Contacts of the helix formed by residues 473 - 485 (chain E) in PDB entry 1MKD
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 ILE 473 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370E MET* 3.8 26.0 - - + -
373E HIS* 3.6 35.6 + - + +
374E MET* 4.5 9.9 - - + -
416E LEU* 3.9 14.8 - - + -
469E PHE* 3.0 33.4 + - + +
471E ASP 3.6 0.4 - - - -
472E TYR* 1.3 97.6 - - + +
474E VAL* 1.3 66.9 + - - +
475E HIS 3.6 1.1 - - - -
476E PRO* 3.3 4.3 - - - +
477E LEU* 3.2 24.3 + - - +
389J VAL* 6.2 0.9 - - + -
390J THR 5.8 1.3 - - - +
391J SER* 4.7 15.3 - - - +
393J GLY* 6.2 1.6 - - - -
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Residues in contact with VAL 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E LEU* 3.7 18.8 - - + +
419E PRO* 4.1 10.5 - - + -
420E THR* 4.4 1.1 - - + -
469E PHE* 3.1 48.7 + - + +
470E ILE* 3.9 9.0 - - - -
473E ILE* 1.3 74.8 - - + +
475E HIS* 1.3 59.0 + - - +
477E LEU* 3.2 5.8 + - - +
478E TRP* 2.9 51.1 + - + -
496E LEU* 3.8 22.0 - - + -
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Residues in contact with HIS 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E ILE* 2.6 34.4 + - + +
471E ASP* 4.7 3.8 - - - +
474E VAL* 1.3 74.7 - - - +
476E PRO* 1.3 65.8 - - + +
479E GLU* 2.9 67.2 + - + +
493E LEU* 3.6 13.6 - - + +
496E LEU* 3.7 14.9 - - + +
497E GLU* 3.0 41.0 + - + -
500E ARG* 6.2 3.4 - - - -
486J HIS* 6.3 0.2 - - + -
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Residues in contact with PRO 476 (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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377E LEU* 3.8 19.6 - - + +
381E LYS* 5.1 5.0 - - - +
470E ILE 3.3 2.9 - - - +
471E ASP 3.2 28.0 - - - +
472E TYR* 3.6 13.5 - - - +
473E ILE 3.3 12.8 - - - +
475E HIS* 1.3 93.8 - - + +
477E LEU* 1.3 58.0 + - - +
479E GLU* 3.9 12.2 - - - +
480E THR* 2.8 27.5 + - - -
486J HIS* 4.4 10.5 - - + +
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Residues in contact with LEU 477 (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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373E HIS* 3.9 8.7 - - + -
377E LEU* 3.9 20.1 - - + +
380E LEU* 4.5 4.0 - - + -
409E ASN* 4.2 14.6 - - - +
412E HIS* 3.5 34.3 - - + +
413E CYS* 3.7 34.3 - - - -
416E LEU* 3.8 22.4 - - + -
473E ILE 3.2 14.3 + - - +
474E VAL* 3.6 3.1 - - - +
476E PRO* 1.3 80.1 - - - +
478E TRP* 1.3 64.6 + - + +
480E THR* 3.2 6.6 + - - -
481E TRP* 2.9 23.9 + - - +
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Residues in contact with TRP 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E TRP* 3.8 25.4 - + - -
272E LEU* 4.0 9.6 - - + -
413E CYS* 3.3 40.3 + - + +
416E LEU 3.3 18.3 + - - -
417E SER* 4.0 12.6 - - - -
420E THR* 3.7 15.6 - - + +
474E VAL* 2.9 44.5 + - + +
477E LEU* 1.3 77.0 - - + +
479E GLU* 1.3 55.9 + - - +
481E TRP* 3.7 31.8 - + - +
482E ALA* 2.7 36.0 + - + +
489E ALA* 5.0 3.1 - - + -
492E ILE* 3.8 28.3 - - + -
493E LEU* 4.4 9.9 - - + +
496E LEU* 4.0 14.6 - - + -
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Residues in contact with GLU 479 (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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475E HIS* 2.9 46.1 + - + +
476E PRO* 3.9 9.8 - - - +
478E TRP* 1.3 75.9 - - - +
480E THR* 1.3 63.7 + - - +
482E ALA* 3.4 7.8 + - - +
483E ASP* 3.1 32.2 + - - +
493E LEU* 4.3 14.2 - - + +
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Residues in contact with THR 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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377E LEU* 3.4 13.2 - - + +
380E LEU* 3.4 27.8 - - + -
381E LYS* 3.8 30.3 - - + +
384E VAL* 3.7 16.4 - - + +
476E PRO 2.8 14.1 + - - -
477E LEU 3.2 8.9 + - - -
479E GLU* 1.3 77.3 - - - +
481E TRP* 1.3 65.5 + - - +
483E ASP* 3.0 18.5 + - - +
484E LEU* 3.1 10.9 + - - +
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Residues in contact with TRP 481 (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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272E LEU* 4.1 25.0 - - + +
275E THR* 5.0 2.5 + - + +
278E LEU* 4.2 5.8 - - + -
380E LEU* 4.1 8.2 - - + +
406E VAL* 3.8 31.9 - - + -
409E ASN* 4.4 11.2 - - + -
410E MET* 3.8 46.2 - - + -
413E CYS* 3.8 26.7 - - - -
477E LEU 2.9 13.8 + - - +
478E TRP* 3.3 29.1 + + - +
480E THR* 1.3 76.7 - - - +
482E ALA* 1.3 64.5 + - - +
484E LEU* 3.1 18.1 + - + +
485E VAL* 3.1 57.7 + - + +
489E ALA* 4.2 5.7 - - + +
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Residues in contact with ALA 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 TRP* 2.7 22.1 + - + +
479E GLU 3.5 6.3 - - - +
480E THR 3.2 0.2 - - - -
481E TRP* 1.3 73.8 - - - +
483E ASP* 1.3 57.9 + - - +
485E VAL* 3.6 0.9 - - - +
486E HIS* 2.9 34.3 + - - +
487E PRO* 4.6 2.1 - - - +
489E ALA* 3.7 28.9 - - + +
490E GLN* 5.1 3.1 - - - +
493E LEU* 3.8 25.6 - - + -
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Residues in contact with ASP 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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384E VAL* 3.5 23.5 - - + +
387E LYS* 3.1 18.2 + - - -
479E GLU* 3.1 24.8 + - - +
480E THR* 3.0 15.0 + - - +
482E ALA* 1.3 75.8 - - - +
484E LEU* 1.3 66.6 + - - +
486E HIS* 3.2 16.9 + - - +
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Residues in contact with LEU 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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277E ALA* 4.8 0.7 - - - +
380E LEU* 4.2 15.0 - - + -
383E MET* 4.3 29.4 - - + +
384E VAL* 4.1 17.0 - - + +
387E LYS* 3.6 20.4 + - + +
395E LEU* 3.7 43.1 - - + +
397E LEU* 6.2 0.9 - - + -
406E VAL* 4.3 16.2 - - + -
480E THR 3.1 7.8 + - - +
481E TRP* 3.1 35.0 + - + +
483E ASP* 1.3 82.4 - - - +
485E VAL* 1.3 60.2 + - + +
486E HIS 3.4 0.2 - - - -
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Residues in contact with VAL 485 (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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275E THR* 4.2 16.2 - - + +
277E ALA* 3.7 23.8 - - + -
278E LEU* 4.4 7.4 - - + -
395E LEU* 4.8 1.1 - - + -
481E TRP* 3.1 53.4 + - + +
482E ALA 4.1 0.4 - - - +
484E LEU* 1.3 85.8 - - + +
486E HIS* 1.3 65.7 + - - +
488E ASP* 2.9 26.2 + - + +
489E ALA* 3.8 22.0 - - + +
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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