Contacts of the helix formed by residues 393 - 412 (chain B) in PDB entry 6B0Z
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 393 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B GLU* 2.9 38.7 + - + +
325B THR 3.1 16.2 - - - +
326B SER* 4.0 3.8 - - - -
373B THR* 5.1 0.2 - - - -
388B ARG* 3.8 2.0 - - - +
391B TYR* 4.9 0.9 - - - -
392B LEU* 1.3 75.4 - - - +
394B THR* 1.3 65.8 + - - +
395B PHE* 3.0 15.2 + - - +
396B GLU* 2.7 53.1 + - - +
397B PHE* 3.0 22.6 + - - +
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Residues in contact with THR 394 (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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18B MET* 4.5 7.9 - - + -
21B ILE* 5.9 0.2 - - + -
22B ILE* 4.1 24.0 - - + -
25B LEU* 4.9 9.6 - - + -
325B THR* 2.9 28.8 + - - -
326B SER* 3.8 1.4 - - - +
327B THR* 2.7 44.1 + - - +
329B PRO* 5.7 1.6 - - + +
373B THR* 5.1 0.4 - - - -
393B ASN* 1.3 72.2 - - - +
395B PHE* 1.3 71.4 + - + +
397B PHE* 3.6 4.8 + - - +
398B MET* 3.3 25.7 + - + +
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 5.3 1.3 - - + -
21B ILE* 4.4 15.0 - - + -
25B LEU* 3.8 34.8 - - + -
29B LYS* 5.5 1.4 - - - +
319B TYR* 4.1 30.7 - + - -
325B THR* 4.6 8.1 - - - -
393B ASN* 3.0 12.8 + - + +
394B THR* 1.3 88.3 - - + +
396B GLU* 1.3 61.8 + - + +
398B MET* 3.4 5.5 + - - +
399B ASP* 2.9 37.7 + - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 2.8 21.1 + - - -
392B LEU* 3.7 27.2 - - + +
393B ASN* 2.7 56.1 + - - +
395B PHE* 1.3 72.9 - - + +
397B PHE* 1.3 56.1 + - - +
399B ASP* 3.2 10.5 + - - +
400B LYS* 2.8 28.6 + - - +
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Residues in contact with PHE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN* 4.7 0.9 - - - -
329B PRO* 3.5 38.1 - - + -
330B ILE* 3.8 11.7 - - + -
366B THR* 3.9 12.8 - - + -
367B ILE* 3.9 20.9 - - + -
371B PHE 3.3 26.0 - - - -
372B MET* 3.7 20.4 - - - -
373B THR* 3.7 17.3 - - + -
376B LEU* 5.8 0.9 - - + -
392B LEU* 4.0 14.1 - - + +
393B ASN 3.0 16.2 + - - +
394B THR 3.9 3.4 - - - +
396B GLU* 1.3 78.0 - - - +
398B MET* 1.3 57.3 + - - +
400B LYS* 3.1 3.4 + - + +
401B LEU* 2.8 54.0 + - + +
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Residues in contact with MET 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 5.1 2.7 - - + -
25B LEU* 3.9 40.6 - - + +
26B ILE* 3.9 14.8 - - + +
29B LYS* 4.2 18.6 - - + +
30B LEU* 3.8 29.8 - - + +
329B PRO* 3.7 35.9 - - + -
333B ILE* 4.6 0.4 - - - -
394B THR* 3.3 19.8 + - + +
395B PHE* 3.8 6.1 - - - +
396B GLU 3.4 0.2 - - - -
397B PHE* 1.3 76.1 - - - +
399B ASP* 1.3 63.6 + - - +
401B LEU* 3.3 8.9 + - + +
402B GLY* 2.9 20.8 + - - -
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 3.0 29.3 + - - +
395B PHE* 2.9 22.1 + - - +
396B GLU* 3.3 13.4 - - - +
398B MET* 1.3 76.4 - - - +
400B LYS* 1.3 57.3 + - - +
402B GLY* 3.2 3.1 + - - -
403B GLU* 2.9 43.9 + - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B THR* 3.9 20.4 - - + -
371B PHE* 3.7 49.2 - - + -
392B LEU* 4.2 11.2 - - + -
396B GLU 2.8 17.2 + - - +
397B PHE* 3.1 9.4 + - - +
399B ASP* 1.3 72.9 - - - +
401B LEU* 1.3 62.2 - - - +
403B GLU* 3.2 21.2 + - - +
404B ASN* 3.0 43.6 + - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.1 12.1 - - + -
329B PRO* 4.4 2.9 - - + -
330B ILE* 4.2 2.2 - - + -
333B ILE* 3.6 29.6 - - + -
359B LEU* 6.0 1.6 - - + -
362B VAL* 3.9 10.1 - - + +
363B SER* 3.8 21.8 - - - +
366B THR* 3.4 33.7 - - + +
397B PHE* 2.8 52.9 + - + +
398B MET* 3.7 8.5 - - - +
400B LYS* 1.3 72.9 - - - +
402B GLY* 1.3 58.3 + - - +
404B ASN* 3.4 0.7 + - - +
405B LEU* 2.8 32.1 + - - +
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 4.6 10.5 - - - -
30B LEU* 3.8 16.5 - - - +
34B TYR* 4.4 2.6 + - - -
398B MET 2.9 14.8 + - - -
399B ASP* 3.6 3.6 - - - -
401B LEU* 1.3 77.1 - - - +
403B GLU* 1.3 62.2 + - - +
405B LEU* 4.1 1.8 - - - +
406B LYS* 3.2 23.6 + - - +
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP* 2.9 33.6 + - - +
400B LYS* 3.2 25.5 + - + +
402B GLY* 1.3 79.4 - - - +
404B ASN* 1.3 65.2 + - - +
406B LYS* 3.6 6.3 + - - +
407B ILE* 3.3 29.5 + - + +
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Residues in contact with ASN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B VAL* 4.1 15.4 - - + +
365B GLU* 6.3 0.4 - - - +
366B THR* 3.0 26.5 + - - +
369B ALA* 6.3 0.8 - - - +
371B PHE* 5.5 1.0 - - - -
400B LYS* 3.0 46.2 + - - +
401B LEU 4.0 2.7 - - - +
403B GLU* 1.3 76.4 - - - +
405B LEU* 1.3 55.8 + - - +
407B ILE* 3.2 15.1 + - - +
408B LYS* 2.7 36.6 + - - +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS 4.6 0.4 - - - +
30B LEU* 3.5 44.9 - - + +
34B TYR* 3.6 20.6 - - + +
355B PHE* 4.4 3.6 - - + -
358B ALA 4.8 0.2 - - - +
359B LEU* 4.0 31.4 - - + +
362B VAL* 3.9 21.2 - - + +
401B LEU 2.8 18.6 + - - +
402B GLY* 4.1 3.6 - - - +
404B ASN* 1.3 77.8 - - - +
406B LYS* 1.3 61.9 + - - +
408B LYS* 5.0 0.2 - - + -
409B LEU* 3.0 47.2 + - + +
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Residues in contact with LYS 406 (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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34B TYR* 3.4 26.4 + - + +
402B GLY 3.2 14.6 + - - +
403B GLU* 3.8 6.7 - - - +
405B LEU* 1.3 79.8 - - - +
407B ILE* 1.3 64.0 + - + +
409B LEU* 3.8 1.4 + - - +
410B ALA* 3.3 23.4 + - + +
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Residues in contact with ILE 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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403B GLU* 3.3 18.8 + - + +
404B ASN* 3.2 18.2 + - - +
406B LYS* 1.3 79.0 - - + +
408B LYS* 1.3 65.8 + - - +
410B ALA* 3.0 6.8 + - - +
411B GLN* 3.0 47.4 + - + +
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 5.7 3.5 - - + -
358B ALA* 4.2 20.4 - - + -
361B GLU* 3.1 33.7 + - - -
362B VAL* 3.5 22.4 - - + -
365B GLU* 2.6 36.7 + - - +
404B ASN 2.7 20.5 + - - +
405B LEU 3.2 3.1 + - - +
407B ILE* 1.3 76.8 - - - +
409B LEU* 1.3 63.6 + - + +
411B GLN* 3.5 12.0 + - - +
412B ALA* 3.5 9.7 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 6.0 0.9 - - + -
34B TYR* 3.6 35.9 - - + -
354B PHE* 4.4 16.4 - - + -
355B PHE* 3.7 32.8 - - + -
358B ALA* 3.9 28.0 - - + -
405B LEU* 3.0 28.4 + - + +
406B LYS 4.5 2.0 - - - +
408B LYS* 1.3 76.4 - - + +
410B ALA* 1.3 62.0 + - - +
412B ALA* 3.4 17.3 - - - +
413B LYS 4.8 0.2 + - - -
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Residues in contact with ALA 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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406B LYS* 3.3 19.5 + - + +
407B ILE* 3.0 5.7 + - - +
409B LEU* 1.3 75.5 - - - +
411B GLN* 1.3 72.5 + - - +
412B ALA 3.0 5.9 + - - -
413B LYS* 3.1 18.9 + - - +
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Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE* 3.0 38.0 + - + +
408B LYS* 3.5 5.4 + - - +
410B ALA* 1.3 83.2 - - - +
412B ALA* 1.3 64.6 + - - +
413B LYS* 3.0 10.7 + - - +
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Residues in contact with ALA 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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354B PHE* 4.1 30.1 - - + -
408B LYS 3.5 7.6 + - - +
409B LEU 3.4 18.6 - - - +
410B ALA 3.0 1.0 + - - -
411B GLN* 1.3 77.1 - - - +
413B LYS* 1.3 90.7 + - + +
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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