Contacts of the helix formed by residues 350 - 367 (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 THR 350 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348J ASN 5.6 0.4 - - - +
349J LEU* 1.3 74.8 - - - +
351J LYS* 1.3 64.6 + - - +
352J LYS* 3.2 26.4 - - - +
353J GLN* 2.9 43.6 + - - +
354J ARG* 2.9 19.8 + - - +
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Residues in contact with LYS 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449I MET* 6.4 0.2 - - - +
349J LEU 3.6 1.0 + - - -
350J THR* 1.3 71.5 - - - +
352J LYS* 1.3 74.4 + - + +
354J ARG* 3.3 15.3 + - - +
355J GLN* 3.1 50.1 + - + +
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Residues in contact with LYS 352 (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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350J THR* 3.1 23.1 - - - +
351J LYS* 1.3 96.4 - - + +
353J GLN* 1.3 63.6 + - + +
355J GLN* 3.2 16.3 + - - +
356J SER* 3.0 26.8 + - - +
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Residues in contact with GLN 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232J PHE* 4.3 20.9 - - - -
285J LEU* 3.7 27.2 - - + +
348J ASN 4.7 0.5 - - - +
349J LEU* 3.4 20.3 - - + +
350J THR* 2.9 47.6 + - + +
352J LYS* 1.3 74.3 - - + +
354J ARG* 1.3 61.0 + - - +
356J SER* 3.2 2.9 + - - -
357J LEU* 2.9 32.7 + - - +
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Residues in contact with ARG 354 (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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344J ASP* 3.6 18.9 + - - -
346J PHE* 2.6 45.8 + - + +
347J GLN* 3.5 11.2 + - - +
349J LEU* 3.5 28.7 - - + +
350J THR 2.9 13.9 + - - +
351J LYS* 3.6 15.3 - - - +
353J GLN* 1.3 76.2 - - - +
355J GLN* 1.3 63.4 + - + +
357J LEU* 3.5 6.7 + - - +
358J ARG* 3.0 24.9 + - - +
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Residues in contact with GLN 355 (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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311I ASN* 5.2 6.2 - - - +
351J LYS* 3.1 46.0 + - + +
352J LYS* 3.5 13.7 - - - +
353J GLN 3.2 0.4 - - - -
354J ARG* 1.3 78.8 - - + +
356J SER* 1.3 61.7 + - - +
358J ARG* 3.4 7.0 + - - +
359J LYS* 3.0 22.2 + - - +
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Residues in contact with SER 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285J LEU* 3.9 16.4 - - - +
352J LYS* 3.0 14.6 + - - +
353J GLN 3.7 6.5 - - - -
355J GLN* 1.3 73.7 - - - +
357J LEU* 1.3 67.4 + - - +
359J LYS* 3.1 6.7 + - - +
360J MET* 2.9 38.1 + - - +
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Residues in contact with LEU 357 (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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285J LEU* 3.9 13.9 - - + -
288J LEU* 3.5 37.5 - - + -
289J ALA* 3.7 17.7 - - + +
292J PHE* 4.7 1.6 - - + -
335J PHE* 5.3 3.4 - - + -
346J PHE* 3.4 41.7 - - + -
349J LEU* 4.7 2.7 - - + -
353J GLN 2.9 17.2 + - - +
354J ARG* 3.8 6.1 - - - +
356J SER* 1.3 75.9 - - - +
358J ARG* 1.3 66.3 + - - +
360J MET* 3.8 9.6 - - - +
361J VAL* 2.9 43.1 + - + +
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Residues in contact with ARG 358 (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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310I ILE* 5.4 0.6 - - - +
317I ALA 3.3 18.6 + - - -
318I LEU* 4.1 9.4 + - - +
321I ASN* 3.6 9.9 + - - +
322I ASP* 2.5 45.5 + - - +
335J PHE* 3.1 61.4 - - + +
354J ARG 3.0 18.7 + - - +
355J GLN* 3.7 7.2 - - - +
357J LEU* 1.3 78.7 - - + +
359J LYS* 1.3 62.9 + - - +
361J VAL* 3.4 1.0 + - - +
362J ILE* 3.0 39.4 + - + +
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Residues in contact with LYS 359 (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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355J GLN 3.0 14.3 + - - +
356J SER* 3.1 10.3 + - - +
358J ARG* 1.3 80.0 - - - +
360J MET* 1.3 57.8 + - + +
362J ILE* 3.4 6.7 + - + +
363J ASP* 2.9 51.6 + - - +
400J TYR* 3.7 29.1 - - + +
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Residues in contact with MET 360 (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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285J LEU* 3.9 24.9 - - + +
286J GLU* 3.9 31.2 - - + +
289J ALA* 3.9 16.6 - - + -
356J SER* 2.9 37.5 + - - +
357J LEU* 3.9 9.6 - - - +
359J LYS* 1.3 75.8 - - + +
361J VAL* 1.3 56.8 - - - +
363J ASP* 3.3 1.0 + - - +
364J ILE* 2.8 39.4 + - + +
400J TYR* 3.7 31.0 - - + +
404J ILE* 3.9 18.2 - - + -
407J LEU* 5.0 3.6 - - - -
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Residues in contact with VAL 361 (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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289J ALA* 3.7 28.9 - - - +
292J PHE* 3.8 20.2 - - + -
293J ALA* 4.2 13.2 - - + -
296J ILE* 4.0 15.5 - - + -
331J LEU* 3.8 11.0 - - + -
335J PHE* 3.5 25.8 - - + -
357J LEU* 2.9 27.8 + - + +
360J MET* 1.3 76.7 - - - +
362J ILE* 1.3 62.2 + - - +
364J ILE* 3.3 1.1 + - - +
365J VAL* 2.9 25.6 + - - +
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Residues in contact with ILE 362 (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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321I ASN* 3.3 41.5 - - + +
322I ASP* 3.8 9.4 - - + +
323I SER* 4.2 3.6 - - - +
331J LEU* 3.7 13.3 - - + +
335J PHE* 3.7 16.4 - - + -
358J ARG* 3.0 44.8 + - + +
359J LYS* 3.7 6.7 - - + +
361J VAL* 1.3 75.7 - - - +
363J ASP* 1.3 68.2 + - - +
366J LEU* 3.0 45.5 + - + +
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Residues in contact with ASP 363 (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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359J LYS* 2.9 36.6 + - - +
360J MET 3.6 4.5 - - - +
362J ILE* 1.3 81.8 - - - +
364J ILE* 1.3 63.2 + - - +
366J LEU* 3.8 7.0 + - - +
367J ALA* 3.4 12.6 + - - +
400J TYR* 2.9 24.3 + - - -
404J ILE* 4.1 12.2 - - + +
408J GLN* 3.1 27.5 - - - +
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Residues in contact with ILE 364 (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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289J ALA* 4.4 1.3 - - + -
290J ALA* 3.9 28.5 - - + +
293J ALA* 3.9 14.1 - - + -
360J MET* 2.8 28.7 + - + +
361J VAL 3.8 2.7 - - - +
363J ASP* 1.3 73.9 - - - +
365J VAL* 1.3 67.4 + - - +
367J ALA* 2.9 18.7 + - - +
368J THR* 3.5 6.8 + - - +
404J ILE* 4.2 11.9 - - + -
407J LEU* 4.0 30.3 - - + +
408J GLN* 3.9 12.8 - - + +
411J VAL* 3.5 37.0 - - + -
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Residues in contact with VAL 365 (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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293J ALA* 3.7 33.9 - - + +
296J ILE* 4.4 3.4 - - + +
297J HIS* 4.1 26.0 - - + +
327J GLU* 3.9 17.0 - - + +
330J HIS* 4.5 3.8 - - + -
331J LEU* 3.5 34.5 - - + +
361J VAL* 2.9 21.5 + - + +
364J ILE* 1.3 71.9 - - + +
366J LEU* 1.3 58.3 + - - +
368J THR* 2.6 36.1 + - - +
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Residues in contact with LEU 366 (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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321I ASN* 5.5 0.4 - - + -
323I SER* 4.2 14.4 - - - +
324J SER* 4.3 7.8 + - - +
327J GLU* 4.2 7.2 - - + -
328J ASN* 3.9 38.6 - - - +
331J LEU* 3.7 17.7 - - + -
362J ILE* 3.0 38.2 + - + +
363J ASP* 4.2 6.7 - - - +
365J VAL* 1.3 75.6 - - - +
367J ALA* 1.3 59.8 + - - +
369J ASP* 3.4 12.3 - - - +
372J LYS* 3.4 26.5 - - - +
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Residues in contact with ALA 367 (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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363J ASP 3.4 11.9 + - - +
364J ILE 2.9 13.7 + - - +
366J LEU* 1.3 76.7 - - - +
368J THR* 1.3 58.8 + - - +
369J ASP 3.1 11.8 + - - +
372J LYS* 4.6 8.6 - - - +
376J LEU* 3.6 31.9 - - + +
408J GLN* 3.7 26.2 - - + +
412J HIS* 3.9 8.7 + - - -
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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