Contacts of the helix formed by residues 320 - 331 (chain B) in PDB entry 5E9W
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 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B THR 3.5 1.4 + - - -
319B PRO* 1.3 69.6 - - - +
321B SER* 1.3 66.5 + - - +
322B PHE* 3.1 25.7 + - - +
323B GLU* 3.2 23.3 + - + +
324B LEU* 3.0 23.2 + - - +
326B ARG* 5.8 1.0 - - - +
375B PHE* 6.1 0.2 - - - +
392B LYS* 5.2 4.5 + - - +
394B THR* 3.8 25.5 - - - +
465B SER 5.4 1.2 + - - -
466B ILE 2.7 18.4 + - - +
467B TYR 4.3 1.8 - - - +
468B LEU* 3.8 32.9 - - + +
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Residues in contact with SER 321 (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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319B PRO 3.5 5.1 + - - -
320B ASN* 1.3 71.3 + - - +
322B PHE* 1.3 65.8 + - - +
324B LEU* 3.2 3.5 + - - +
325B ILE* 2.8 37.7 + - - +
372B LEU* 3.6 36.3 - - - -
373B VAL 3.4 24.3 + - - +
374B TYR* 3.8 22.2 - - - -
375B PHE* 4.2 1.6 + - - +
468B LEU* 5.2 0.6 - - - +
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Residues in contact with PHE 322 (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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320B ASN* 3.1 16.7 + - - +
321B SER* 1.3 85.1 + - - +
323B GLU* 1.3 62.0 + - - +
325B ILE* 4.0 5.7 - - + +
326B ARG* 3.0 42.2 + - - +
374B TYR* 3.6 37.7 - + - -
375B PHE* 5.2 4.9 - - + -
376B PRO* 4.3 16.8 - - + -
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Residues in contact with GLU 323 (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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320B ASN* 3.2 27.8 + - + +
322B PHE* 1.3 77.6 - - - +
324B LEU* 1.3 62.7 + - - +
326B ARG* 3.4 25.8 + - - +
327B ARG* 2.5 80.1 + - - +
465B SER* 3.8 15.3 - - - +
466B ILE* 4.2 7.4 - - + +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PRO* 3.8 16.2 - - + +
320B ASN 3.0 14.1 + - - +
321B SER* 3.5 8.1 - - - +
323B GLU* 1.3 78.3 - - - +
325B ILE* 1.3 63.3 + - - +
327B ARG* 3.4 1.1 + - - -
328B LEU* 3.1 23.9 + - - +
336B PHE* 3.7 27.9 - - + -
343B VAL* 4.5 17.5 - - + -
345B PHE* 4.5 6.5 - - + -
358B TYR* 3.5 33.7 - - + +
360B PHE* 6.3 0.2 - - + -
372B LEU* 3.8 23.1 - - + -
466B ILE* 4.2 23.8 - - + +
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Residues in contact with ILE 325 (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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321B SER* 2.8 28.1 + - - +
322B PHE* 4.1 5.2 - - - +
324B LEU* 1.3 74.1 - - - +
326B ARG* 1.3 64.2 + - - +
328B LEU* 3.3 4.3 + - + +
329B GLU* 3.0 46.1 + - - +
345B PHE* 4.5 8.5 - - + -
351B TYR* 3.7 40.6 - - + +
372B LEU* 3.8 27.4 - - + -
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Residues in contact with ARG 326 (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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320B ASN* 5.8 1.2 - - - +
322B PHE* 3.0 42.6 + - - +
323B GLU* 3.7 25.2 + - - +
324B LEU 3.3 0.2 - - - -
325B ILE* 1.3 79.2 - - - +
327B ARG* 1.3 61.6 + - + +
329B GLU* 4.0 6.2 - - - +
330B ALA* 3.1 27.7 + - + +
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Residues in contact with ARG 327 (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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323B GLU* 2.5 54.7 + - - +
324B LEU* 5.3 0.2 - - - +
325B ILE 3.3 0.2 - - - -
326B ARG* 1.3 76.9 - - + +
328B LEU* 1.3 66.3 + - - +
330B ALA* 3.4 6.4 + - - +
331B SER* 3.2 22.5 + - - -
336B PHE* 3.6 31.2 - - + +
341B TYR* 2.8 35.9 + - - -
451B LEU* 6.1 0.2 - - - +
462B GLU* 2.8 25.9 + - - +
465B SER* 2.9 29.3 + - - -
466B ILE* 3.3 13.4 - - - +
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Residues in contact with LEU 328 (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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324B LEU 3.1 17.3 + - - +
325B ILE* 3.6 5.8 - - + +
327B ARG* 1.3 75.9 - - - +
329B GLU* 1.3 58.1 + - - +
331B SER* 3.1 15.2 + - - -
334B GLU* 3.4 33.4 - - - +
336B PHE* 3.5 13.1 - - + -
345B PHE* 3.7 36.1 - - + -
348B LYS* 2.9 47.6 + - + -
351B TYR* 3.6 33.7 - - + +
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Residues in contact with GLU 329 (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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325B ILE* 3.0 32.4 + - - +
326B ARG* 4.2 4.5 - - - +
328B LEU* 1.3 79.0 - - + +
330B ALA* 1.3 60.7 + - - +
331B SER 3.2 4.6 + - - +
348B LYS* 4.1 13.2 + - + +
349B GLY* 5.2 2.8 + - - -
351B TYR* 3.6 26.7 + - - +
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Residues in contact with ALA 330 (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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326B ARG* 3.1 20.3 + - + +
327B ARG* 3.9 7.2 - - - +
328B LEU 3.2 0.4 - - - -
329B GLU* 1.3 77.3 - - - +
331B SER* 1.3 62.3 + - - +
332B GLU* 3.9 5.7 + - - +
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ARG 3.2 11.3 + - - -
328B LEU* 3.1 14.4 + - - -
329B GLU 3.9 3.6 - - - +
330B ALA* 1.3 82.4 - - - +
332B GLU* 1.3 63.1 + - - +
333B THR* 2.9 16.5 + - - -
335B SER 2.7 28.8 + - - -
336B PHE* 4.3 5.6 - - - -
348B LYS* 3.2 17.8 + - - -
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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