Contacts of the helix formed by residues 489 - 507 (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 ALA 489 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478J TRP* 5.0 2.9 - - + -
481J TRP* 4.2 11.9 - - + +
482J ALA* 3.7 31.6 - - + -
485J VAL* 3.8 13.3 - - + +
487J PRO* 2.9 1.8 + - - +
488J ASP* 1.3 79.0 - - - +
490J GLN* 1.3 63.0 + - - +
491J ASP 3.3 2.9 - - - -
492J ILE* 3.2 21.3 + - + +
493J LEU* 3.0 21.7 + - - +
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Residues in contact with GLN 490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482J ALA* 5.1 3.1 - - - +
486J HIS* 4.7 9.5 + - - -
487J PRO* 2.8 32.4 + - + +
488J ASP 3.3 1.0 + - - -
489J ALA* 1.3 77.6 - - - +
491J ASP* 1.3 63.3 + - - +
493J LEU* 3.4 20.7 + - - +
494J ASP* 3.1 44.1 + - - +
497J GLU* 5.5 0.6 + - - -
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Residues in contact with ASP 491 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488J ASP 4.8 3.6 + - - +
489J ALA 3.3 0.8 - - - -
490J GLN* 1.3 75.4 - - - +
492J ILE* 1.3 71.9 + - + +
494J ASP* 3.1 14.4 + - - +
495J THR* 2.9 28.5 + - - +
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Residues in contact with ILE 492 (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 43.1 - - + +
271J VAL* 6.2 0.9 - - + -
272J LEU* 4.6 7.0 - - + -
420J THR* 3.4 31.7 - - + +
478J TRP* 3.8 30.3 - - + -
488J ASP 5.3 2.7 - - - +
489J ALA* 3.2 19.9 + - + +
491J ASP* 1.3 78.2 - - + +
493J LEU* 1.3 63.3 + - - +
495J THR* 3.3 8.5 + - - -
496J LEU* 3.0 22.0 + - - +
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Residues in contact with LEU 493 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475J HIS* 3.6 33.4 - - + +
478J TRP* 4.4 6.7 - - + +
479J GLU* 4.3 21.8 - - + +
482J ALA* 3.8 26.7 - - + -
489J ALA 3.0 10.8 + - - +
490J GLN* 3.6 25.6 - - - +
492J ILE* 1.3 78.4 - - - +
494J ASP* 1.3 62.4 + - - +
496J LEU* 3.2 14.6 + - + +
497J GLU* 3.0 37.9 + - - +
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Residues in contact with ASP 494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490J GLN* 3.1 43.0 + - - +
491J ASP* 3.4 15.3 - - - +
493J LEU* 1.3 76.5 - - - +
495J THR* 1.3 57.2 + - - +
497J GLU* 3.2 18.7 + - - +
498J ASP* 2.9 38.6 + - - +
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Residues in contact with THR 495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J TRP* 6.1 0.3 - - - -
420J THR 3.4 21.2 + - - +
421J LYS 3.7 9.4 - - - +
422J PRO* 4.5 5.8 - - + -
491J ASP* 2.9 16.4 + - - +
492J ILE* 3.6 8.7 - - - -
494J ASP* 1.3 75.8 - - - +
496J LEU* 1.3 57.6 + - - +
498J ASP* 3.1 11.1 + - + +
499J ASN* 2.8 51.0 + - - +
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Residues in contact with LEU 496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419J PRO* 3.5 43.7 - - + +
420J THR* 3.9 8.2 - - + +
470J ILE* 3.8 16.6 - - + +
474J VAL* 3.8 18.2 - - + -
475J HIS* 3.8 37.9 - - + -
478J TRP* 4.0 17.0 - - + -
492J ILE 3.0 12.7 + - - +
493J LEU* 3.2 12.5 + - + +
495J THR* 1.3 77.5 - - - +
497J GLU* 1.3 58.9 + - - +
499J ASN* 3.3 2.1 + - - +
500J ARG* 3.0 26.5 + - - +
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Residues in contact with GLU 497 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475J HIS* 3.1 37.6 + - + +
490J GLN* 5.5 0.3 + - - -
493J LEU* 3.0 26.1 + - - +
494J ASP* 3.6 21.1 - - - +
496J LEU* 1.3 73.2 - - - +
498J ASP* 1.3 66.7 + - - +
500J ARG* 3.5 9.9 + - - +
501J GLU* 3.3 27.9 + - - +
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Residues in contact with ASP 498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494J ASP* 2.9 25.4 + - - +
495J THR* 3.1 10.9 + - + +
497J GLU* 1.3 73.7 - - - +
499J ASN* 1.3 69.6 + - - +
501J GLU* 3.1 10.1 + - - +
502J TRP* 3.0 20.2 + - - +
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Residues in contact with ASN 499 (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 2.8 26.4 + - - +
421J LYS 2.9 23.2 + - - -
423J LEU* 3.4 27.4 + - + +
426J TYR* 3.7 21.3 - - + -
470J ILE* 4.7 2.0 - - + -
495J THR* 2.8 26.0 + - - +
496J LEU 3.7 4.3 - - - +
498J ASP* 1.3 78.5 - - - +
500J ARG* 1.3 62.2 + - - +
502J TRP* 3.3 7.9 + - - +
503J TYR* 3.1 27.5 + - - +
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Residues in contact with ARG 500 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B HIS* 4.4 11.5 + - - -
487B PRO* 5.7 2.6 - - - +
467J VAL* 3.3 22.9 - - + +
470J ILE* 3.8 28.9 - - + +
471J ASP* 2.7 40.3 + - - +
475J HIS* 6.2 2.9 - - - -
496J LEU 3.0 14.4 + - - +
497J GLU* 3.6 12.6 - - - +
498J ASP 3.1 0.2 - - - -
499J ASN* 1.3 78.1 - - - +
501J GLU* 1.3 87.1 + - - +
503J TYR* 3.4 3.3 + - - +
504J GLN* 2.9 58.5 + - - +
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Residues in contact with GLU 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497J GLU 3.3 12.4 + - - +
498J ASP* 3.1 10.6 + - - +
500J ARG* 1.3 107.6 + - - +
502J TRP* 1.3 61.4 + - - +
504J GLN* 3.4 11.9 - - - +
505J SER* 2.9 31.5 + - - +
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Residues in contact with TRP 502 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502F TRP* 3.2 53.5 + + - -
505F SER* 3.8 22.9 - - - -
506F THR* 4.1 3.8 + - - -
423J LEU* 3.6 30.0 - - + +
427J ARG* 3.2 47.1 - - - -
498J ASP 3.0 12.2 + - - +
499J ASN* 3.5 12.1 - - - +
500J ARG 3.2 0.2 - - - -
501J GLU* 1.3 76.0 - - - +
503J TYR* 1.3 105.4 + + - +
505J SER* 3.2 9.2 + - - -
506J THR* 2.9 38.4 + - + -
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Residues in contact with TYR 503 (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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423J LEU* 4.6 0.9 - - + -
426J TYR* 3.5 46.0 - + - -
427J ARG* 3.7 19.3 + - + +
430J THR* 3.2 31.0 + - + +
431J ASP* 5.5 0.7 + - - -
462J VAL* 4.7 5.4 - - + -
463J GLU* 3.6 34.9 - - + +
466J GLN* 3.9 16.2 - - + -
467J VAL* 4.1 14.1 - - + +
470J ILE* 5.5 0.7 - - + -
499J ASN 3.1 13.8 + - - +
500J ARG* 3.9 4.5 - - - +
502J TRP* 1.3 107.0 - + - +
504J GLN* 1.3 63.2 + - - +
506J THR* 3.2 13.2 + - + -
507J ILE* 3.3 15.2 + - - +
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Residues in contact with GLN 504 (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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467J VAL* 3.8 11.2 - - + +
500J ARG* 2.9 52.6 + - - +
501J GLU* 3.4 18.4 - - - +
503J TYR* 1.3 76.9 - - - +
505J SER* 1.3 63.3 + - - +
507J ILE* 3.0 52.5 + - - +
509J GLN* 4.9 2.9 + - - -
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Residues in contact with SER 505 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F LEU* 4.5 13.1 - - - +
502F TRP* 4.6 12.8 - - - -
501J GLU* 2.9 15.6 + - - +
502J TRP* 3.4 9.9 - - - -
504J GLN* 1.3 78.7 - - - +
506J THR* 1.3 62.5 + - - +
507J ILE 3.1 7.7 + - - +
509J GLN* 5.3 1.4 + - - +
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Residues in contact with THR 506 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F LEU* 4.5 9.6 - - + -
427F ARG* 4.4 19.7 - - - +
502F TRP* 3.1 23.6 + - + +
463J GLU* 3.5 26.0 - - + +
502J TRP* 2.9 28.6 + - + -
503J TYR* 3.2 10.3 + - - -
505J SER* 1.3 75.6 - - - +
507J ILE* 1.3 64.7 + - - +
508J PRO* 3.1 12.6 - - - +
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Residues in contact with ILE 507 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463J GLU* 3.5 14.8 - - + -
464J LYS* 3.7 51.8 - - + +
467J VAL* 3.8 11.0 - - + -
503J TYR 3.3 9.6 + - - +
504J GLN* 3.0 36.3 - - - +
505J SER 3.1 6.4 - - - +
506J THR* 1.3 76.0 - - - +
508J PRO* 1.3 68.6 - - + +
509J GLN* 2.7 35.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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