Contacts of the helix formed by residues 399 - 416 (chain E) 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 ASN 399 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A ASN* 6.5 0.7 - - + -
398E ASP* 1.3 99.1 - - - +
400E TYR* 1.3 61.7 + - - +
401E SER* 2.6 45.9 + - - +
402E ASP* 3.2 22.4 + - - +
403E ARG* 3.0 28.8 + - - +
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Residues in contact with TYR 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E GLU* 5.1 8.3 - - - -
359E LYS* 3.7 30.9 - - + +
360E MET* 3.8 30.9 - - + +
363E ASP* 2.9 24.0 + - - -
399E ASN* 1.3 69.9 - - - +
401E SER* 1.3 58.6 + - - +
402E ASP 2.9 4.5 - - - -
403E ARG* 2.7 25.0 + - + +
404E ILE* 2.7 66.8 + - + +
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Residues in contact with SER 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399E ASN* 2.6 19.6 + - - +
400E TYR* 1.3 85.0 - - - +
402E ASP* 1.3 60.7 + - - +
404E ILE* 3.5 14.8 - - - +
405E GLN* 3.2 31.2 + - - +
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Residues in contact with ASP 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E MET* 3.2 26.4 - - + +
388E LYS* 5.0 3.3 + - - -
397E LEU* 4.1 18.4 - - + +
398E ASP* 3.5 17.2 - - - +
399E ASN* 3.2 27.1 - - - +
400E TYR 2.9 0.8 - - - -
401E SER* 1.3 84.5 + - - +
403E ARG* 1.3 66.1 + - - +
405E GLN* 3.4 5.2 + - - +
406E VAL* 3.2 27.4 + - - +
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Residues in contact with ARG 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E VAL* 3.7 22.4 - - - -
282E PHE* 3.7 13.4 - - + -
283E THR* 5.2 4.9 - - - +
286E GLU* 2.8 36.1 + - - +
397E LEU* 3.4 39.1 + - + -
398E ASP 2.8 29.3 + - - -
399E ASN 3.0 14.1 + - - +
400E TYR* 2.7 28.8 + - + +
402E ASP* 1.3 72.4 - - - +
404E ILE* 1.3 60.1 + - - +
405E GLN 3.1 2.0 - - - -
406E VAL* 3.1 3.8 + - - +
407E LEU* 2.9 32.8 + - + +
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Residues in contact with ILE 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E MET* 3.9 37.0 - - + +
363E ASP* 4.0 14.4 - - + +
364E ILE* 4.1 13.2 - - + -
400E TYR* 2.7 59.8 + - + +
401E SER* 3.5 18.2 - - - +
403E ARG* 1.3 74.0 - - - +
405E GLN* 1.3 60.6 + - + +
407E LEU* 3.8 8.2 - - + +
408E GLN* 2.9 36.1 + - - +
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Residues in contact with GLN 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E LEU* 5.2 1.3 - - + -
379E ASP* 3.7 44.4 + - + +
380E LEU* 5.8 0.7 - - + -
383E MET* 3.1 30.9 - - + +
401E SER* 3.2 20.4 + - - +
402E ASP* 3.4 7.1 + - - +
403E ARG 3.1 0.4 - - - -
404E ILE* 1.3 84.0 - - + +
406E VAL* 1.3 57.1 + - - +
408E GLN* 3.4 16.1 + - - +
409E ASN* 2.9 46.2 + - - +
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Residues in contact with VAL 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E LEU* 4.6 6.7 - - + -
282E PHE* 3.9 22.0 - - + -
380E LEU* 5.4 2.2 - - + -
383E MET* 3.8 20.2 - - - -
395E LEU* 5.7 0.9 - - + -
397E LEU* 3.6 20.0 - - + -
402E ASP 3.2 15.9 - - - +
403E ARG 3.1 6.9 + - - +
405E GLN* 1.3 75.6 - - - +
407E LEU* 1.3 59.2 + - - +
409E ASN* 3.4 5.0 + - - +
410E MET* 2.8 32.0 + - + +
481E TRP* 3.8 25.7 - - + -
484E LEU* 4.3 14.4 - - + -
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Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E LEU* 4.1 13.0 - - + -
282E PHE* 3.6 31.0 - - + -
286E GLU* 4.0 35.4 - - + +
290E ALA* 4.1 17.5 - - + -
360E MET* 5.0 4.0 - - - -
364E ILE* 4.0 23.3 - - + -
403E ARG* 2.9 19.3 + - + +
404E ILE* 3.8 15.9 - - + +
406E VAL* 1.3 75.8 - - - +
408E GLN* 1.3 63.2 + - - +
410E MET* 3.2 9.8 + - - +
411E VAL* 3.0 28.4 + - - +
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Residues in contact with GLN 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E ASP* 3.1 38.7 - - - +
364E ILE* 4.0 15.3 - - + +
367E ALA* 3.7 20.1 - - + +
368E THR* 6.1 0.2 - - - +
376E LEU* 4.1 17.1 - - + +
404E ILE* 2.9 29.9 + - + +
405E GLN* 3.5 18.3 - - - +
406E VAL 3.2 0.2 - - - -
407E LEU* 1.3 77.6 - - - +
409E ASN* 1.3 62.9 + - - +
411E VAL* 3.3 2.3 + - - +
412E HIS* 3.0 23.9 + - - +
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Residues in contact with ASN 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E LEU* 3.3 46.5 + - - +
380E LEU* 3.6 44.3 - - + +
405E GLN* 2.9 31.6 + - - +
406E VAL 3.9 3.1 - - - +
408E GLN* 1.3 79.4 - - - +
410E MET* 1.3 57.9 + - - +
412E HIS* 3.4 6.3 - - - +
413E CYS* 2.8 34.4 + - - -
477E LEU* 4.2 10.4 - - - +
481E TRP* 4.4 5.2 - - + -
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Residues in contact with MET 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E THR* 4.3 11.0 - - + +
272E LEU* 3.7 30.2 - - + +
273E LEU* 3.5 42.4 - - + -
278E LEU* 3.4 32.8 - - + -
282E PHE* 4.3 7.6 - - + -
290E ALA* 5.4 0.9 - - - -
406E VAL* 2.8 20.6 + - + +
407E LEU* 3.4 13.0 - - + +
408E GLN 3.1 0.2 - - - -
409E ASN* 1.3 75.9 - - - +
411E VAL* 1.3 58.7 + - - +
413E CYS* 3.0 8.2 + - - +
414E ALA* 2.9 26.3 + - - +
481E TRP* 3.8 19.2 - - + -
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Residues in contact with VAL 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E VAL* 4.4 9.0 - - + -
269E THR* 4.0 11.2 - - + +
290E ALA* 4.0 14.8 - - + +
293E ALA 5.2 0.9 - - - -
294E SER* 3.7 33.0 - - - +
297E HIS* 5.3 1.8 - - + -
364E ILE* 3.5 30.7 - - + -
368E THR* 4.3 16.2 - - + -
407E LEU 3.0 14.9 + - - +
408E GLN 4.0 1.1 - - - +
410E MET* 1.3 75.8 - - + +
412E HIS* 1.3 56.5 + - - +
414E ALA* 3.3 6.9 + - - +
415E ASP* 2.8 28.9 + - + +
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Residues in contact with HIS 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ALA 3.9 16.1 + - - +
368E THR* 4.5 13.6 + - - +
369E ASP 5.2 0.2 - - - -
370E MET* 3.8 16.8 - - - -
373E HIS* 2.8 36.9 + - + +
376E LEU* 4.0 18.2 - - + -
408E GLN 3.0 17.8 + - - +
409E ASN* 3.4 9.0 - - - +
411E VAL* 1.3 78.0 - - - +
413E CYS* 1.3 55.2 + - - +
415E ASP* 3.3 10.2 + - - +
416E LEU* 3.0 51.7 + - + +
477E LEU* 3.5 29.8 - - + -
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Residues in contact with CYS 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E LEU* 4.2 4.3 - - + -
380E LEU* 5.7 0.2 - - - -
409E ASN 2.8 20.9 + - - -
410E MET* 3.0 10.3 + - - +
412E HIS* 1.3 74.1 - - - +
414E ALA* 1.3 64.4 + - - +
416E LEU 3.1 4.9 + - - -
417E SER 3.0 17.8 + - - -
477E LEU* 3.7 33.7 - - - -
478E TRP* 3.3 32.7 - - + -
481E TRP* 3.8 33.9 - - + -
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Residues in contact with ALA 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E ASP* 5.4 0.9 - - - +
265E VAL* 3.8 22.4 - - + +
268E SER* 3.9 15.6 - - - -
269E THR* 3.4 29.2 - - - +
272E LEU* 4.2 5.3 - - + +
410E MET 2.9 11.6 + - - +
411E VAL 3.5 7.2 - - - +
413E CYS* 1.3 76.7 - - - +
415E ASP* 1.3 61.3 + - - +
417E SER* 2.8 28.5 + - - -
418E ASN* 5.5 0.7 + - - -
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Residues in contact with ASP 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E TYR* 4.3 7.3 + - - -
261E HIS* 2.9 18.2 + - - -
265E VAL* 3.9 9.8 - - + +
297E HIS* 2.8 16.6 + - + +
368E THR* 4.1 21.7 - - + +
411E VAL 2.8 20.9 + - - +
412E HIS* 3.6 10.9 + - - +
414E ALA* 1.3 73.5 - - - +
416E LEU* 1.3 69.1 + - + +
417E SER 3.4 1.6 + - - -
418E ASN* 5.2 2.3 + - - +
2009E ZN 2.3 35.7 - - - -
3005E ZAR 5.9 1.6 - - - -
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Residues in contact with LEU 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E MET* 4.0 15.3 - - + -
412E HIS* 3.0 46.3 + - + +
413E CYS 3.1 4.9 + - - +
415E ASP* 1.3 87.2 - - + +
417E SER* 1.3 57.6 + - - +
418E ASN* 3.6 2.6 + - - -
419E PRO* 4.0 4.3 - - - +
469E PHE* 3.7 26.2 - - + -
473E ILE* 3.9 21.1 - - + -
474E VAL* 3.7 19.9 - - + +
477E LEU* 3.8 17.7 - - + -
478E TRP* 3.3 13.5 + - - -
3005E ZAR 4.8 13.9 - - + -
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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
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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