Contacts of the helix formed by residues 473 - 485 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B MET* 3.8 25.8 - - + -
373B HIS* 3.7 36.1 + - + +
374B MET* 4.5 9.6 - - + -
416B LEU* 3.8 15.3 - - + -
469B PHE* 3.0 33.2 + - + +
472B TYR* 1.3 97.9 - - + +
474B VAL* 1.3 67.9 + - - +
475B HIS 3.5 0.9 - - - -
476B PRO* 3.3 3.9 - - - +
477B LEU* 3.2 24.7 + - - +
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 3.8 18.4 - - + +
419B PRO* 4.1 10.3 - - + -
420B THR* 4.4 0.9 - - + -
469B PHE* 3.1 49.6 + - + +
470B ILE* 3.9 9.4 - - - -
473B ILE* 1.3 74.9 - - + +
475B HIS* 1.3 59.1 + - - +
477B LEU* 3.3 5.4 + - - +
478B TRP* 2.9 49.4 + - + +
496B LEU* 3.8 22.4 - - + -
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Residues in contact with HIS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ILE* 2.7 34.8 + - + +
471B ASP* 4.8 4.0 - - - +
474B VAL* 1.3 73.6 - - - +
476B PRO* 1.3 66.9 - - + +
479B GLU* 2.8 66.9 + - + +
493B LEU* 3.6 8.8 - - + +
496B LEU* 3.7 20.6 - - + +
497B GLU* 3.1 40.1 + - + -
500B ARG* 6.2 2.7 - - - -
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Residues in contact with PRO 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.8 18.8 - - + +
381B LYS* 5.0 4.8 - - - +
470B ILE 3.4 2.2 - - - +
471B ASP 3.2 28.0 - - - +
472B TYR* 3.6 14.4 - - - +
473B ILE* 3.3 12.3 - - - +
475B HIS* 1.3 94.1 - - + +
477B LEU* 1.3 58.6 + - - +
479B GLU* 3.9 11.7 - - - +
480B THR* 2.8 27.5 + - - -
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 3.9 8.7 - - + -
377B LEU* 3.8 19.0 - - + +
380B LEU* 4.5 4.7 - - + +
409B ASN* 4.3 14.8 - - - +
412B HIS* 3.4 35.0 - - + +
413B CYS* 3.7 33.2 - - - -
416B LEU* 3.8 23.1 - - + -
473B ILE 3.2 14.3 + - - +
474B VAL* 3.6 2.7 - - - +
475B HIS 3.1 0.6 - - - -
476B PRO* 1.3 78.1 - - - +
478B TRP* 1.3 65.5 - - + +
480B THR* 3.1 6.8 + - - -
481B TRP* 2.9 23.7 + - - +
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Residues in contact with TRP 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.8 24.7 - + - -
272B LEU* 4.0 9.2 - - + -
413B CYS* 3.3 38.9 + - + +
416B LEU 3.2 19.1 + - - -
417B SER* 3.9 13.2 - - - -
420B THR* 3.6 16.4 - - + +
474B VAL* 2.9 44.2 + - + +
477B LEU* 1.3 76.4 - - + +
479B GLU* 1.3 56.1 + - - +
481B TRP* 3.7 32.4 - + - +
482B ALA* 2.7 35.7 + - - +
489B ALA* 5.0 3.6 - - + -
492B ILE* 3.8 28.0 - - + -
493B LEU* 4.4 8.6 - - + +
496B LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B HIS* 2.8 51.6 + - + +
476B PRO* 3.9 10.1 - - - +
478B TRP* 1.3 72.5 - - - +
480B THR* 1.3 64.1 + - - +
482B ALA* 3.3 7.7 + - - +
483B ASP* 3.1 33.2 + - - +
493B LEU* 4.3 13.3 - - + +
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Residues in contact with THR 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B LEU* 3.4 14.1 - - + +
380B LEU* 3.4 28.0 - - + -
381B LYS* 3.8 30.3 - - + +
384B VAL* 3.7 16.8 - - + +
476B PRO 2.8 14.3 + - - -
477B LEU 3.1 8.8 + - - -
479B GLU* 1.3 81.3 + - - +
481B TRP* 1.3 61.9 + - - +
483B ASP* 3.1 22.8 - - - +
484B LEU* 3.1 5.7 + - - +
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Residues in contact with TRP 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 4.1 24.8 - - + +
275B THR* 4.9 2.1 + - + +
278B LEU* 4.2 5.8 - - + -
380B LEU* 4.2 8.7 - - + +
406B VAL* 3.8 31.9 - - + -
409B ASN* 4.4 9.2 - - + -
410B MET* 3.8 47.3 - - + -
413B CYS* 3.8 26.2 - - - -
477B LEU 2.9 13.5 + - - +
478B TRP* 3.3 28.5 + + - +
480B THR* 1.3 75.4 - - - +
482B ALA* 1.3 65.4 + - - +
484B LEU* 3.1 20.4 + - + +
485B VAL* 3.1 56.1 + - + +
489B ALA* 4.1 6.1 - - + +
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B TRP* 2.7 21.9 + - + +
479B GLU 3.5 6.1 - - - +
480B THR 3.2 0.2 - - - -
481B TRP* 1.3 72.8 - - - +
483B ASP* 1.3 56.6 + - - +
485B VAL* 3.6 1.0 - - - +
486B HIS* 2.9 35.5 + - + +
487B PRO* 4.6 1.9 - - - +
489B ALA* 3.7 28.7 - - + +
490B GLN* 5.1 3.1 - - - +
493B LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B VAL* 3.5 23.5 - - + +
387B LYS* 3.1 16.6 + - - -
479B GLU* 3.1 23.3 + - - +
480B THR* 3.1 15.9 + - - +
481B TRP 3.0 0.2 - - - -
482B ALA* 1.3 75.8 - - - +
484B LEU* 1.3 66.8 + - - +
486B HIS* 3.1 21.4 + - - +
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ALA* 4.8 0.7 - - - +
380B LEU* 4.2 14.8 - - + -
383B MET* 4.3 29.4 - - + +
384B VAL* 4.1 18.1 - - + +
387B LYS* 3.6 21.7 + - + +
395B LEU* 3.8 42.7 - - + +
397B LEU* 6.2 0.9 - - + -
406B VAL* 4.3 15.0 - - + -
480B THR 3.1 8.2 + - - +
481B TRP* 3.1 35.6 + - + +
483B ASP* 1.3 82.0 - - - +
485B VAL* 1.3 60.8 + - + +
486B HIS 3.6 0.3 + - - -
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B THR* 4.1 17.3 - - + +
277B ALA* 3.8 24.0 - - + -
278B LEU* 4.4 7.9 - - + -
395B LEU* 4.8 1.8 - - + -
481B TRP* 3.1 56.3 + - + +
482B ALA 4.1 0.2 - - - +
484B LEU* 1.3 84.1 - - + +
486B HIS* 1.3 66.7 + - - +
488B ASP* 2.9 26.2 + - + +
489B ALA* 3.8 19.5 - - + +
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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