Contacts of the helix formed by residues 461 - 473 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459J ASN 4.1 4.9 + - - -
460J ALA* 1.3 75.7 + - - +
462J VAL* 1.3 65.5 + - - +
463J GLU* 3.1 7.4 - - - -
464J LYS* 2.8 50.5 + - - +
465J SER* 2.9 18.9 + - - -
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Residues in contact with VAL 462 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430J THR* 3.8 27.1 - - + -
431J ASP* 5.7 3.4 - - - +
434J MET* 3.9 33.9 - - + -
438J PHE* 4.8 5.4 - - + -
460J ALA* 3.6 7.3 + - + +
461J SER* 1.3 72.5 - - - +
463J GLU* 1.3 77.9 + - - +
465J SER* 3.4 7.0 + - - -
466J GLN* 3.1 23.4 + - - +
503J TYR* 4.7 5.8 - - + -
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Residues in contact with GLU 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461J SER* 2.9 5.4 + - - -
462J VAL* 1.3 88.7 + - - +
464J LYS* 1.3 65.0 + - + +
466J GLN* 3.1 5.5 + - - +
467J VAL* 3.1 24.3 + - - +
503J TYR* 3.6 23.4 - - + +
506J THR* 3.5 43.6 - - + +
507J ILE* 3.5 22.4 - - + -
508J PRO* 3.9 14.9 - - + +
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Residues in contact with LYS 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461J SER* 2.8 34.5 + - - +
463J GLU* 1.3 75.3 - - - +
465J SER* 1.3 58.4 + - - +
467J VAL* 3.1 3.9 + - - +
468J GLY* 2.8 27.9 + - - -
507J ILE* 3.7 43.3 - - + +
508J PRO* 5.3 6.5 - - + -
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Residues in contact with SER 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434J MET* 5.2 1.0 - - - +
454J MET* 3.5 45.2 - - - +
460J ALA* 5.9 0.2 - - - +
461J SER* 2.9 19.3 + - - -
462J VAL* 3.6 12.1 + - - -
464J LYS* 1.3 78.0 - - - +
466J GLN* 1.3 58.8 + - - +
468J GLY* 3.3 1.6 + - - +
469J PHE* 2.7 31.8 + - - +
3010J ZAR 4.1 3.0 - - - +
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Residues in contact with GLN 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426J TYR* 2.6 32.7 + - - +
430J THR* 3.4 32.3 - - + +
433J ILE* 4.6 3.2 - - - +
434J MET* 4.8 5.1 - - - -
462J VAL 3.1 14.5 + - - +
463J GLU 3.1 8.6 + - - +
465J SER* 1.3 74.5 - - - +
467J VAL* 1.3 59.9 + - - +
469J PHE* 3.2 7.8 + - - +
470J ILE* 2.9 37.5 + - + +
503J TYR* 3.9 23.1 - - + -
3010J ZAR 3.0 45.4 + - - +
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Residues in contact with VAL 467 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463J GLU 3.1 15.0 + - - +
464J LYS* 3.1 7.6 + - - +
466J GLN* 1.3 75.9 - - - +
468J GLY* 1.3 58.0 + - - +
470J ILE* 3.4 5.7 + - - +
471J ASP* 2.9 38.1 + - - +
500J ARG* 3.3 44.2 - - + +
503J TYR* 4.1 5.4 - - + -
504J GLN* 3.8 38.4 - - - +
507J ILE* 3.8 10.3 - - + -
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Residues in contact with GLY 468 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464J LYS 2.8 15.2 + - - -
465J SER* 3.7 1.8 - - - -
467J VAL* 1.3 75.3 - - - +
469J PHE* 1.3 59.2 + - - +
471J ASP* 3.1 3.2 + - - -
472J TYR* 2.8 60.0 + - - +
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Residues in contact with PHE 469 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370J MET* 5.4 3.1 - - + -
416J LEU* 3.7 25.4 - - + -
419J PRO* 4.1 14.1 - - + -
465J SER 2.7 21.5 + - - +
466J GLN* 3.5 12.1 - - - +
468J GLY* 1.3 71.7 - - - +
470J ILE* 1.3 58.2 + - - +
472J TYR* 5.2 0.2 - - - -
473J ILE* 3.0 50.5 + - + +
474J VAL* 3.1 35.1 + - + -
3010J ZAR 3.6 72.7 - + - -
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Residues in contact with ILE 470 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419J PRO* 4.0 22.0 - - + -
426J TYR* 3.5 26.2 - - + +
466J GLN* 2.9 21.5 + - + +
467J VAL* 3.7 3.8 - - - +
469J PHE* 1.3 77.2 - - + +
471J ASP* 1.3 60.8 + - - +
474J VAL* 3.9 5.8 - - - -
475J HIS* 2.7 44.4 + - + +
476J PRO* 3.4 1.0 - - - +
496J LEU* 3.8 23.6 - - + +
499J ASN 4.7 0.4 - - - +
500J ARG* 3.8 46.7 - - + +
503J TYR* 5.5 1.3 - - + -
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Residues in contact with ASP 471 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B HIS* 3.6 21.1 - - + +
467J VAL* 2.9 26.3 + - - +
468J GLY* 3.7 6.2 + - - +
470J ILE* 1.3 78.4 - - - +
472J TYR* 1.3 74.7 + - + +
475J HIS* 4.7 4.6 - - - +
476J PRO* 3.2 19.8 - - - +
500J ARG* 2.7 45.2 + - - -
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Residues in contact with TYR 472 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B LYS* 4.5 20.9 - - + -
389B VAL* 4.9 22.2 - - + -
391B SER 5.3 6.3 - - - -
392B SER 5.9 0.4 - - - -
393B GLY* 4.6 21.5 + - - -
486B HIS* 3.7 26.4 + - + -
487B PRO* 4.9 2.9 - - - +
373J HIS* 4.5 3.1 + - - -
374J MET* 4.7 7.1 - - - +
468J GLY* 2.8 42.5 + - - +
469J PHE* 5.2 0.2 - - - -
471J ASP* 1.3 88.6 + - + +
473J ILE* 1.3 76.8 + - + +
476J PRO* 3.6 12.4 - - - +
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Residues in contact with ILE 473 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370J MET* 3.8 25.8 - - + -
373J HIS* 3.6 36.1 + - + +
374J MET* 4.6 9.4 - - + -
416J LEU* 3.9 14.4 - - + -
469J PHE* 3.0 33.2 + - + +
471J ASP 3.7 0.2 - - - -
472J TYR* 1.3 97.2 - - + +
474J VAL* 1.3 69.0 + - - +
475J HIS 3.5 1.1 - - - -
476J PRO* 3.3 4.7 - - - +
477J LEU* 3.1 24.1 + - - +
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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