Contacts of the helix formed by residues 461 - 473 (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 SER 461 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459E ASN 4.1 4.7 + - - -
460E ALA* 1.3 75.0 + - - +
462E VAL* 1.3 66.9 + - - +
463E GLU* 3.1 7.9 - - - -
464E LYS* 2.8 50.3 + - - +
465E SER* 2.9 18.1 + - - -
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Residues in contact with VAL 462 (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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430E THR* 3.8 27.1 - - + -
431E ASP* 5.7 3.4 - - - +
434E MET* 3.9 34.3 - - + -
438E PHE* 4.9 4.9 - - + -
460E ALA* 3.6 7.9 + - + +
461E SER* 1.3 72.8 - - - +
463E GLU* 1.3 78.2 + - - +
465E SER* 3.4 7.3 + - - -
466E GLN* 3.1 23.2 + - - +
503E TYR* 4.7 6.1 - - + -
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Residues in contact with GLU 463 (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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461E SER* 2.9 5.0 + - - -
462E VAL* 1.3 87.4 + - - +
464E LYS* 1.3 64.8 + - + +
466E GLN* 3.1 4.9 + - - +
467E VAL* 3.1 24.6 + - - +
503E TYR* 3.6 22.2 - - + +
506E THR* 3.5 44.2 - - + +
507E ILE* 3.5 22.0 - - + -
508E PRO* 3.9 14.9 - - + +
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Residues in contact with LYS 464 (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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461E SER* 2.8 34.0 + - - +
463E GLU* 1.3 76.2 - - + +
465E SER* 1.3 57.5 + - - +
467E VAL* 3.1 4.1 + - - +
468E GLY* 2.8 27.2 + - - -
507E ILE* 3.7 42.8 - - + +
508E PRO* 5.3 6.3 - - + -
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Residues in contact with SER 465 (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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434E MET* 5.2 1.3 - - - +
454E MET* 3.5 45.3 - - - +
460E ALA* 5.9 0.2 - - - +
461E SER* 2.9 20.3 + - - -
462E VAL* 3.6 12.1 - - - -
464E LYS* 1.3 76.1 - - - +
466E GLN* 1.3 54.3 + - - +
468E GLY* 3.3 1.4 + - - +
469E PHE* 2.7 37.1 + - - +
3005E ZAR 4.1 3.6 - - - +
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Residues in contact with GLN 466 (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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426E TYR* 2.7 31.4 + - - +
430E THR* 3.5 30.4 - - + +
433E ILE* 4.6 3.4 - - - +
434E MET* 4.7 5.7 - - - -
462E VAL 3.1 16.1 + - - +
463E GLU 3.1 7.4 + - - +
465E SER* 1.3 73.2 - - - +
467E VAL* 1.3 62.7 + - - +
469E PHE* 3.1 8.1 + - - +
470E ILE* 2.9 36.7 + - - +
503E TYR* 3.9 23.3 - - + -
3005E ZAR 3.0 47.5 + - - +
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Residues in contact with VAL 467 (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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463E GLU 3.1 15.1 + - - +
464E LYS* 3.1 7.6 + - - +
466E GLN* 1.3 75.7 - - - +
468E GLY* 1.3 57.4 + - - +
470E ILE* 3.5 5.7 + - - +
471E ASP* 2.9 39.1 + - - +
500E ARG* 3.3 44.0 - - + +
503E TYR* 4.0 5.2 - - + -
504E GLN* 3.8 33.7 - - - +
507E ILE* 3.8 14.8 - - + -
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Residues in contact with GLY 468 (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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464E LYS 2.8 14.5 + - - -
465E SER* 3.7 3.1 - - - -
467E VAL* 1.3 75.6 - - - +
469E PHE* 1.3 58.2 + - - +
471E ASP* 3.1 3.0 + - - -
472E TYR* 2.8 59.7 + - - -
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Residues in contact with PHE 469 (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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370E MET* 5.4 2.7 - - + -
416E LEU* 3.7 26.2 - - + -
419E PRO* 4.1 14.8 - - + -
465E SER 2.7 21.2 + - - +
466E GLN* 3.5 13.2 - - - +
468E GLY* 1.3 71.6 - - - +
470E ILE* 1.3 58.1 + - - +
472E TYR* 5.1 0.4 - - - -
473E ILE* 3.0 51.6 + - + +
474E VAL* 3.1 34.4 + - + -
3005E ZAR 3.6 71.8 - + - -
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Residues in contact with ILE 470 (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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419E PRO* 4.0 22.4 - - + -
426E TYR* 3.4 26.7 - - + +
466E GLN* 2.9 21.5 + - + +
467E VAL* 3.7 4.5 - - - +
469E PHE* 1.3 79.1 - - + +
471E ASP* 1.3 62.6 + - - +
474E VAL* 3.9 5.8 - - - -
475E HIS* 2.6 45.1 + - + +
476E PRO* 3.3 1.2 - - - +
496E LEU* 3.9 23.6 - - + +
499E ASN 4.9 0.2 - - - +
500E ARG* 3.8 45.8 - - + +
503E TYR* 5.5 1.6 - - + -
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Residues in contact with ASP 471 (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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467E VAL* 2.9 28.0 + - - +
468E GLY* 3.1 6.4 + - - +
470E ILE* 1.3 77.7 - - - +
472E TYR* 1.3 55.6 + - + +
475E HIS* 4.7 4.1 - - - +
476E PRO* 3.2 12.5 - - - +
500E ARG* 2.7 46.1 + - - -
486J HIS* 2.7 29.7 - - + -
487J PRO* 3.7 28.6 - - + +
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Residues in contact with TYR 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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373E HIS* 4.5 3.1 + - - -
374E MET* 4.7 6.9 - - - +
468E GLY* 2.8 44.4 + - - +
471E ASP* 1.3 75.2 - - + +
473E ILE* 1.3 76.6 + - + +
476E PRO* 3.6 12.2 - - - +
276J PRO* 5.6 0.8 - - + +
392J SER 5.0 10.5 - - - +
393J GLY* 5.4 14.4 - - - -
486J HIS* 2.7 23.8 - - - -
487J PRO* 2.1 43.4 - - + +
488J ASP* 3.1 21.6 + - - -
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Residues in contact with ILE 473 (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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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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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