Contacts of the helix formed by residues 407 - 424 (chain B) in PDB entry 1LK9
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 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ARG* 4.3 8.5 - - - +
42B ASN* 3.6 29.9 + - - +
67B LEU* 3.8 30.3 - - + +
68B PHE* 4.7 3.6 - - - +
70B GLU* 5.4 1.1 - - - +
325B ARG* 3.5 3.2 + - - +
406B LYS* 1.3 82.8 - - - +
408B GLN* 1.3 64.9 + - - +
409B ASP* 3.3 10.7 + - - +
410B ASP* 2.8 39.7 + - - +
411B PHE* 3.0 11.1 + - - +
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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
----------------------------------------------------------
68B PHE* 5.7 0.2 - - - +
321B LYS* 6.1 3.4 - - - +
325B ARG* 3.3 22.0 - - - +
407B THR* 1.3 74.0 - - - +
409B ASP* 1.3 59.0 + - - +
411B PHE* 3.2 6.8 + - - +
412B ASP* 2.7 60.1 + - - +
1F NAG 3.0 35.9 - - - +
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Residues in contact with ASP 409 (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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22B GLU 4.2 2.2 - - - +
23B HIS* 2.7 38.4 + - - -
42B ASN* 2.7 31.5 + - + +
45B TYR* 3.6 10.6 + - + -
407B THR* 3.1 9.4 + - - +
408B GLN* 1.3 80.3 - - - +
410B ASP* 1.3 62.3 - - - +
412B ASP* 3.3 11.0 + - - +
413B GLN* 3.0 43.5 + - - +
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Residues in contact with ASP 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASN* 5.3 0.3 - - - +
43B THR* 2.6 36.7 + - - +
59B ALA* 4.8 0.9 - - - +
60B ASP 3.7 15.2 + - - +
61B VAL* 4.1 8.8 - - + +
67B LEU* 4.9 1.7 - - - +
406B LYS* 3.3 29.9 - - + +
407B THR* 2.8 43.1 + - - +
409B ASP* 1.3 77.1 - - - +
411B PHE* 1.3 56.7 + - - +
413B GLN* 3.3 7.5 + - - +
414B LEU* 2.9 28.9 + - - +
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Residues in contact with PHE 411 (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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61B VAL* 5.5 1.1 - - - -
325B ARG* 3.4 70.4 - - + +
328B ASN* 4.0 8.7 - - + -
329B ILE* 4.4 3.4 - - + -
403B SER 5.7 1.1 - - - -
404B LEU* 4.2 24.2 - - + -
407B THR 3.0 12.2 + - - +
408B GLN* 3.6 13.0 - - - +
410B ASP* 1.3 75.6 - - - +
412B ASP* 1.3 58.8 + - - +
414B LEU* 3.2 12.3 + - + +
415B MET* 2.9 62.2 + - + +
1F NAG 3.6 28.7 - - - -
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Residues in contact with ASP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLN* 2.7 54.4 + - - +
409B ASP* 3.7 11.9 - - - +
411B PHE* 1.3 75.3 - - - +
413B GLN* 1.3 57.3 + - + +
415B MET* 3.4 6.6 + - - +
416B TYR* 2.9 29.7 + - - +
1F NAG 4.0 6.4 - - - +
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Residues in contact with GLN 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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43B THR* 2.9 37.7 + - - +
44B CYS* 3.7 21.7 - - - +
45B TYR* 3.5 22.6 + - - -
53B LYS* 4.7 10.7 - - + +
57B CYS 5.3 0.3 - - - +
59B ALA* 3.8 17.6 - - + -
409B ASP* 3.0 23.1 + - - +
410B ASP* 3.7 6.5 - - - +
412B ASP* 1.3 73.9 - - + +
414B LEU* 1.3 70.7 + - - +
416B TYR* 3.3 6.9 + - - +
417B TYR* 3.2 32.9 + - + -
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Residues in contact with LEU 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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59B ALA* 3.7 8.4 - - - +
61B VAL* 4.0 27.6 - - + -
329B ILE* 3.9 25.6 - - + -
385B ILE* 3.8 34.5 - - + -
402B LEU* 4.1 17.5 - - + -
403B SER 4.5 0.7 - - - +
404B LEU* 4.2 15.9 - - + -
410B ASP 2.9 14.3 + - - +
411B PHE* 3.4 16.4 - - + +
413B GLN* 1.3 78.6 - - - +
415B MET* 1.3 58.6 + - + +
417B TYR* 3.8 1.2 - - - +
418B LEU* 2.9 35.4 + - + +
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Residues in contact with MET 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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328B ASN* 3.5 33.9 - - + +
329B ILE* 3.9 24.0 - - - -
332B LEU* 3.6 13.9 - - + +
411B PHE* 2.9 52.7 + - + +
412B ASP* 3.8 5.6 - - - +
414B LEU* 1.3 77.0 - - + +
416B TYR* 1.3 63.9 + - - +
418B LEU* 3.8 3.4 - - - +
419B LYS* 3.0 61.2 + - - +
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Residues in contact with TYR 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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412B ASP 2.9 18.6 + - - +
413B GLN* 3.5 7.4 - - - +
414B LEU 3.2 0.2 - - - -
415B MET* 1.3 79.0 - - - +
417B TYR* 1.3 99.2 + + - +
419B LYS* 3.5 21.1 - - + +
420B ASP* 4.0 12.5 + - - +
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Residues in contact with TYR 417 (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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54B ILE 5.3 0.2 + - - -
56B GLY* 3.2 24.1 + - - -
57B CYS 2.7 29.3 + - - -
59B ALA* 3.6 11.7 - - + -
383B GLY 3.3 22.4 - - - +
384B ARG* 3.2 36.1 - - + -
385B ILE* 3.7 12.6 - - + -
413B GLN* 3.2 25.3 + - + +
416B TYR* 1.3 105.4 - + - +
418B LEU* 1.3 66.6 + - - +
419B LYS 3.3 0.3 + - - -
420B ASP* 3.3 15.5 + - + +
421B MET* 3.4 14.9 + - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 3.7 36.3 - - + -
332B LEU* 3.9 15.3 - - + -
333B LEU* 3.8 26.5 - - + -
339B PHE* 4.4 5.2 - - + -
380B PHE* 4.0 28.9 - - + -
385B ILE* 3.9 6.4 - - + +
402B LEU* 4.7 3.6 - - + -
414B LEU* 2.9 25.2 + - + +
415B MET* 3.8 6.1 - - - +
417B TYR* 1.3 76.6 - - - +
419B LYS* 1.3 58.0 + - - +
421B MET* 3.0 11.8 + - - +
422B VAL* 2.8 37.4 + - + +
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Residues in contact with LYS 419 (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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332B LEU* 3.6 26.7 - - + +
415B MET* 3.0 59.2 + - - +
416B TYR* 3.5 14.8 - - + +
418B LEU* 1.3 76.9 - - - +
420B ASP* 1.3 66.5 + - - +
422B VAL* 3.3 2.6 + - - +
423B LYS* 3.2 32.9 + - + +
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Residues in contact with ASP 420 (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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416B TYR* 4.0 13.2 + - - +
417B TYR* 3.3 10.4 + - - +
418B LEU 3.3 0.4 - - - -
419B LYS* 1.3 78.1 - - - +
421B MET* 1.3 64.3 + - + +
423B LYS* 3.0 33.1 + - - +
424B ALA* 3.3 22.0 + - - +
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Residues in contact with MET 421 (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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338B ARG* 2.9 39.0 + - - +
339B PHE* 3.6 28.5 - - + -
379B THR* 3.9 22.4 - - + +
380B PHE* 3.9 27.6 - - + -
383B GLY* 3.8 24.2 - - - -
385B ILE* 3.7 27.1 - - - -
417B TYR 3.4 9.6 + - - +
418B LEU* 3.0 10.4 + - + +
420B ASP* 1.3 78.0 - - + +
422B VAL* 1.3 63.2 + - - +
423B LYS 3.5 0.3 + - - -
424B ALA* 3.5 6.4 + - - -
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Residues in contact with VAL 422 (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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332B LEU* 3.3 42.2 - - + +
333B LEU* 4.0 24.5 - - + +
335B GLN* 4.0 13.0 - - + +
336B SER* 2.8 46.5 + - - +
338B ARG* 4.7 0.7 - - - +
339B PHE* 4.1 12.3 - - + -
418B LEU* 2.8 21.4 + - + +
419B LYS 3.8 4.0 - - - +
421B MET* 1.3 78.6 - - - +
423B LYS* 1.3 62.1 + - + +
424B ALA 3.6 4.7 + - - +
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Residues in contact with LYS 423 (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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336B SER* 5.3 0.7 - - - -
419B LYS* 3.2 16.9 + - - +
420B ASP* 3.0 41.9 + - - +
422B VAL* 1.3 77.4 - - + +
424B ALA* 1.3 68.7 + - - +
425B LYS* 3.8 1.6 + - - +
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Residues in contact with ALA 424 (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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336B SER* 5.5 0.9 - - - -
338B ARG* 3.8 13.5 - - - +
370B TRP* 3.6 12.4 - - + -
420B ASP 3.3 13.9 + - - +
421B MET* 3.6 13.5 - - - +
422B VAL 3.3 7.9 - - - +
423B LYS* 1.3 84.3 - - - +
425B LYS* 1.3 68.7 + - - +
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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