Contacts of the helix formed by residues 399 - 416 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C ASP* 1.3 97.4 - - - +
400C TYR* 1.3 63.0 - - - +
401C SER* 2.6 45.9 + - - +
402C ASP* 3.2 21.4 + - - +
403C ARG* 3.0 29.6 + - - +
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Residues in contact with TYR 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLU* 5.2 7.9 - - - -
359C LYS* 3.7 29.6 - - + +
360C MET* 3.8 30.8 - - + +
363C ASP* 2.9 24.0 + - - -
399C ASN* 1.3 70.6 - - - +
401C SER* 1.3 59.0 + - - +
402C ASP 2.9 4.3 - - - -
403C ARG* 2.7 24.7 + - + +
404C ILE* 2.7 66.4 + - + +
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Residues in contact with SER 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ASN* 2.6 19.4 + - - +
400C TYR* 1.3 84.3 - - - +
402C ASP* 1.3 60.7 + - - +
404C ILE* 3.5 14.2 - - - +
405C GLN* 3.2 31.8 + - - +
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Residues in contact with ASP 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C MET* 3.2 26.9 - - + +
388C LYS* 5.0 3.3 + - - -
396C LEU 5.1 0.2 - - - +
397C LEU* 4.1 18.7 - - + +
398C ASP* 3.5 17.0 - - - +
399C ASN* 3.2 27.5 + - - +
400C TYR 2.9 0.6 - - - -
401C SER* 1.3 83.0 + - - +
403C ARG* 1.3 66.7 + - - +
405C GLN* 3.4 5.2 + - - +
406C VAL* 3.2 27.8 + - - +
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Residues in contact with ARG 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 3.7 22.6 + - - -
282C PHE* 3.7 11.7 - - + -
283C THR* 5.3 5.0 - - - +
286C GLU* 2.8 37.3 + - - +
397C LEU* 3.4 37.5 + - + -
398C ASP 2.8 28.5 + - - -
399C ASN 3.0 14.1 + - - +
400C TYR* 2.7 29.1 + - + +
402C ASP* 1.3 72.5 - - - +
404C ILE* 1.3 63.7 + - - +
405C GLN 3.1 2.0 - - - -
406C VAL* 3.2 4.0 + - - +
407C LEU* 3.0 28.0 + - + +
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Residues in contact with ILE 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C MET* 3.9 37.0 - - + +
363C ASP* 4.1 14.8 - - + +
364C ILE* 4.2 12.8 - - + -
400C TYR* 2.7 59.3 + - + +
401C SER* 3.5 17.9 - - - +
403C ARG* 1.3 73.2 - - - +
405C GLN* 1.3 61.3 + - - +
407C LEU* 4.4 9.2 - - + -
408C GLN* 2.9 34.5 + - - +
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Residues in contact with GLN 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C LEU* 5.2 2.0 - - + -
379C ASP* 3.7 43.7 + - + +
380C LEU* 5.1 0.6 - - - -
383C MET* 3.1 29.5 - - + +
401C SER* 3.2 20.4 + - - +
402C ASP* 3.4 8.0 + - - +
403C ARG 3.1 0.2 - - - -
404C ILE* 1.3 82.1 - - + +
406C VAL* 1.3 58.6 + - - +
408C GLN* 3.4 15.7 + - - +
409C ASN* 2.9 46.5 + - - +
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Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 4.6 6.7 - - + -
282C PHE* 3.8 22.2 - - + -
380C LEU* 5.4 2.5 - - + -
383C MET* 3.7 20.9 - - - -
395C LEU* 5.7 0.4 - - + -
397C LEU* 3.6 20.4 - - + -
402C ASP 3.2 15.7 - - - +
403C ARG 3.2 6.4 + - - +
405C GLN* 1.3 75.6 - - - +
407C LEU* 1.3 59.7 + - - +
409C ASN* 3.4 4.6 + - - +
410C MET* 2.8 31.3 + - + +
481C TRP* 3.8 24.9 - - + -
484C LEU* 4.3 13.9 - - + -
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C LEU* 4.1 12.6 - - + -
282C PHE* 3.6 30.7 - - + -
286C GLU* 4.1 34.8 - - + +
290C ALA* 4.0 18.4 - - + -
360C MET* 5.0 3.6 - - + -
364C ILE* 4.0 24.0 - - + -
403C ARG* 3.0 21.2 + - + +
404C ILE* 3.9 15.7 - - + +
406C VAL* 1.3 75.5 - - - +
408C GLN* 1.3 63.1 + - - +
410C MET* 3.4 8.3 - - - +
411C VAL* 3.0 28.6 + - - +
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Residues in contact with GLN 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ASP* 3.0 37.8 - - - +
364C ILE* 3.9 16.6 - - + +
367C ALA* 3.7 21.0 - - + +
368C THR* 6.1 0.2 - - - +
376C LEU* 4.1 16.3 - - + +
404C ILE* 2.9 31.8 + - + +
405C GLN* 3.5 19.3 + - - +
407C LEU* 1.3 78.5 - - - +
409C ASN* 1.3 63.0 + - - +
411C VAL* 3.3 2.4 + - - +
412C HIS* 3.0 23.4 + - - +
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Residues in contact with ASN 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C LEU* 3.2 48.1 + - - +
380C LEU* 3.7 42.8 - - + +
405C GLN* 2.9 31.8 + - - +
406C VAL 3.9 3.1 - - - +
408C GLN* 1.3 79.3 - - - +
410C MET* 1.3 57.8 + - - +
412C HIS* 3.4 6.5 - - - +
413C CYS* 2.8 35.5 + - - -
477C LEU* 4.3 9.5 - - - +
481C TRP* 4.4 5.2 - - + -
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Residues in contact with MET 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C THR* 4.3 11.4 - - + +
272C LEU* 3.7 29.4 - - + +
273C LEU* 3.4 43.3 - - + -
278C LEU* 3.4 33.2 - - + -
282C PHE* 4.3 7.2 - - + -
290C ALA* 5.3 0.9 - - - -
406C VAL* 2.8 19.8 + - + +
407C LEU* 3.4 13.7 - - + +
408C GLN 3.1 0.2 - - - -
409C ASN* 1.3 77.6 - - - +
411C VAL* 1.3 59.9 + - + +
413C CYS* 3.0 7.4 + - - +
414C ALA* 2.8 26.9 + - - +
481C TRP* 3.7 18.1 - - + -
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Residues in contact with VAL 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C VAL* 4.4 9.9 - - + -
269C THR* 3.9 11.2 - - + +
290C ALA* 4.0 15.0 - - + +
293C ALA 5.3 0.2 - - - -
294C SER* 3.7 32.3 - - - +
297C HIS* 5.2 2.5 - - + -
364C ILE* 3.5 32.3 - - + +
368C THR* 4.2 17.0 - - + -
407C LEU 3.0 14.1 + - - +
408C GLN 4.0 1.1 - - - +
410C MET* 1.3 77.7 - - + +
412C HIS* 1.3 58.1 + - - +
414C ALA* 3.5 6.5 - - - +
415C ASP* 2.8 27.6 + - + +
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Residues in contact with HIS 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C ALA 3.9 17.7 + - - +
368C THR* 4.5 13.5 + - - +
370C MET* 3.8 17.5 - - - -
373C HIS* 2.8 36.5 + - + +
376C LEU* 4.0 20.2 - - + -
408C GLN 3.0 17.1 + - - +
409C ASN* 3.4 9.0 - - - +
411C VAL* 1.3 75.8 - - - +
413C CYS* 1.3 59.2 + - - +
415C ASP* 3.3 9.6 + - - +
416C LEU* 3.0 50.6 + - + +
477C LEU* 3.4 29.2 - - + -
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Residues in contact with CYS 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 4.2 5.4 - - + -
409C ASN 2.8 20.8 + - - +
410C MET 3.0 8.3 + - - +
412C HIS* 1.3 72.9 - - - +
414C ALA* 1.3 67.1 + - - +
416C LEU 3.1 4.7 + - - -
417C SER 3.0 18.5 + - - -
477C LEU* 3.7 33.2 - - - -
478C TRP* 3.3 32.2 - - + -
481C TRP* 3.8 35.2 - - - -
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Residues in contact with ALA 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C ASP* 5.4 0.9 - - - +
265C VAL* 3.8 23.9 - - + +
268C SER* 3.8 13.9 - - - -
269C THR* 3.5 28.9 - - - +
272C LEU* 4.2 4.9 - - + +
410C MET 2.8 12.2 + - - +
411C VAL 3.5 6.5 - - - +
413C CYS* 1.3 77.0 - - - +
415C ASP* 1.3 60.9 + - - +
417C SER* 2.8 27.8 + - - -
418C ASN* 5.5 0.7 + - - -
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Residues in contact with ASP 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C TYR* 4.3 7.1 + - - -
261C HIS* 2.9 19.9 + - - -
265C VAL* 3.9 9.4 - - + +
297C HIS* 2.8 17.5 + - + +
368C THR* 4.1 21.4 - - + +
411C VAL* 2.8 21.7 + - + +
412C HIS* 3.6 10.8 + - - +
414C ALA* 1.3 72.4 - - - +
416C LEU* 1.3 67.6 + - + +
417C SER 3.4 1.4 + - - -
418C ASN* 5.1 2.4 + - - +
2005C ZN 2.2 36.6 - - - -
3003C ZAR 6.0 1.6 - - - -
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Residues in contact with LEU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C MET* 4.0 14.6 - - - -
412C HIS* 3.0 47.2 + - + +
413C CYS 3.1 5.1 + - - +
415C ASP* 1.3 87.6 - - + +
417C SER* 1.3 57.3 + - - +
418C ASN* 3.6 3.1 + - - +
419C PRO* 4.0 4.4 - - - +
469C PHE* 3.7 26.2 - - + -
473C ILE* 3.8 22.0 - - + -
474C VAL* 3.7 19.9 - - + +
477C LEU* 3.8 17.9 - - + -
478C TRP* 3.2 13.7 + - - -
3003C ZAR 4.8 13.5 - - + -
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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