Contacts of the helix formed by residues 329 - 340 (chain B) in PDB entry 4M83
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 ASP 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B PHE* 5.2 4.5 - - - -
327B ALA* 3.0 6.3 + - - +
328B VAL* 1.3 93.7 + - - +
330B GLN* 1.3 67.7 + - - +
331B PHE 3.4 2.5 - - - -
332B GLY* 3.8 4.1 + - - -
333B ASN* 3.5 26.3 + - - +
501B ERY 4.2 29.2 - - + +
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Residues in contact with GLN 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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242B PHE* 3.9 15.9 - - - -
305B HIS* 2.8 59.3 + - - +
306B ALA* 3.1 19.1 - - - +
307B GLY* 3.1 9.4 - - - -
325B PRO* 3.5 11.6 - - + +
326B GLN 4.3 1.6 - - - +
327B ALA* 3.1 28.0 + - - +
329B ASP* 1.3 83.3 + - - +
331B PHE* 1.3 60.4 + - - +
333B ASN* 3.9 2.9 - - - +
334B ALA* 2.9 29.3 + - - +
502B UDP 3.8 6.1 + - - -
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Residues in contact with PHE 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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325B PRO* 3.5 39.3 - - + -
326B GLN 3.6 10.8 - - - -
327B ALA 2.9 31.9 - - - -
328B VAL* 3.3 32.8 - - + -
330B GLN* 1.3 76.3 - - - +
332B GLY* 1.3 60.0 + - - +
334B ALA* 3.1 3.9 + - - +
335B ASP* 2.6 35.7 + - - +
345B LYS* 4.4 7.9 - - - +
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Residues in contact with GLY 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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171A GLU 4.8 0.9 - - - +
328B VAL 5.2 1.0 + - - -
329B ASP 3.8 7.3 + - - -
330B GLN 3.3 0.4 - - - -
331B PHE* 1.3 79.0 - - - +
333B ASN* 1.3 63.0 + - - +
335B ASP* 3.1 10.8 + - - +
336B MET* 3.0 24.6 + - - +
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Residues in contact with ASN 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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196B LEU* 4.8 4.1 - - + +
306B ALA* 3.2 30.6 + - - +
307B GLY* 4.0 1.0 - - - -
308B ALA* 3.8 23.4 - - - +
311B SER* 3.9 9.9 - - - +
329B ASP* 3.5 21.2 + - - +
330B GLN* 3.5 4.4 + - - +
331B PHE 3.3 0.4 - - - -
332B GLY* 1.3 76.4 - - - +
334B ALA* 1.3 62.4 + - - +
336B MET* 3.2 10.4 + - - +
337B LEU* 3.0 26.0 + - - +
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Residues in contact with ALA 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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306B ALA* 4.0 4.2 - - + +
323B ALA* 3.6 29.9 - - + +
325B PRO* 4.0 9.0 - - + -
330B GLN 2.9 15.6 + - - +
331B PHE 3.1 8.9 + - - +
333B ASN* 1.3 76.0 - - - +
335B ASP* 1.3 58.2 + - - +
337B LEU* 3.3 4.6 + - - +
338B GLN* 2.9 29.8 + - - +
345B LYS* 3.7 22.6 - - + +
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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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122A ARG* 5.2 13.3 + - - +
170A LYS 3.3 2.4 - - - +
171A GLU 3.3 19.7 - - - +
172A ASN* 3.0 21.6 - - - +
173A GLY* 3.2 15.8 + - - +
331B PHE* 2.6 33.8 + - - +
332B GLY* 3.1 8.9 + - - +
334B ALA* 1.3 75.9 - - - +
336B MET* 1.3 59.1 + - - +
338B GLN* 4.6 2.9 + - - -
339B GLY 2.8 26.5 + - - -
345B LYS* 4.8 12.0 + - - +
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Residues in contact with MET 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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170A LYS* 4.4 3.9 - - + +
171A GLU* 3.8 28.0 - - - +
195B ALA 3.6 12.6 - - - +
196B LEU* 3.4 49.6 - - + +
197B GLN 3.7 3.8 - - - +
198B PRO* 3.6 30.7 - - + -
332B GLY 3.0 16.6 + - - +
333B ASN* 3.2 11.0 + - - +
335B ASP* 1.3 75.8 - - - +
337B LEU* 1.3 64.5 + - - +
339B GLY* 3.3 1.0 + - - -
340B LEU* 3.0 29.7 + - + +
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Residues in contact with LEU 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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196B LEU* 4.0 10.8 - - + -
304B THR* 4.8 1.1 - - + -
306B ALA* 4.1 14.1 - - + -
311B SER* 3.8 22.9 - - - +
315B LEU* 3.7 32.8 - - + -
321B MET* 3.8 36.1 - - + -
323B ALA* 4.6 9.4 - - + -
333B ASN 3.0 16.7 + - - +
334B ALA* 3.6 6.5 - - - +
336B MET* 1.3 76.6 - - - +
338B GLN* 1.3 62.5 + - - +
340B LEU* 3.3 17.8 + - + +
342B VAL* 3.5 15.6 + - + +
343B ALA* 3.7 13.8 + - + -
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Residues in contact with GLN 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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172A ASN 5.2 0.2 + - - -
173A GLY* 2.8 29.9 + - - +
175A THR* 3.1 18.0 - - + +
334B ALA 2.9 17.3 + - - +
335B ASP* 4.0 4.0 + - - +
337B LEU* 1.3 75.4 - - - +
339B GLY* 1.3 58.5 + - - +
341B GLY* 2.9 18.5 + - - -
343B ALA* 3.5 21.2 - - - +
344B ARG* 3.0 25.4 + - - +
345B LYS* 2.9 37.8 + - + +
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Residues in contact with GLY 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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170A LYS* 3.0 57.1 - - - +
173A GLY* 3.6 9.8 - - - -
175A THR* 3.9 11.1 - - - +
335B ASP 2.8 11.3 + - - -
336B MET 3.7 1.1 - - - -
338B GLN* 1.3 77.8 - - - +
340B LEU* 1.3 58.3 + - - +
341B GLY 3.1 1.1 + - - -
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Residues in contact with LEU 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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170A LYS* 4.1 20.6 + - - +
195B ALA* 3.7 41.7 - - + +
196B LEU* 4.5 1.8 - - + -
315B LEU* 4.3 14.8 - - + -
336B MET* 3.0 20.9 + - + +
337B LEU* 3.5 15.0 - - - +
338B GLN 3.1 0.4 - - - -
339B GLY* 1.3 76.6 - - - +
341B GLY* 1.3 59.0 + - - +
342B VAL* 3.6 14.4 + - + +
372B ARG* 3.2 24.7 + - - -
375B ARG* 4.4 10.1 + - - +
376B ILE* 4.1 21.6 - - + +
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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