Contacts of the helix formed by residues 379 - 397 (chain B) in PDB entry 5UO5
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 SER 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B ARG* 2.7 45.2 + - - +
377B PHE 3.2 1.0 + - - -
378B GLY* 1.3 82.1 - - - +
380B LYS* 1.3 60.7 + - - +
381B ALA* 3.4 8.5 + - - +
382B HIS* 3.0 17.6 + - - +
383B MET* 2.9 30.2 + - - +
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Residues in contact with LYS 380 (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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379B SER* 1.3 74.8 - - - +
381B ALA* 1.3 62.0 + - - +
383B MET* 3.5 9.0 + - - +
384B GLU* 3.0 56.1 + - - +
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Residues in contact with ALA 381 (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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371B TYR* 3.4 22.5 + - + +
376B ARG* 5.9 2.0 - - + -
379B SER* 3.2 6.3 + - - +
380B LYS* 1.3 79.7 - - - +
382B HIS* 1.3 57.7 + - - +
384B GLU* 3.6 7.5 + - - +
385B ARG* 3.0 30.0 + - - +
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Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ILE* 3.9 8.0 - - + +
368B ASP* 2.7 38.5 + - - -
371B TYR* 3.7 31.6 - + + -
376B ARG 3.6 7.0 - - - +
377B PHE* 3.7 24.3 - + - -
378B GLY* 2.8 25.5 + - - -
379B SER* 3.0 22.9 + - - +
380B LYS 3.2 0.2 - - - -
381B ALA* 1.3 75.3 - - - +
383B MET* 1.3 66.5 + - + +
385B ARG* 3.1 2.8 + - - +
386B LEU* 3.1 32.6 + - + +
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Residues in contact with MET 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLY* 4.5 15.9 - - - +
379B SER 2.9 20.9 + - - +
380B LYS* 3.8 7.4 - - - +
382B HIS* 1.3 76.9 - - - +
384B GLU* 1.3 61.7 + - - +
386B LEU* 3.2 12.2 + - + +
387B GLU* 3.2 21.2 + - - +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LYS* 3.0 48.3 + - - +
381B ALA* 4.0 6.6 - - - +
383B MET* 1.3 74.9 - - - +
385B ARG* 1.3 60.6 + - - +
387B GLU* 3.5 10.2 - - + +
388B GLU* 2.9 30.6 + - - +
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Residues in contact with ARG 385 (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 ILE* 3.9 20.5 - - + +
371B TYR* 3.8 17.7 - - + +
381B ALA 3.0 19.3 + - - +
382B HIS 3.1 4.5 + - - +
384B GLU* 1.3 76.7 - - - +
386B LEU* 1.3 65.1 + - - +
388B GLU* 3.0 34.2 + - - +
389B VAL* 3.0 52.3 + - - +
392B GLU* 4.7 5.3 + - - -
399B TYR* 4.3 3.8 - - - -
400B GLN 3.1 25.1 + - - -
401B LEU* 3.9 0.6 - - - +
402B LYS* 3.4 24.1 - - - +
405B GLU* 2.6 42.9 + - - +
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Residues in contact with LEU 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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360B PHE* 4.0 14.9 - - + -
364B LYS* 3.9 39.5 - - + -
367B ILE* 4.0 24.0 - - + -
368B ASP* 3.8 8.5 - - - +
382B HIS* 3.1 36.6 + - + +
383B MET* 3.2 10.7 + - - +
385B ARG* 1.3 77.7 - - - +
387B GLU* 1.3 64.5 + - - +
389B VAL* 3.3 5.9 + - + +
390B ASN* 3.2 21.2 + - - +
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Residues in contact with GLU 387 (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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383B MET 3.2 9.4 + - - +
384B GLU* 3.5 15.3 - - + +
386B LEU* 1.3 77.9 - - - +
388B GLU* 1.3 65.8 + - - +
390B ASN* 3.1 12.6 + - - -
391B LYS* 3.1 54.0 + - + +
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Residues in contact with GLU 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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384B GLU 2.9 20.0 + - - +
385B ARG* 3.0 36.2 + - - +
387B GLU* 1.3 74.0 - - - +
389B VAL* 1.3 62.4 + - - +
391B LYS* 3.4 7.8 + - - +
392B GLU* 3.2 27.2 + - - +
402B LYS* 3.5 23.7 + - - -
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PHE* 4.5 5.6 - - + -
363B ALA* 3.9 19.3 - - + -
367B ILE* 4.4 12.3 - - + -
385B ARG* 3.0 57.1 + - + +
386B LEU* 3.7 6.5 - - + +
388B GLU* 1.3 75.4 - - - +
390B ASN* 1.3 58.0 + - - +
392B GLU* 3.3 9.6 + - - +
393B ILE* 3.0 45.8 + - + +
399B TYR* 3.9 17.5 - - + -
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Residues in contact with ASN 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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360B PHE* 3.2 52.0 - - + +
386B LEU 3.2 7.2 + - - +
387B GLU* 3.1 10.1 + - - +
389B VAL* 1.3 75.0 - - - +
391B LYS* 1.3 70.8 + - - +
393B ILE* 3.4 4.3 + - - +
394B ASP* 3.0 39.2 + - - +
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Residues in contact with LYS 391 (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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387B GLU* 3.1 69.2 + - + +
388B GLU* 3.8 7.6 - - - +
390B ASN* 1.3 93.2 + - - +
392B GLU* 1.3 52.9 + - - +
394B ASP* 3.8 5.1 - - - +
395B THR* 2.5 45.0 + - + +
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Residues in contact with GLU 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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385B ARG* 4.7 9.0 + - - -
388B GLU* 3.2 19.9 + - + +
389B VAL* 3.6 6.0 - - - +
390B ASN 3.2 0.6 - - - -
391B LYS* 1.3 79.1 - - - +
393B ILE* 1.3 59.3 + - - +
395B THR* 3.6 4.7 + - - -
396B THR* 2.5 45.8 + - + +
398B THR 2.8 8.7 - - - +
399B TYR* 3.2 17.0 - - + +
400B GLN* 2.9 39.1 + - - +
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Residues in contact with ILE 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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356B LYS* 3.6 38.2 - - + +
359B LEU* 4.0 24.0 - - + -
360B PHE* 3.9 33.4 - - + -
363B ALA* 4.2 1.3 - - + -
389B VAL* 3.0 32.8 + - + +
390B ASN* 3.9 3.8 - - - +
391B LYS 3.3 0.2 - - - -
392B GLU* 1.3 77.4 - - - +
394B ASP* 1.3 61.7 + - - +
397B SER* 2.8 27.7 + - - -
398B THR 3.3 14.1 - - - +
399B TYR* 4.0 10.3 - - + -
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Residues in contact with ASP 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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356B LYS* 2.9 36.2 + - - +
390B ASN* 3.0 28.8 + - - +
391B LYS* 3.8 7.6 - - - +
393B ILE* 1.3 79.7 - - - +
395B THR* 1.3 61.3 + - + +
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Residues in contact with THR 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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356B LYS* 5.4 0.7 - - - -
391B LYS* 2.5 28.1 + - + +
392B GLU* 3.6 5.9 + - - -
394B ASP* 1.3 81.8 - - + +
396B THR* 1.3 70.7 + - - +
397B SER 3.9 0.2 - - - -
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Residues in contact with THR 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 GLU* 2.5 28.3 + - + +
395B THR* 1.3 92.1 - - - +
397B SER* 1.3 67.4 + - - +
398B THR* 2.9 30.6 + - - +
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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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355B THR* 5.1 1.8 - - - -
356B LYS* 3.1 36.5 + - - +
359B LEU* 3.6 13.8 - - - +
393B ILE* 2.8 25.0 + - - -
395B THR 3.9 0.2 - - - -
396B THR* 1.3 72.6 - - - +
398B THR* 1.3 59.3 - - - +
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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