Contacts of the helix formed by residues 330 - 341 (chain B) in PDB entry 1EQR
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 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B LEU* 1.3 73.0 - - - +
331B ARG* 1.3 59.3 + - + +
332B LYS* 3.0 28.3 - - + +
333B GLN* 2.9 31.4 + - + +
334B ILE* 2.5 41.9 + - - +
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Residues in contact with ARG 331 (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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329B LEU 4.0 1.0 + - - -
330B THR* 1.3 74.2 - - + +
332B LYS* 1.3 54.8 + - - +
334B ILE* 3.2 10.2 + - - +
335B ASP* 2.5 59.6 + - - +
353B LYS* 6.0 0.4 - - - +
116C ASN 5.3 1.4 + - - -
117C THR* 4.5 8.7 - - - +
118C GLU* 2.9 65.5 + - - +
121C ARG* 5.3 3.2 - - - +
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Residues in contact with LYS 332 (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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330B THR* 3.0 15.8 - - + +
331B ARG* 1.3 81.7 - - - +
333B GLN* 1.3 73.5 + - + +
335B ASP* 2.9 21.7 + - - +
336B GLU* 3.0 45.5 + - + +
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Residues in contact with GLN 333 (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 SER 4.7 2.4 - - - +
329B LEU* 3.3 27.7 - - + +
330B THR* 2.9 37.6 + - - +
332B LYS* 1.3 86.5 - - + +
334B ILE* 1.3 63.5 + - - +
335B ASP 3.0 5.8 + - - -
336B GLU* 3.2 22.4 + - - +
337B TYR* 3.3 25.5 + - + -
417B LEU* 5.7 4.2 - - - +
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Residues in contact with ILE 334 (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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329B LEU* 3.6 34.5 - - + +
330B THR 2.5 34.5 + - - +
331B ARG* 3.5 9.6 - - - +
333B GLN* 1.3 72.0 - - - +
335B ASP* 1.3 58.0 + - - +
337B TYR* 4.4 7.5 - - - +
338B GLY* 3.3 18.9 + - - -
349B LEU* 5.0 4.6 - - + +
351B TYR* 3.8 33.2 - - + +
353B LYS* 4.2 9.2 - - - +
391B MET* 3.4 26.2 - - + -
393B PHE* 4.0 13.2 - - + -
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Residues in contact with ASP 335 (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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331B ARG* 2.5 50.1 + - - +
332B LYS* 2.9 9.8 + - - +
334B ILE* 1.3 81.2 - - - +
336B GLU* 1.3 58.7 + - - +
337B TYR 3.3 0.2 - - - -
338B GLY* 3.1 2.6 + - - +
339B ASN* 2.7 39.0 + - - +
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Residues in contact with GLU 336 (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 LYS* 3.0 52.1 + - + +
333B GLN* 3.2 13.0 + - - +
335B ASP* 1.3 75.2 - - - +
337B TYR* 1.3 59.6 + - + +
339B ASN* 2.7 16.5 + - - +
340B PHE* 2.6 35.4 + - - +
412B LYS* 5.9 6.0 - - - -
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Residues in contact with TYR 337 (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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329B LEU* 4.1 23.7 - - + +
333B GLN* 3.3 23.8 + - + +
334B ILE 4.4 2.2 - - - +
336B GLU* 1.3 85.8 - - + +
338B GLY* 1.3 64.9 + - - +
340B PHE* 3.9 4.9 - - + -
341B VAL* 3.0 28.8 + - - +
349B LEU* 3.8 18.2 - - + -
393B PHE* 4.2 19.5 - + + -
409B LEU* 3.8 16.8 - - + -
412B LYS* 4.1 22.4 - - + -
413B VAL* 3.7 26.6 - - + +
416B ASP* 2.5 43.0 + - - +
417B LEU* 4.7 5.3 - - + +
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Residues in contact with GLY 338 (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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334B ILE 3.3 14.2 + - - -
335B ASP* 3.1 8.4 + - - -
336B GLU 3.1 1.2 - - - -
337B TYR* 1.3 80.1 - - - +
339B ASN* 1.3 57.5 + - - +
341B VAL* 3.1 11.3 - - - +
342B LYS* 2.9 30.8 + - - +
349B LEU* 3.9 17.9 - - - +
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Residues in contact with ASN 339 (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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335B ASP* 2.7 29.8 + - - +
336B GLU* 2.7 11.3 + - - +
338B GLY* 1.3 75.8 - - - +
340B PHE* 1.3 56.4 + - - +
342B LYS* 2.5 45.1 + - - +
343B ILE* 3.6 4.3 + - - +
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Residues in contact with PHE 340 (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 GLU 2.6 18.6 + - - +
337B TYR* 3.6 9.0 - - - +
339B ASN* 1.3 71.9 - - - +
341B VAL* 1.3 67.9 + - + +
343B ILE* 3.1 40.8 + - + +
344B TYR* 3.6 35.2 - + - -
405B ALA 4.8 0.7 - - - -
408B ALA* 3.7 36.6 - - + -
409B LEU* 3.7 15.9 - - + -
412B LYS* 3.7 43.5 - - + -
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Residues in contact with VAL 341 (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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337B TYR 3.0 9.3 + - - +
338B GLY 3.1 21.1 - - - +
339B ASN 2.9 0.2 + - - -
340B PHE* 1.3 77.4 - - + +
342B LYS* 1.3 62.7 + - + +
343B ILE 3.1 0.2 - - - -
344B TYR* 3.2 16.5 + - - +
345B GLY 3.5 0.2 + - - -
346B ALA* 3.0 40.4 + - + +
348B GLY 3.7 14.6 - - - +
349B LEU* 4.0 12.3 - - + -
405B ALA* 4.1 13.4 - - + +
406B MET* 5.0 0.7 - - - -
409B LEU* 3.5 41.5 - - + -
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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