Contacts of the helix formed by residues 330 - 340 (chain A) in PDB entry 2AZE
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 LEU 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LEU* 5.1 0.2 - - + -
227A ILE* 4.2 17.4 - - + +
230A GLN* 3.9 17.9 - - - +
326A VAL* 3.6 15.0 - - + -
327A PRO* 2.8 39.6 + - + +
329A ALA* 1.3 77.5 - - + +
331A GLU* 1.3 64.2 + - - +
332A PRO* 3.4 2.0 - - - -
333A TYR* 3.3 10.2 + - + +
334A VAL* 3.0 21.7 + - - +
223B LEU* 3.8 45.5 - - + +
226B ILE* 4.0 15.7 - - + -
227B CYS* 4.3 9.9 - - + -
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ARG* 2.7 52.5 + - + +
326A VAL* 3.2 15.7 - - - +
327A PRO 3.6 2.8 + - - -
328A LYS* 3.1 36.3 + - + +
330A LEU* 1.3 77.2 - - - +
332A PRO* 1.4 66.2 - - + +
334A VAL* 3.1 7.4 + - - +
335A THR* 3.0 25.6 + - - +
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Residues in contact with PRO 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A LYS 3.7 4.5 - - - +
329A ALA 3.6 16.2 - - - +
330A LEU 3.6 1.1 - - - -
331A GLU* 1.4 94.4 - - + +
333A TYR* 1.3 56.1 + - - +
335A THR* 3.2 11.0 + - - +
336A GLU* 3.0 34.2 + - - +
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Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLN* 3.4 37.1 + - - +
223A LEU* 3.5 30.3 - - + -
224A GLN* 3.6 23.8 - - + -
227A ILE* 3.7 22.7 - - + -
329A ALA 5.7 0.2 - - - +
330A LEU* 3.3 11.6 + - + +
331A GLU 3.2 0.4 - - - -
332A PRO* 1.3 76.7 - - - +
334A VAL* 1.3 60.3 + - - +
336A GLU* 3.0 14.8 + - + +
337A MET* 2.8 34.8 + - - +
342A VAL* 3.7 21.5 - - + +
346A PHE* 4.1 27.6 - + - -
220B LEU* 4.6 0.7 - - + -
223B LEU* 4.3 16.2 - - + -
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 3.9 24.2 - - + -
231A ILE* 4.6 3.6 - - + -
309A LEU* 3.9 15.3 - - + +
319A LEU* 4.3 12.8 - - + -
322A ALA* 4.5 8.1 - - + +
323A ARG* 4.3 21.3 - - + +
326A VAL* 3.8 24.0 - - + -
330A LEU 3.0 18.6 + - - +
331A GLU* 3.1 9.4 + - - +
333A TYR* 1.3 74.1 - - - +
335A THR* 1.3 57.7 + - - +
337A MET* 3.1 11.8 + - - +
338A ALA* 2.9 26.9 + - - +
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 5.5 0.2 - - - -
323A ARG* 2.7 34.2 + - - +
331A GLU* 3.0 13.1 + - - +
332A PRO* 3.3 14.4 - - - +
334A VAL* 1.3 74.3 - - - +
336A GLU* 1.3 65.3 + - - +
338A ALA* 3.3 13.4 + - - +
339A GLN* 3.1 41.9 + - + +
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A PRO* 3.0 22.4 + - - +
333A TYR* 3.1 20.9 - - + +
335A THR* 1.3 78.1 - - - +
337A MET* 1.3 61.7 + - - +
339A GLN* 3.1 14.5 + - - +
340A GLY* 3.2 11.3 + - - -
341A THR* 3.0 48.4 + - - +
342A VAL* 4.0 15.9 - - + +
346A PHE* 6.4 1.6 - - + -
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Residues in contact with MET 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLN* 3.6 53.6 - - + +
227A ILE* 4.0 21.5 - - + -
228A LEU* 3.6 22.9 - - + -
309A LEU* 3.7 31.7 - - + +
312A GLY* 4.0 11.6 + - - -
333A TYR* 2.8 37.3 + - + +
334A VAL* 3.5 7.6 - - - +
336A GLU* 1.3 77.0 - - - +
338A ALA* 1.3 60.0 + - - +
339A GLN 3.5 0.5 + - - -
340A GLY* 3.5 8.8 + - - -
342A VAL* 4.3 8.2 - - + +
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU* 3.7 10.3 - - + +
312A GLY* 3.7 23.3 - - - +
314A CYS* 4.9 4.9 - - + -
319A LEU* 3.8 31.9 - - + -
334A VAL 2.9 13.5 + - - +
335A THR* 3.5 11.7 - - - +
336A GLU 3.2 0.6 - - - -
337A MET* 1.3 76.7 - - - +
339A GLN* 1.3 60.6 + - + +
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLY* 6.0 0.2 - - - -
335A THR* 3.1 34.8 - - + +
336A GLU* 3.1 6.5 + - - +
338A ALA* 1.3 78.5 - - + +
340A GLY* 1.3 56.3 + - - +
341A THR* 3.1 37.9 + - + +
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Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLY* 5.6 1.4 - - - -
336A GLU 3.2 5.7 + - - -
337A MET 3.5 7.2 + - - -
338A ALA 3.5 2.8 + - - -
339A GLN* 1.3 76.2 - - - +
341A THR* 1.3 55.3 + - - +
342A VAL* 2.8 25.6 + - - +
343A GLY 4.5 1.7 + - - -
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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