Contacts of the helix formed by residues 383 - 397 (chain B) in PDB entry 2W8D
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 LYS 383 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375B GLU 2.7 26.6 + - - +
376B ASN* 2.9 24.7 + - - +
377B THR 4.4 8.5 - - - -
378B LYS* 4.4 12.3 - - + +
381B GLY 3.6 0.4 + - - -
382B MSE 1.3 71.4 - - - +
384B ASP* 1.3 65.4 + - - +
385B LYS 3.4 0.7 + - - -
386B PRO* 3.5 10.6 - - + +
387B PHE* 3.2 21.7 + - - +
410B SER* 3.3 9.0 - - - +
417B MSE 4.0 14.8 - - + -
418B ASP* 3.8 15.6 + - - +
421B ASP* 3.2 38.4 + - - +
443B TYR* 3.5 15.7 - - - +
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Residues in contact with ASP 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B MSE 4.0 0.7 - - - +
383B LYS* 1.3 73.2 - - - +
385B LYS* 1.3 57.0 + - - +
387B PHE* 3.5 9.2 - - + +
388B PHE* 2.9 43.4 + - + -
408B THR* 3.7 19.2 - - - -
409B LEU* 3.0 15.7 + - - +
410B SER* 3.0 41.2 + - - +
411B ASN 4.4 2.1 + - - -
443B TYR* 4.0 3.2 + - + -
444B LEU* 3.7 16.3 - - + +
447B SER* 3.8 21.3 - - - +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 1.3 77.3 - - - +
386B PRO* 1.4 66.8 - - + +
389B LYS* 3.1 12.2 + - - +
421B ASP 3.3 23.2 + - - -
443B TYR* 3.4 29.9 + - + +
446B GLN* 3.4 35.7 + - - -
447B SER* 4.2 14.3 + - - +
450B GLN* 3.1 42.6 + - + +
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Residues in contact with PRO 386 (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 ASN* 3.5 36.8 - - + +
382B MSE 4.1 11.7 - - + -
383B LYS* 3.5 19.1 - - + +
385B LYS* 1.4 93.4 - - + +
387B PHE* 1.3 59.0 + - - +
389B LYS* 4.2 9.9 - - + -
390B GLU* 2.8 42.9 + - - +
443B TYR* 4.1 5.4 - - - +
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 3.5 25.1 - - + -
343B HIS* 3.7 13.9 - - - -
344B GLY* 3.9 13.2 - - - -
370B TYR* 3.3 39.0 - + - -
382B MSE 4.0 17.6 - - + +
383B LYS 3.2 20.9 + - - +
384B ASP* 3.5 16.4 - - - +
386B PRO* 1.3 79.2 - - - +
388B PHE* 1.3 84.8 + + - +
391B SER* 2.6 38.3 + - - -
406B PHE* 4.1 9.2 - + + -
407B ILE 4.3 15.3 - - - -
408B THR* 4.8 2.2 - - - -
409B LEU* 6.4 0.7 - - + -
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Residues in contact with PHE 388 (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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250B VAL* 4.0 13.5 - - + -
384B ASP* 2.9 29.1 + - + +
387B PHE* 1.3 83.3 - + - +
389B LYS* 1.3 66.5 + - - +
391B SER* 3.2 11.1 + - - -
392B MSE 3.4 20.1 + - - +
406B PHE* 3.8 22.4 - + + -
408B THR* 4.0 28.9 - - + -
444B LEU* 5.4 0.4 - - + -
447B SER* 3.8 30.7 - - - -
448B ILE* 4.8 5.8 - - + -
450B GLN* 3.7 15.0 - - - +
451B PHE* 3.3 53.2 - + + -
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Residues in contact with LYS 389 (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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385B LYS 3.1 17.8 + - - +
386B PRO* 3.8 9.9 - - + +
388B PHE* 1.3 76.5 - - - +
390B GLU* 1.3 65.7 + - + +
392B MSE 3.4 23.3 + - + +
393B PRO* 3.8 4.2 - - - +
450B GLN* 3.5 17.6 - - - +
454B ASP* 4.8 4.9 - - - +
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Residues in contact with GLU 390 (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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369B TYR 4.7 2.9 - - - +
370B TYR* 3.4 26.1 - - + +
371B ASP* 3.2 36.5 + - - +
376B ASN* 4.8 3.8 - - - +
382B MSE 3.6 11.6 - - - +
386B PRO* 2.8 26.3 + - - +
389B LYS* 1.3 80.4 - - + +
391B SER* 1.3 62.7 + - - +
392B MSE 3.3 0.4 + - - -
393B PRO* 3.5 11.4 - - - +
394B LEU* 4.0 13.5 - - - +
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Residues in contact with SER 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 4.1 2.9 - - - -
370B TYR* 2.9 25.9 + - - -
387B PHE* 2.6 30.5 + - - -
388B PHE* 3.2 7.6 + - - -
390B GLU* 1.3 76.7 - - - +
392B MSE 1.3 55.3 + - - +
394B LEU* 3.1 10.7 + - - +
395B LEU* 2.8 35.1 + - - +
406B PHE* 3.7 26.5 - - - -
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Residues in contact with MSE 392 (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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388B PHE 3.4 20.2 - - - +
389B LYS* 3.5 8.5 - - - +
391B SER* 1.3 77.3 - - - +
393B PRO* 1.4 67.0 - - + +
395B LEU* 3.1 9.4 + - + -
396B GLU* 2.7 65.2 + - - +
451B PHE* 3.8 25.6 - - - -
454B ASP* 3.7 37.7 - - + +
455B LEU* 3.6 27.8 - - + -
458B ASP* 3.9 8.5 - - - +
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Residues in contact with PRO 393 (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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389B LYS 3.8 6.1 - - - +
390B GLU* 3.5 15.3 - - - +
392B MSE 1.4 93.3 - - + +
394B LEU* 1.3 64.0 + - + +
396B GLU* 3.5 10.5 + - + +
397B SER* 3.1 26.7 + - - -
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Residues in contact with LEU 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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342B PHE* 3.8 12.1 - - + -
365B PHE* 4.0 34.7 - - + -
369B TYR* 4.0 35.7 - - + +
370B TYR* 4.5 13.0 - - + +
390B GLU 4.0 17.0 - - - +
391B SER* 3.1 6.2 + - - +
393B PRO* 1.3 79.6 - - + +
395B LEU* 1.3 60.8 + - - +
397B SER* 2.8 20.3 + - - +
398B LEU* 3.4 17.3 - - - +
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Residues in contact with LEU 395 (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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248B ILE* 4.3 8.7 - - + -
342B PHE* 4.1 9.8 - - + -
391B SER 2.8 19.2 + - - +
392B MSE 3.1 12.3 + - + +
394B LEU* 1.3 69.4 - - - +
396B GLU* 1.3 66.3 + - - +
397B SER 3.1 2.6 + - - -
398B LEU* 3.2 23.0 + - + +
402B PHE* 3.7 26.5 - - + -
404B THR* 3.8 24.5 - - + +
406B PHE* 3.8 24.7 - - + -
451B PHE* 4.5 0.9 - - + -
455B LEU* 3.7 29.8 - - + -
460B LEU* 4.2 13.9 - - + +
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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
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392B MSE 2.7 51.1 + - - +
393B PRO* 3.9 9.5 - - + +
395B LEU* 1.3 72.4 - - - +
397B SER* 1.3 56.7 + - - +
398B LEU 3.3 8.6 + - - +
400B GLN* 5.7 2.4 + - - -
458B ASP* 2.9 47.9 - - + +
460B LEU* 3.6 17.8 - - + +
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Residues in contact with SER 397 (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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365B PHE* 5.7 1.2 - - - -
393B PRO 3.1 13.5 + - - -
394B LEU* 2.8 24.0 + - - +
395B LEU 3.1 0.2 - - - -
396B GLU* 1.3 75.2 - - - +
398B LEU* 1.3 63.3 + - - +
399B PRO* 3.7 7.3 - - - +
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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