Contacts of the helix formed by residues 473 - 485 (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 ILE 473 (chain J).
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Specific contacts
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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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Residues in contact with VAL 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416J LEU* 3.7 18.6 - - + +
419J PRO* 4.1 10.3 - - + -
420J THR* 4.4 1.3 - - + -
469J PHE* 3.1 49.1 + - + +
470J ILE* 3.9 9.2 - - - -
473J ILE* 1.3 74.2 - - + +
475J HIS* 1.3 58.0 + - - +
477J LEU* 3.3 5.9 + - - +
478J TRP* 2.9 50.8 + - + +
496J LEU* 3.8 22.4 - - + -
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Residues in contact with HIS 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470J ILE* 2.7 34.5 + - + +
471J ASP* 4.7 4.0 - - - +
474J VAL* 1.3 73.6 - - - +
476J PRO* 1.3 66.1 - - + +
479J GLU* 2.8 68.6 + - + +
493J LEU* 3.6 13.9 - - + +
496J LEU* 3.8 14.3 - - + +
497J GLU* 3.1 39.9 + - + +
500J ARG* 6.2 3.6 - - - -
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Residues in contact with PRO 476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377J LEU* 3.7 19.3 - - + +
381J LYS* 5.1 4.4 - - - +
470J ILE 3.4 2.2 - - - +
471J ASP 3.2 28.3 - - - +
472J TYR* 3.6 13.9 - - - +
473J ILE 3.3 12.6 - - - +
475J HIS* 1.3 92.3 - - + +
477J LEU* 1.3 58.6 + - - +
479J GLU* 3.9 11.6 - - - +
480J THR* 2.8 27.4 + - - -
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Residues in contact with LEU 477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373J HIS* 3.9 9.0 - - + -
377J LEU* 3.9 19.7 - - + +
380J LEU* 4.5 4.9 - - + +
409J ASN* 4.3 14.6 - - - +
412J HIS* 3.5 34.1 - - + +
413J CYS* 3.7 33.9 - - - -
416J LEU* 3.8 23.1 - - + -
473J ILE 3.1 17.5 + - - +
474J VAL* 3.6 3.1 - - - +
476J PRO* 1.3 77.8 - - - +
478J TRP* 1.3 63.8 + - + +
480J THR* 3.2 6.8 + - - -
481J TRP* 2.9 23.2 + - - +
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Residues in contact with TRP 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J TRP* 3.8 25.1 - + - -
272J LEU* 4.0 9.4 - - + -
413J CYS* 3.3 40.2 + - + +
416J LEU 3.2 18.4 + - - -
417J SER* 3.9 12.3 - - - -
420J THR* 3.6 15.5 - - + +
474J VAL* 2.9 44.9 + - + +
477J LEU* 1.3 77.4 - - + +
479J GLU* 1.3 56.3 + - - +
481J TRP* 3.6 32.0 - + + +
482J ALA* 2.7 36.0 + - - +
489J ALA* 5.0 3.4 - - + -
492J ILE* 3.8 27.8 - - + -
493J LEU* 4.4 8.7 - - + +
496J LEU* 4.0 14.6 - - + -
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Residues in contact with GLU 479 (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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475J HIS* 2.8 47.9 + - + +
476J PRO* 3.9 9.7 - - - +
478J TRP* 1.3 76.0 - - - +
480J THR* 1.3 63.8 + - - +
482J ALA* 3.3 2.9 + - - +
483J ASP* 3.1 33.3 + - - +
493J LEU* 4.3 18.2 - - + +
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Residues in contact with THR 480 (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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377J LEU* 3.4 13.0 - - + +
380J LEU* 3.4 28.3 - - + -
381J LYS* 3.8 29.9 - - + +
384J VAL* 3.7 17.8 - - + +
476J PRO 2.8 18.5 + - - -
477J LEU 3.2 8.9 + - - -
479J GLU* 1.3 77.0 - - - +
481J TRP* 1.3 65.0 + - - +
483J ASP* 3.1 18.6 + - - +
484J LEU* 3.1 10.4 + - - +
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Residues in contact with TRP 481 (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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272J LEU* 4.1 23.3 - - + +
275J THR* 4.9 3.7 - - + +
278J LEU* 4.2 5.8 - - + -
380J LEU* 4.1 8.9 - - + +
406J VAL* 3.8 31.9 - - + -
409J ASN* 4.4 9.9 - - + -
410J MET* 3.7 46.9 - - + -
413J CYS* 3.8 26.0 - - - -
477J LEU 2.9 13.3 + - - +
478J TRP* 3.7 27.8 - + - +
480J THR* 1.3 75.8 - - - +
482J ALA* 1.3 65.8 + - - +
484J LEU* 3.1 27.4 + - + +
485J VAL* 3.1 49.5 + - + +
489J ALA* 4.2 6.5 - - + +
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Residues in contact with ALA 482 (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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478J TRP 2.7 21.9 + - - +
479J GLU 3.5 6.3 - - - +
480J THR 3.2 0.2 - - - -
481J TRP* 1.3 73.0 - - - +
483J ASP* 1.3 57.5 + - - +
485J VAL* 3.6 1.3 - - - +
486J HIS* 2.8 35.3 + - + +
487J PRO* 4.5 2.3 - - + +
489J ALA* 3.7 28.4 - - + +
490J GLN* 5.1 3.4 - - - +
493J LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 483 (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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381E LYS* 5.8 1.9 + - - -
384J VAL* 3.5 23.9 - - + +
387J LYS* 3.1 18.3 + - - -
479J GLU* 3.1 23.8 + - - +
480J THR* 3.1 14.5 + - - +
482J ALA* 1.3 76.3 - - - +
484J LEU* 1.3 65.6 + - - +
486J HIS* 3.2 19.2 + - - +
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Residues in contact with LEU 484 (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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277J ALA* 4.8 0.5 - - - +
380J LEU* 4.2 15.3 - - + -
383J MET* 4.3 28.5 - - + +
384J VAL* 4.1 18.5 - - + +
387J LYS* 3.7 19.5 + - + +
395J LEU* 3.7 44.8 - - + +
397J LEU* 6.2 0.9 - - + -
406J VAL* 4.3 16.4 - - + -
480J THR 3.1 8.1 + - - +
481J TRP* 3.5 33.7 - - + +
483J ASP* 1.3 82.4 - - - +
485J VAL* 1.3 62.3 + - + +
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Residues in contact with VAL 485 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J THR* 4.1 14.6 - - + +
277J ALA* 3.7 23.7 - - + +
278J LEU* 4.4 7.6 - - + -
395J LEU* 4.8 1.3 - - + -
481J TRP* 3.1 54.9 + - + +
482J ALA 4.0 0.4 - - - +
484J LEU* 1.3 85.8 - - + +
486J HIS* 1.3 67.2 + - - +
488J ASP* 2.9 27.6 + - + +
489J ALA* 3.8 20.0 - - + +
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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