Contacts of the helix formed by residues 461 - 473 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ASN 4.1 5.2 + - - -
460A ALA* 1.3 75.2 + - - +
462A VAL* 1.3 66.5 + - - +
463A GLU* 3.1 7.4 - - - -
464A LYS* 2.8 49.9 + - - +
465A SER* 2.9 17.9 + - - -
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Residues in contact with VAL 462 (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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430A THR* 3.8 27.4 - - + -
431A ASP* 5.7 3.4 - - - +
434A MET* 3.9 34.5 - - + -
438A PHE* 4.8 5.4 - - + -
460A ALA* 3.6 8.2 - - + +
461A SER* 1.3 72.4 - - - +
463A GLU* 1.3 77.1 + - - +
465A SER* 3.4 7.6 + - - -
466A GLN* 3.1 23.2 + - - +
503A TYR* 4.7 6.1 - - + -
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Residues in contact with GLU 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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461A SER* 2.9 6.6 + - - -
462A VAL* 1.3 87.1 + - - +
464A LYS* 1.3 66.7 + - + +
466A GLN* 3.1 4.7 + - - +
467A VAL* 3.1 24.9 + - - +
503A TYR* 3.6 22.7 - - + +
506A THR* 3.5 43.2 - - + +
507A ILE* 3.5 22.0 - - + -
508A PRO* 3.9 15.2 - - + +
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Residues in contact with LYS 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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461A SER* 2.8 35.4 + - - +
463A GLU* 1.3 75.6 - - + +
465A SER* 1.3 58.9 + - - +
467A VAL* 3.1 3.4 + - - +
468A GLY* 2.8 28.2 + - - -
507A ILE* 3.7 42.6 - - + +
508A PRO* 5.3 6.5 - - + -
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Residues in contact with SER 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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434A MET* 5.2 1.4 - - - +
454A MET* 3.5 45.0 - - - +
460A ALA* 5.9 0.3 - - - +
461A SER* 2.9 20.2 + - - -
462A VAL* 3.5 11.6 + - - -
464A LYS* 1.3 77.6 - - - +
466A GLN* 1.3 52.9 + - - +
468A GLY* 3.3 1.8 + - - +
469A PHE* 2.7 36.7 + - - +
3001A ZAR 4.1 3.7 - - - +
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Residues in contact with GLN 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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426A TYR* 2.7 31.8 + - - +
430A THR* 3.4 33.8 - - + +
433A ILE* 4.6 3.6 - - - +
434A MET* 4.8 5.1 - - - -
462A VAL 3.1 18.2 + - - +
463A GLU 3.1 7.2 + - - +
465A SER* 1.3 74.2 - - - +
467A VAL* 1.3 62.6 + - - +
469A PHE* 3.3 7.5 + - - +
470A ILE* 2.9 37.3 + - - +
503A TYR* 3.9 22.7 - - + -
3001A ZAR 3.0 46.1 + - - +
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Residues in contact with VAL 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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463A GLU 3.1 15.1 + - - +
464A LYS* 3.5 6.7 - - - +
466A GLN* 1.3 75.9 - - - +
468A GLY* 1.3 59.0 + - - +
470A ILE* 3.4 5.5 + - - +
471A ASP* 2.9 38.5 + - - +
500A ARG* 3.2 45.5 - - + +
503A TYR* 4.0 5.8 - - + -
504A GLN* 3.8 38.8 - - - +
507A ILE* 3.8 9.6 - - + -
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Residues in contact with GLY 468 (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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464A LYS 2.8 14.1 + - - -
465A SER* 3.7 2.5 - - - -
467A VAL* 1.3 75.6 - - - +
469A PHE* 1.3 59.3 + - - +
471A ASP* 3.1 3.2 + - - -
472A TYR* 2.8 60.1 + - - +
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Residues in contact with PHE 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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370A MET* 5.4 3.4 - - + -
416A LEU* 3.6 25.4 - - + -
419A PRO* 4.1 14.1 - - + -
465A SER 2.7 21.7 + - - +
466A GLN* 3.6 11.7 - - - +
468A GLY* 1.3 71.0 - - - +
470A ILE* 1.3 56.4 + - - +
472A TYR* 5.4 0.2 - - - -
473A ILE* 3.0 50.7 + - + +
474A VAL* 3.1 34.9 + - + -
3001A ZAR 3.6 71.1 - + - -
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Residues in contact with ILE 470 (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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419A PRO* 4.0 21.5 - - + -
426A TYR* 3.4 27.6 - - + +
466A GLN* 2.9 22.1 + - + +
467A VAL* 3.8 4.5 - - - +
469A PHE* 1.3 78.1 - - + +
471A ASP* 1.3 62.1 + - - +
474A VAL* 4.0 6.3 - - - -
475A HIS* 2.7 45.2 + - + +
476A PRO* 3.4 1.0 - - - +
496A LEU* 3.9 24.2 - - + +
500A ARG* 3.9 44.9 - - + +
503A TYR* 5.5 1.3 - - + -
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Residues in contact with ASP 471 (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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467A VAL* 2.9 25.8 + - - +
468A GLY* 3.1 6.7 + - - +
470A ILE* 1.3 77.7 - - - +
472A TYR* 1.3 72.7 + - + +
475A HIS* 4.7 4.1 - - - +
476A PRO* 3.2 19.8 - - - +
500A ARG* 2.7 45.6 + - - -
486I HIS* 5.1 9.2 - - + -
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Residues in contact with TYR 472 (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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373A HIS* 4.5 2.8 + - - -
374A MET* 4.7 7.3 - - - +
468A GLY* 2.8 47.1 + - - +
469A PHE* 5.2 0.7 - - - -
471A ASP* 1.3 83.2 + - + +
473A ILE* 1.3 76.3 + - + +
476A PRO* 3.6 12.0 - - - +
387I LYS* 6.3 1.1 - - - -
486I HIS* 3.0 49.4 + + + -
487I PRO* 3.7 12.8 - - - +
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Residues in contact with ILE 473 (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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370A MET* 3.8 25.1 - - + -
373A HIS* 3.6 36.2 + - + +
374A MET* 4.5 9.6 - - + -
416A LEU* 3.9 15.5 - - + -
469A PHE* 3.0 33.9 + - + +
471A ASP 3.7 0.2 - - - -
472A TYR* 1.3 98.4 - - + +
474A VAL* 1.3 67.5 + - - +
475A HIS 3.5 0.9 - - - -
476A PRO* 3.3 5.1 - - - +
477A LEU* 3.1 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
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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