE* 3.4 30.7 - - + +
496E LEU* 3.5 17.7 - - + +
27Y ILE* 4.6 20.6 - - + -
31Y ILE* 3.8 28.9 - - + -
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Residues in contact with ASP 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489E LEU 3.1 11.0 + - - +
490E TRP* 3.1 8.3 - - - +
492E LEU* 1.4 71.9 - - - +
494E GLY* 1.4 58.1 + - - +
495E ILE 3.4 1.1 - - - -
496E LEU* 3.8 7.4 - - + +
497E VAL* 3.2 18.8 + - + -
498E ARG* 2.6 66.4 + - - +
31Y ILE* 4.6 13.0 - - + +
34Y ARG* 2.6 36.6 + - + -
35Y ILE* 5.8 0.9 - - + -
38Y PHE* 3.3 12.1 - - - -
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Residues in contact with GLY 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490E TRP 3.2 12.2 + - - -
491E GLY* 3.2 10.3 + - - -
493E ASP* 1.4 78.6 + - - +
495E ILE* 1.3 60.1 + - - +
496E LEU 3.3 1.3 + - - -
498E ARG* 3.8 28.0 - - - +
499E LEU* 3.9 11.8 - - - +
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Residues in contact with ILE 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E GLY 3.6 11.9 + - - +
492E LEU* 3.4 32.1 - - + +
494E GLY* 1.3 74.9 - - - +
496E LEU* 1.4 72.6 + - + +
499E LEU* 3.3 23.6 - - + +
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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
------------------------------------------------------------
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