Contacts of the helix formed by residues 461 - 473 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459D ASN 4.4 4.2 + - - -
460D ALA* 1.3 76.5 + - - +
462D VAL* 1.3 65.9 + - - +
463D GLU* 3.1 7.9 - - - -
464D LYS* 2.9 51.1 + - - +
465D SER* 2.9 18.0 + - - -
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Residues in contact with VAL 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D THR* 3.8 27.1 - - + -
431D ASP* 5.6 3.4 - - - +
434D MET* 3.8 35.7 - - + -
438D PHE* 4.8 4.5 - - + -
460D ALA* 3.6 8.6 + - + +
461D SER* 1.3 72.3 - - - +
463D GLU* 1.3 76.9 + - - +
465D SER* 3.4 7.8 + - - -
466D GLN* 3.1 23.7 + - - +
503D TYR* 4.7 5.8 - - + -
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Residues in contact with GLU 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D SER* 2.9 7.8 + - - -
462D VAL* 1.3 86.8 + - - +
464D LYS* 1.3 65.0 + - + +
466D GLN* 3.2 4.9 + - - +
467D VAL* 3.1 25.1 + - - +
503D TYR* 3.6 22.7 - - + +
506D THR* 3.5 43.5 - - + +
507D ILE* 3.5 22.2 - - + -
508D PRO* 3.9 15.5 - - + +
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Residues in contact with LYS 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D SER* 2.9 35.4 + - - +
463D GLU* 1.3 74.7 - - + +
465D SER* 1.3 57.6 + - - +
467D VAL* 3.2 2.9 + - - +
468D GLY* 2.8 27.7 + - - -
507D ILE* 3.7 43.7 - - + -
508D PRO* 5.3 6.1 - - + -
392K SER 5.6 1.0 - - - +
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Residues in contact with SER 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D MET* 5.2 1.2 - - - +
454D MET* 3.5 46.2 - - - +
460D ALA* 5.9 0.2 - - - +
461D SER* 2.9 19.2 + - - -
462D VAL* 3.6 12.7 + - - -
464D LYS* 1.3 78.1 - - - +
466D GLN* 1.3 59.5 + - - +
468D GLY* 3.3 1.7 + - - -
469D PHE* 2.8 31.1 + - - +
3004D ZAR 4.2 1.9 - - - +
391K SER 5.6 2.7 - - - +
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Residues in contact with GLN 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D TYR* 2.7 32.9 + - - +
430D THR* 3.4 32.1 - - + +
433D ILE* 4.6 3.2 - - - +
434D MET* 4.8 5.3 - - - -
462D VAL 3.1 15.9 + - - +
463D GLU 3.2 7.1 + - - +
465D SER* 1.3 72.5 - - - +
467D VAL* 1.3 62.1 + - - +
469D PHE* 3.5 6.8 - - - +
470D ILE* 2.9 37.4 + - - +
503D TYR* 3.9 23.1 - - + -
3004D ZAR 3.1 46.0 + - - +
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Residues in contact with VAL 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D GLU 3.1 15.7 + - - +
464D LYS* 3.2 7.4 + - - +
466D GLN* 1.3 74.7 - - - +
468D GLY* 1.3 57.3 + - - +
470D ILE* 3.4 6.3 + - - +
471D ASP* 2.9 38.2 + - - +
500D ARG* 3.3 44.4 - - + +
503D TYR* 4.1 5.6 - - + -
504D GLN* 3.8 38.1 - - - +
507D ILE* 3.9 9.9 - - + -
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Residues in contact with GLY 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D LYS 2.8 14.3 + - - -
465D SER 3.7 2.7 - - - -
467D VAL* 1.3 74.9 - - - +
469D PHE* 1.3 58.6 + - - +
471D ASP* 3.1 3.1 + - - -
472D TYR* 2.8 59.5 + - - +
391K SER 4.7 6.7 - - - -
392K SER 5.2 2.9 - - - -
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Residues in contact with PHE 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D MET* 5.5 3.6 - - + -
416D LEU* 3.7 25.6 - - + -
419D PRO* 4.1 14.8 - - + -
465D SER 2.8 21.2 + - - +
466D GLN* 3.5 12.1 - - - +
468D GLY* 1.3 70.3 - - - +
470D ILE* 1.3 58.0 + - - +
472D TYR* 5.2 0.4 - - - -
473D ILE* 3.0 45.3 + - + +
474D VAL* 3.1 38.9 + - + -
3004D ZAR 3.6 71.6 - + - -
391K SER 5.2 1.0 + - - -
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Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D PRO* 4.0 22.0 - - + -
426D TYR* 3.4 27.1 - - + +
466D GLN* 2.9 21.0 + - + +
467D VAL* 3.7 4.3 - - - +
469D PHE* 1.3 78.3 - - + +
471D ASP* 1.3 61.6 + - - +
474D VAL* 3.9 6.1 - - + -
475D HIS* 2.7 44.0 + - + +
476D PRO* 3.4 0.7 - - - +
496D LEU* 3.9 22.0 - - + +
499D ASN 4.7 0.2 - - - -
500D ARG* 3.9 46.4 - - + +
503D TYR* 5.5 1.3 - - + -
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Residues in contact with ASP 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D VAL* 2.9 27.1 + - - +
468D GLY* 3.7 5.6 - - - +
470D ILE* 1.3 79.1 - - - +
472D TYR* 1.3 75.0 + - + +
475D HIS* 4.7 3.8 - - - +
476D PRO* 3.2 20.1 - - - +
500D ARG* 2.8 45.1 + - - -
486K HIS* 4.1 22.7 + - + +
487K PRO* 4.6 5.0 - - - +
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Residues in contact with TYR 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D HIS* 4.6 2.9 + - - -
374D MET* 4.7 7.3 - - - +
468D GLY* 2.8 43.6 + - - +
471D ASP* 1.3 88.8 + - + +
473D ILE* 1.3 77.1 + - + +
476D PRO* 3.6 12.2 - - - +
387K LYS* 5.0 10.5 - - - -
389K VAL* 3.7 36.3 - - + +
390K THR 4.3 1.8 - - - +
391K SER* 3.9 12.8 - - - -
392K SER 4.2 1.9 + - - -
393K GLY* 3.0 40.8 + - - -
486K HIS* 4.1 18.9 + - + -
487K PRO* 5.6 1.0 - - - +
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Residues in contact with ILE 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D MET* 3.8 25.6 - - + -
373D HIS* 3.6 36.3 + - + +
374D MET* 4.5 10.3 - - + -
416D LEU* 3.9 14.8 - - + -
469D PHE* 3.0 33.9 + - + +
471D ASP 3.7 0.2 - - - -
472D TYR* 1.3 97.1 - - + +
474D VAL* 1.3 67.0 + - - +
476D PRO* 3.3 5.1 - - - +
477D LEU* 3.1 24.3 + - - +
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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