Contacts of the helix formed by residues 399 - 416 (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 ASN 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B ASP* 1.3 97.8 - - - +
400B TYR* 1.3 63.4 + - - +
401B SER* 2.6 46.3 + - - +
402B ASP* 3.2 24.0 + - - +
403B ARG* 3.0 27.1 + - - +
398I ASP* 5.5 6.7 - - - +
399I ASN* 5.8 7.0 - - + -
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Residues in contact with TYR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 5.1 7.6 - - - -
359B LYS* 3.8 29.0 - - + +
360B MET* 3.8 31.5 - - + +
363B ASP* 2.9 24.2 + - - -
399B ASN* 1.3 70.1 - - - +
401B SER* 1.3 58.5 + - - +
402B ASP 2.9 4.7 - - - -
403B ARG* 2.7 25.1 + - + +
404B ILE* 2.7 65.3 + - + +
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASN* 2.6 22.2 + - - +
400B TYR* 1.3 84.0 - - - +
402B ASP* 1.3 61.5 + - - +
404B ILE* 3.6 14.7 - - - +
405B GLN* 3.2 32.0 + - - +
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Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B MET* 3.2 27.3 - - + +
388B LYS* 5.0 3.5 + - - -
397B LEU* 4.1 18.0 - - + +
398B ASP* 3.5 16.8 - - - +
399B ASN* 3.2 27.5 - - - +
400B TYR 2.9 0.8 - - - -
401B SER* 1.3 85.7 + - - +
403B ARG* 1.3 63.8 + - - +
405B GLN* 3.4 4.7 + - - +
406B VAL* 3.2 27.7 + - - +
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Residues in contact with ARG 403 (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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281B VAL* 3.7 23.3 + - - -
282B PHE* 3.7 12.4 - - + -
283B THR* 5.2 5.5 - - - +
286B GLU* 2.8 36.9 + - - +
397B LEU* 3.4 38.2 + - + -
398B ASP 2.8 28.9 + - - -
399B ASN* 3.0 13.9 + - - +
400B TYR* 2.7 28.8 + - + +
402B ASP* 1.3 72.1 - - - +
404B ILE* 1.3 59.4 + - - +
405B GLN 3.1 1.6 - - - -
406B VAL* 3.1 4.3 + - - +
407B LEU* 3.0 32.5 + - + +
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Residues in contact with ILE 404 (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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360B MET* 3.9 37.5 - - + +
363B ASP* 4.1 13.7 - - + +
364B ILE* 4.2 12.3 - - + -
400B TYR* 2.7 59.7 + - + +
401B SER* 3.6 16.8 - - - +
403B ARG* 1.3 74.4 - - - +
405B GLN* 1.3 60.5 + - + +
407B LEU* 4.3 9.2 - - + -
408B GLN* 2.9 37.1 + - - +
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Residues in contact with GLN 405 (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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376B LEU* 5.2 1.6 - - + -
379B ASP* 3.7 44.5 + - + +
380B LEU* 5.1 0.8 - - - -
383B MET* 3.0 30.6 - - + +
401B SER* 3.2 20.9 + - - +
402B ASP* 3.4 6.9 + - - +
403B ARG 3.1 0.2 - - - -
404B ILE* 1.3 82.6 - - + +
406B VAL* 1.3 62.7 + - - +
408B GLN* 3.5 15.7 + - - +
409B ASN* 2.9 42.2 + - - +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 4.6 7.0 - - + -
282B PHE* 3.8 21.3 - - + -
380B LEU* 5.5 2.5 - - + -
383B MET* 3.8 21.1 - - - -
395B LEU* 5.7 0.7 - - + -
397B LEU* 3.6 19.7 - - + -
402B ASP 3.2 15.7 - - - +
403B ARG 3.1 7.3 + - - +
405B GLN* 1.3 75.4 - - - +
407B LEU* 1.3 60.8 + - - +
409B ASN* 3.4 4.6 + - - +
410B MET* 2.8 28.8 + - + +
481B TRP* 3.8 24.8 - - + -
484B LEU* 4.3 14.4 - - + -
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Residues in contact with LEU 407 (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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273B LEU* 4.1 14.8 - - + -
282B PHE* 3.6 29.2 - - + -
286B GLU* 4.0 36.1 - - + +
290B ALA* 4.0 17.9 - - + -
360B MET* 5.0 3.8 - - - -
364B ILE* 4.1 22.7 - - + -
403B ARG* 3.0 20.8 + - + +
404B ILE* 3.8 15.0 - - + +
406B VAL* 1.3 74.4 - - - +
408B GLN* 1.3 65.9 + - - +
410B MET* 3.5 8.4 - - - +
411B VAL* 3.0 29.5 + - - +
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Residues in contact with GLN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ASP* 3.0 38.5 - - - +
364B ILE* 4.0 15.9 - - + +
367B ALA* 3.7 20.6 - - + +
368B THR* 6.0 0.3 - - - +
376B LEU* 4.1 17.3 - - + +
404B ILE* 2.9 31.7 + - + +
405B GLN* 3.5 18.9 - - - +
407B LEU* 1.3 78.7 - - - +
409B ASN* 1.3 62.9 + - - +
411B VAL* 3.8 2.3 - - - +
412B HIS* 3.0 23.4 + - - +
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Residues in contact with ASN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 3.2 48.4 + - - +
377B LEU 4.3 0.5 + - - -
380B LEU* 3.8 42.1 - - + +
405B GLN* 2.9 32.2 + - - +
406B VAL 3.9 3.1 - - - +
408B GLN* 1.3 78.9 - - - +
410B MET* 1.3 57.8 + - - +
412B HIS* 3.4 7.1 - - - +
413B CYS* 2.8 35.1 + - - -
477B LEU* 4.3 9.2 - - - +
481B TRP* 4.4 5.2 - - + -
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Residues in contact with MET 410 (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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269B THR* 4.2 11.7 - - + +
272B LEU* 3.7 29.9 - - + +
273B LEU* 3.5 43.1 - - + -
278B LEU* 3.4 33.2 - - + -
282B PHE* 4.3 7.2 - - + -
290B ALA* 5.4 0.7 - - - -
406B VAL* 2.8 20.2 + - + +
407B LEU* 3.5 13.5 - - + +
408B GLN 3.1 0.2 - - - -
409B ASN* 1.3 77.2 - - - +
411B VAL* 1.3 58.8 + - - +
413B CYS* 3.0 6.7 + - - +
414B ALA* 2.8 27.4 + - - +
481B TRP* 3.8 18.6 - - + -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B VAL* 4.4 8.3 - - + -
269B THR* 3.9 12.1 - - + +
290B ALA* 4.0 15.5 - - + +
293B ALA 5.2 0.7 - - - -
294B SER* 3.7 31.9 - - - +
297B HIS* 5.2 2.9 - - + -
364B ILE* 3.5 30.1 - - + -
368B THR* 4.3 16.8 - - + -
407B LEU 3.0 15.3 + - - +
408B GLN 4.0 1.1 - - - +
410B MET* 1.3 76.5 - - + +
412B HIS* 1.3 56.8 + - - +
414B ALA* 3.5 6.5 - - - +
415B ASP* 2.8 27.7 + - - +
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Residues in contact with HIS 412 (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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367B ALA 3.9 16.5 + - - +
368B THR* 4.5 13.8 + - - +
370B MET* 3.9 17.0 - - - -
373B HIS* 2.9 37.3 + - + +
376B LEU* 4.0 18.8 - - + -
408B GLN 3.0 17.7 + - - +
409B ASN* 3.4 9.2 - - - +
410B MET 3.1 0.2 - - - -
411B VAL* 1.3 75.8 - - - +
413B CYS* 1.3 59.9 + - - +
415B ASP* 3.2 8.9 + - - +
416B LEU* 3.0 51.1 + - + +
477B LEU* 3.4 29.2 - - + -
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Residues in contact with CYS 413 (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* 4.2 4.9 - - + -
409B ASN* 2.8 20.3 + - - -
410B MET* 3.4 8.7 - - - +
412B HIS* 1.3 73.4 - - - +
414B ALA* 1.3 66.8 + - - +
416B LEU 3.1 4.5 + - - -
417B SER 3.0 17.5 + - - -
477B LEU* 3.7 32.5 - - - -
478B TRP* 3.3 34.8 - - + -
481B TRP* 3.8 34.8 - - + -
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Residues in contact with ALA 414 (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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264B ASP* 5.5 0.9 - - - +
265B VAL* 3.8 24.6 - - + +
268B SER* 3.9 14.0 - - - -
269B THR* 3.4 28.9 - - - +
272B LEU* 4.2 4.9 - - + +
410B MET 2.8 11.1 + - - +
411B VAL 3.5 7.2 - - - +
413B CYS* 1.3 75.8 - - - +
415B ASP* 1.3 62.7 + - - +
417B SER* 2.9 26.8 + - - -
418B ASN* 5.5 0.9 + - - -
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Residues in contact with ASP 415 (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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256B TYR* 4.3 6.8 + - - -
261B HIS* 3.0 17.8 + - - -
265B VAL* 3.9 9.8 - - + +
297B HIS* 2.7 18.5 + - + +
368B THR* 4.0 20.4 - - + +
411B VAL 2.8 19.2 + - - +
412B HIS* 3.5 10.9 + - - +
413B CYS 3.2 0.2 - - - -
414B ALA* 1.3 78.3 - - - +
416B LEU* 1.3 68.1 + - + +
417B SER 3.7 1.0 + - - -
418B ASN* 5.2 2.8 + - - +
2003B ZN 2.1 36.5 - - - -
2004B MG 4.1 2.9 - - - -
3002B ZAR 6.0 0.9 - - - -
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Residues in contact with LEU 416 (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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370B MET* 4.0 14.4 - - - -
412B HIS* 3.0 47.9 + - + +
413B CYS 3.1 5.1 + - - +
415B ASP* 1.3 87.8 - - + +
417B SER* 1.3 57.2 + - - +
418B ASN* 3.6 2.9 - - - +
419B PRO* 4.0 4.3 - - - +
469B PHE* 3.6 27.4 - - + -
473B ILE* 3.8 21.1 - - + -
474B VAL* 3.8 18.6 - - + +
477B LEU* 3.8 17.5 - - + -
478B TRP* 3.2 14.0 + - - -
3002B 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
------------------------------------------------------------
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