Contacts of the helix formed by residues 399 - 416 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398K ASP* 1.3 98.5 - - - +
400K TYR* 1.3 61.0 + - - +
401K SER* 2.6 45.5 + - - +
402K ASP* 3.3 22.9 + - - +
403K ARG* 3.0 28.7 + - - +
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Residues in contact with TYR 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286K GLU* 5.1 7.9 - - - -
359K LYS* 3.7 30.3 - - + +
360K MET* 3.8 30.5 - - + +
363K ASP* 2.9 24.4 + - - -
399K ASN* 1.3 70.7 - - - +
401K SER* 1.3 61.9 - - - +
402K ASP 2.9 4.5 - - - -
403K ARG* 2.7 22.6 + - + +
404K ILE* 2.7 66.2 + - + +
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Residues in contact with SER 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399K ASN* 2.6 21.5 + - - +
400K TYR* 1.3 84.7 - - - +
402K ASP* 1.3 60.6 + - - +
404K ILE* 3.6 15.3 - - - +
405K GLN* 3.2 31.3 + - - +
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Residues in contact with ASP 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383K MET* 3.2 26.7 - - + +
388K LYS* 5.0 3.3 + - - -
397K LEU* 4.1 18.8 - - + +
398K ASP* 3.5 17.3 - - - +
399K ASN* 3.3 27.0 - - - +
400K TYR 2.8 0.8 + - - -
401K SER* 1.3 83.1 + - - +
403K ARG* 1.3 65.7 + - - +
405K GLN* 3.4 5.0 + - - +
406K VAL* 3.2 28.1 + - - +
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Residues in contact with ARG 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K VAL* 3.7 23.5 + - - -
282K PHE* 3.7 12.6 - - + -
283K THR* 5.3 5.5 - - - +
286K GLU* 2.8 36.7 + - - +
397K LEU* 3.4 38.8 + - + -
398K ASP 2.9 28.3 + - - -
399K ASN 3.0 13.7 + - - +
400K TYR* 2.7 24.9 + - + +
402K ASP* 1.3 77.9 - - - +
404K ILE* 1.3 64.2 + - - +
405K GLN 3.1 1.8 - - - -
406K VAL* 3.1 4.2 + - - +
407K LEU* 3.0 28.2 + - + +
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Residues in contact with ILE 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360K MET* 3.9 37.2 - - + +
363K ASP* 4.0 15.0 - - + +
364K ILE* 4.2 13.0 - - + -
400K TYR* 2.7 60.3 + - + +
401K SER* 3.6 17.0 - - - +
403K ARG* 1.3 72.5 - - - +
405K GLN* 1.3 60.2 + - + +
407K LEU* 4.3 9.0 - - + -
408K GLN* 2.9 42.8 + - - +
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Residues in contact with GLN 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376K LEU* 5.2 1.8 - - + -
379K ASP* 3.7 43.9 + - + +
380K LEU* 5.0 1.0 - - + -
383K MET* 3.1 29.1 - - + +
401K SER* 3.2 20.4 + - - +
402K ASP* 3.4 7.5 + - - +
404K ILE* 1.3 84.3 - - + +
406K VAL* 1.3 57.5 + - - +
408K GLN* 3.4 15.9 + - - +
409K ASN* 2.9 46.7 + - - +
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Residues in contact with VAL 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278K LEU* 4.6 7.4 - - + -
282K PHE* 3.8 22.2 - - + -
380K LEU* 5.4 2.5 - - + -
383K MET* 3.7 20.6 - - - -
397K LEU* 3.6 20.6 - - + -
402K ASP 3.2 15.5 - - - +
403K ARG 3.1 6.8 + - - +
405K GLN* 1.3 75.6 - - - +
407K LEU* 1.3 59.6 + - - +
409K ASN* 3.4 4.4 + - - +
410K MET* 2.8 31.4 + - + +
481K TRP* 3.8 24.7 - - + -
484K LEU* 4.3 14.1 - - + -
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Residues in contact with LEU 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K LEU* 4.1 15.7 - - + -
282K PHE* 3.6 28.3 - - + -
286K GLU* 4.1 35.2 - - + +
290K ALA* 4.0 18.2 - - + -
360K MET* 5.0 4.9 - - - -
364K ILE* 4.0 22.4 - - + -
403K ARG 3.0 20.0 + - - +
404K ILE* 3.8 15.0 - - + +
406K VAL* 1.3 74.9 - - - +
408K GLN* 1.3 65.6 + - - +
410K MET* 3.4 8.0 - - - +
411K VAL* 3.0 29.3 + - - +
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Residues in contact with GLN 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363K ASP* 3.1 38.4 - - - +
364K ILE* 3.9 15.5 - - + +
367K ALA* 3.7 20.6 - - + +
368K THR* 6.0 0.3 - - - +
376K LEU* 4.1 16.1 - - + +
404K ILE* 2.9 31.3 + - + +
405K GLN* 3.5 18.8 + - - +
406K VAL 3.2 0.2 - - - -
407K LEU* 1.3 78.9 - - - +
409K ASN* 1.3 64.0 + - - +
411K VAL* 3.3 2.4 + - - +
412K HIS* 2.9 23.8 + - - +
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Residues in contact with ASN 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376K LEU* 3.2 47.5 + - - +
380K LEU* 3.7 42.7 - - + +
405K GLN* 2.9 31.8 + - - +
406K VAL 3.9 3.1 - - - +
408K GLN* 1.3 79.8 - - - +
410K MET* 1.3 57.2 + - - +
412K HIS* 3.4 6.5 - - - +
413K CYS* 2.8 35.1 + - - -
477K LEU* 4.3 10.5 - - + +
481K TRP* 4.4 5.6 - - + -
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Residues in contact with MET 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K THR* 4.2 11.4 - - + +
272K LEU* 3.7 28.9 - - + +
273K LEU* 3.5 45.1 - - + -
278K LEU* 3.4 33.4 - - + -
282K PHE* 4.3 7.0 - - + -
290K ALA* 5.4 0.9 - - - -
406K VAL* 2.8 20.8 + - + +
407K LEU* 3.4 12.3 - - + +
408K GLN 3.1 0.2 - - - -
409K ASN* 1.3 77.3 - - - +
411K VAL* 1.3 59.2 + - - +
413K CYS* 3.0 8.4 + - - +
414K ALA* 2.9 26.0 + - - +
481K TRP* 3.7 18.1 - - + -
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Residues in contact with VAL 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K VAL* 4.4 10.1 - - + -
269K THR* 4.0 10.3 - - + +
290K ALA* 4.0 15.5 - - + +
293K ALA 5.3 0.2 - - - -
294K SER* 3.7 31.9 - - - +
297K HIS* 5.2 2.9 - - + -
364K ILE* 3.5 30.1 - - + -
368K THR* 4.3 15.9 - - + -
407K LEU 3.0 14.0 + - - +
408K GLN 4.0 1.1 - - - +
410K MET* 1.3 76.6 - - + +
412K HIS* 1.3 53.0 + - - +
414K ALA* 3.3 6.8 + - - +
415K ASP* 2.8 32.2 + - - +
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Residues in contact with HIS 412 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367K ALA 3.9 16.8 + - - +
368K THR* 4.5 13.5 + - - +
369K ASP 5.2 0.2 - - - -
370K MET* 3.9 16.8 - - - -
373K HIS* 2.8 37.3 + - + +
376K LEU* 4.0 19.3 - - + -
408K GLN 2.9 17.3 + - - +
409K ASN* 3.4 9.2 - - - +
411K VAL* 1.3 78.3 - - - +
413K CYS* 1.3 56.1 + - - +
415K ASP* 3.3 9.5 + - - +
416K LEU* 3.0 49.7 + - + +
477K LEU* 3.5 29.2 - - + -
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Residues in contact with CYS 413 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K LEU* 4.2 4.7 - - + -
409K ASN 2.8 20.0 + - - +
410K MET* 3.0 9.4 + - - +
412K HIS* 1.3 74.9 - - - +
414K ALA* 1.3 65.6 + - - +
416K LEU 3.0 4.9 + - - -
417K SER 3.0 18.5 + - - -
477K LEU* 3.7 32.5 - - - -
478K TRP* 3.3 32.6 - - + -
481K TRP* 3.8 34.8 - - + -
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Residues in contact with ALA 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K ASP* 5.4 0.7 - - - +
265K VAL* 3.8 25.6 - - + +
268K SER* 3.9 13.2 - - - -
269K THR* 3.4 29.4 - - - +
272K LEU* 4.2 5.3 - - + +
410K MET 2.9 12.2 + - - +
411K VAL 3.5 6.7 - - - +
413K CYS* 1.3 75.6 - - - +
415K ASP* 1.3 62.1 + - - +
417K SER* 2.9 27.3 + - - -
418K ASN* 5.4 0.5 + - - -
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Residues in contact with ASP 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K TYR* 4.3 6.9 + - - -
261K HIS* 3.0 18.2 + - - -
265K VAL* 3.9 10.1 - - + +
297K HIS* 2.7 19.0 + - + +
368K THR* 4.1 21.0 - - + +
411K VAL 2.8 17.2 + - - +
412K HIS* 3.5 11.5 + - - +
414K ALA* 1.3 75.5 - - - +
416K LEU* 1.3 68.3 + - + +
417K SER 3.4 1.4 + - - -
418K ASN* 5.3 2.4 + - - +
2021K ZN 2.2 36.0 - - - -
3011K ZAR 6.0 0.5 - - - -
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Residues in contact with LEU 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370K MET* 4.1 14.4 - - - -
412K HIS* 3.0 47.0 + - + +
413K CYS 3.0 5.4 + - - +
415K ASP* 1.3 88.3 - - + +
417K SER* 1.3 57.9 + - - +
418K ASN* 3.6 3.5 + - - +
419K PRO* 4.0 4.1 - - - +
469K PHE* 3.6 26.7 - - + -
473K ILE* 3.9 20.4 - - + -
474K VAL* 3.7 20.2 - - + +
477K LEU* 3.8 17.5 - - + -
478K TRP* 3.2 13.0 + - - -
3011K ZAR 4.9 13.7 - - + -
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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
------------------------------------------------------------
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