Contacts of the helix formed by residues 327 - 338 (chain B) in PDB entry 3AGZ
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 PRO 327 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A VAL 5.4 0.2 - - - +
339A PRO* 5.9 6.3 - - + -
325B ARG* 4.3 4.7 - - + +
326B ILE* 1.4 96.8 - - + +
328B GLN* 1.3 64.9 + - - +
329B THR* 3.4 5.4 - - - +
330B SER* 3.2 25.9 + - - +
331B ARG* 3.2 17.3 + - - +
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Residues in contact with GLN 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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326B ILE 4.7 0.4 - - - -
327B PRO* 1.3 73.2 - - - +
329B THR* 1.3 63.5 + - - +
331B ARG* 3.1 38.9 + - - +
332B THR* 3.0 26.4 + - - +
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Residues in contact with THR 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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337A VAL* 5.9 2.9 - - + -
327B PRO* 3.4 4.1 - - - +
328B GLN* 1.3 77.3 - - - +
330B SER* 1.3 67.0 + - - +
331B ARG 3.2 0.2 + - - -
332B THR* 3.5 5.8 + - - -
333B VAL* 3.2 36.7 + - + +
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Residues in contact with SER 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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337A VAL* 3.0 42.5 + - - +
326B ILE* 3.5 23.1 - - - -
327B PRO* 3.2 19.3 + - - +
328B GLN 3.4 0.4 - - - -
329B THR* 1.3 77.7 - - - +
331B ARG* 1.3 56.5 + - - +
333B VAL* 3.4 2.4 + - - +
334B LEU* 3.0 39.2 + - - +
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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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266A LEU 3.9 9.3 + - - +
267A CYS* 3.6 44.3 + - + +
268A GLY* 5.5 0.2 - - - -
286A LYS* 3.0 46.9 + - - +
287A ASP* 5.3 0.6 + - - +
326B ILE* 3.4 27.8 + - + +
327B PRO 3.2 8.8 + - - +
328B GLN* 3.1 30.9 + - - +
330B SER* 1.3 77.4 - - - +
332B THR* 1.3 56.4 + - - +
334B LEU* 3.4 6.5 + - - -
335B GLU* 3.1 32.5 + - - +
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Residues in contact with THR 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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328B GLN* 3.0 23.6 + - - +
329B THR* 4.0 7.0 + - - -
331B ARG* 1.3 72.4 - - - +
333B VAL* 1.3 66.6 - - - +
335B GLU* 3.3 15.3 + - + +
336B GLN* 3.2 21.0 + - - +
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Residues in contact with VAL 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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333A VAL* 4.0 22.0 - - + -
337A VAL* 4.0 35.4 - - + -
329B THR* 3.2 27.2 + - + +
330B SER 3.6 4.5 - - - +
332B THR* 1.3 75.4 - - - +
334B LEU* 1.3 62.0 + - - +
336B GLN* 3.2 10.7 + - - +
337B VAL* 2.9 39.3 + - + +
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Residues in contact with LEU 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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263A ARG* 4.0 1.6 - - - +
266A LEU* 4.4 19.3 - - + +
267A CYS* 4.0 15.0 - - - -
334A LEU* 3.8 27.1 - - + -
337A VAL* 4.4 14.8 - - + +
338A LEU* 4.4 18.6 - - + -
266B LEU* 6.0 0.7 - - + -
326B ILE* 4.4 18.4 - - + -
330B SER* 3.0 36.1 + - - +
331B ARG* 4.4 2.7 - - - +
332B THR 3.4 0.2 - - - -
333B VAL* 1.3 75.5 - - - +
335B GLU* 1.3 62.1 + - - +
337B VAL* 4.3 4.7 - - + -
338B LEU* 3.2 43.9 + - + +
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Residues in contact with GLU 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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263A ARG* 3.5 41.5 + - - +
267A CYS* 3.7 33.6 - - + +
331B ARG* 3.1 23.3 + - - +
332B THR* 3.4 15.7 - - + +
334B LEU* 1.3 78.7 - - - +
336B GLN* 1.3 59.5 + - - +
338B LEU 4.4 2.3 + - - +
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Residues in contact with GLN 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 THR 3.2 9.5 + - - +
333B VAL* 3.2 13.0 + - - +
335B GLU* 1.3 79.3 - - - +
337B VAL* 1.3 74.9 + - + +
338B LEU 5.3 0.7 - - - +
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Residues in contact with VAL 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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330A SER* 3.9 17.6 + - - +
333A VAL* 3.9 30.3 - - + -
334A LEU* 3.6 33.2 - - + -
333B VAL* 2.9 24.0 + - + +
334B LEU* 4.3 5.2 - - - -
336B GLN* 1.3 96.9 - - + +
338B LEU* 1.3 64.2 + - - +
339B PRO* 3.3 9.4 - - - +
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Residues in contact with LEU 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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262A LEU* 4.0 24.0 - - + +
263A ARG* 4.0 37.9 - - + +
266A LEU* 4.2 14.8 - - + -
267A CYS* 5.3 0.2 - - - -
323A PRO* 4.8 9.0 - - + -
326A ILE* 5.1 3.4 - - + -
334A LEU* 4.4 21.3 - - + -
266B LEU* 5.5 1.8 - - + -
334B LEU* 3.2 44.6 + - + +
335B GLU 4.4 1.7 + - - +
336B GLN 3.7 1.7 - - - +
337B VAL* 1.3 75.5 - - - +
339B PRO* 1.4 74.7 - - + +
340B ILE* 3.1 15.4 + - - +
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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