Contacts of the helix formed by residues 318 - 333 (chain A) in PDB entry 1AOX
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 GLU 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER 3.7 0.7 - - - +
156A ILE* 3.5 21.6 - - + +
157A TYR 2.8 46.8 + - - +
158A PRO* 4.3 2.7 - - + +
161A ALA* 3.4 25.3 - - + +
162A VAL* 4.7 6.3 - - + -
254A ASP* 4.5 2.6 - - - +
282A VAL* 3.8 15.9 - - + +
284A GLY* 3.5 10.3 - - - -
285A TYR 4.4 2.8 + - - -
288A ARG* 3.0 31.5 + - - -
317A ASP* 1.3 74.0 - - - +
319A ALA* 1.3 60.2 + - - +
321A LEU* 3.2 25.1 - - - +
322A LEU 4.7 0.2 + - - -
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Residues in contact with ALA 319 (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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158A PRO* 5.6 3.1 - - + +
161A ALA* 4.0 11.6 - - + +
317A ASP* 3.3 15.3 + - - +
318A GLU* 1.3 72.7 - - - +
320A ALA* 1.3 60.0 + - - +
321A LEU 3.1 6.3 + - - -
322A LEU* 3.8 16.1 + - - +
323A GLU* 5.0 1.0 + - - +
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Residues in contact with ALA 320 (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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315A VAL* 4.0 18.0 - - + +
316A SER* 3.9 16.2 - - - +
317A ASP* 3.1 25.5 + - - +
319A ALA* 1.3 76.9 - - - +
321A LEU* 1.3 59.9 + - - +
322A LEU 3.4 0.4 - - - -
323A GLU* 2.9 41.5 - - - +
324A LYS* 4.2 0.9 + - - +
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Residues in contact with LEU 321 (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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161A ALA 4.6 0.7 - - - +
162A VAL* 4.1 27.4 - - + -
165A PHE* 3.5 46.3 - - + -
252A VAL* 4.6 9.0 - - + -
280A ILE* 4.1 25.4 - - + -
282A VAL* 4.2 13.7 - - + -
315A VAL* 4.1 21.1 - - + -
317A ASP 3.7 1.4 + - - -
318A GLU* 3.2 21.9 + - - +
319A ALA 3.1 0.8 - - - -
320A ALA* 1.3 76.6 - - - +
322A LEU* 1.3 56.5 + - - +
324A LYS* 2.7 33.2 + - + +
325A ALA 3.4 3.8 + - - -
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 4.8 4.0 + - - +
164A ASN* 3.2 47.3 - - + +
165A PHE* 4.1 9.1 - - - +
168A LYS* 4.8 10.0 - - + +
318A GLU 4.7 0.4 + - - -
319A ALA 3.8 11.8 + - - +
320A ALA 3.4 0.2 - - - -
321A LEU* 1.3 79.4 - - - +
323A GLU* 1.3 60.8 + - - +
324A LYS 3.1 1.1 + - - -
325A ALA* 3.3 17.7 + - - +
326A GLY 4.5 1.2 + - - -
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Residues in contact with GLU 323 (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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315A VAL* 5.9 0.3 - - - +
319A ALA 5.1 0.9 - - - +
320A ALA* 2.9 37.7 - - - +
322A LEU* 1.3 75.0 - - - +
324A LYS* 1.3 76.3 + - - +
325A ALA 3.4 0.4 + - - -
326A GLY* 4.7 2.6 + - - -
327A THR* 3.9 10.6 + - - +
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Residues in contact with LYS 324 (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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165A PHE* 4.4 7.3 - - + -
280A ILE* 5.6 3.8 - - + -
313A PHE* 3.4 45.3 - - + +
314A ASN 5.0 10.1 + - - +
315A VAL* 4.3 20.9 - - + -
320A ALA 4.6 0.2 - - - +
321A LEU* 2.7 16.6 + - + +
323A GLU* 1.3 96.9 + - - +
325A ALA* 1.3 63.3 + - - +
326A GLY 3.4 1.8 - - - -
327A THR* 3.4 14.0 - - + +
328A LEU* 3.1 25.5 + - - +
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Residues in contact with ALA 325 (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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165A PHE* 3.8 26.5 - - + +
168A LYS* 3.8 13.4 - - + +
169A PHE* 3.7 36.1 - - - +
172A GLY* 6.2 0.3 - - - -
321A LEU 3.4 2.4 + - - -
322A LEU* 3.3 15.6 + - - +
324A LYS* 1.3 78.4 - - - +
326A GLY* 1.3 62.3 + - - +
328A LEU* 3.6 3.9 + - - +
329A GLY* 3.3 16.5 + - - -
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Residues in contact with GLY 326 (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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168A LYS 5.3 2.0 + - - -
172A GLY* 6.4 2.0 - - - -
322A LEU 4.5 2.0 + - - -
323A GLU 4.7 2.4 + - - -
324A LYS 3.4 0.2 - - - -
325A ALA* 1.3 75.9 - - - +
327A THR* 1.3 64.4 + - - +
328A LEU 3.1 2.0 - - - -
329A GLY* 3.2 3.2 + - - -
330A GLU* 3.1 25.1 + - - +
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Residues in contact with THR 327 (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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313A PHE* 3.9 20.3 - - + -
323A GLU 3.9 7.5 + - - +
324A LYS* 3.4 37.2 - - + +
326A GLY* 1.3 70.0 - - - +
328A LEU* 1.3 59.0 + - - +
330A GLU* 3.6 21.2 + - - +
331A GLN* 3.1 35.0 + - - +
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Residues in contact with LEU 328 (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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165A PHE* 4.0 12.3 - - + -
169A PHE* 3.7 22.9 - - + -
250A VAL* 3.9 17.5 - - + -
278A PHE* 3.4 39.7 - - + -
280A ILE* 3.8 27.4 - - + -
313A PHE* 3.9 17.9 - - + -
324A LYS 3.1 17.2 + - - +
325A ALA* 3.7 6.1 - - - +
326A GLY 3.1 0.8 - - - -
327A THR* 1.3 76.7 - - - +
329A GLY* 1.3 64.9 + - - +
331A GLN* 3.1 3.2 + - - +
332A ILE* 3.0 26.0 + - + +
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Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 4.1 7.3 - - - -
172A GLY* 4.8 9.2 - - - -
173A LEU* 4.1 20.6 - - - +
325A ALA 3.3 8.1 + - - -
326A GLY* 3.2 6.7 + - - -
328A LEU* 1.3 78.5 - - - +
330A GLU* 1.3 56.3 + - - +
332A ILE* 2.9 20.7 + - - +
333A PHE* 3.0 20.6 + - - -
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Residues in contact with GLU 330 (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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326A GLY 3.1 13.8 + - - +
327A THR* 3.6 27.3 + - - +
329A GLY* 1.3 74.2 - - - +
331A GLN* 1.3 64.6 + - + +
333A PHE* 3.4 17.6 - - + +
334A SER* 2.8 28.4 + - - -
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Residues in contact with GLN 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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278A PHE* 3.8 25.7 - - + -
310A ARG* 3.6 39.2 + - - +
313A PHE* 4.2 15.9 - - + -
327A THR* 3.1 28.1 + - - +
328A LEU* 3.1 7.6 + - - +
330A GLU* 1.3 80.2 - - - +
332A ILE* 1.3 66.0 + - - +
334A SER* 3.2 25.6 + - - -
335A ILE* 3.2 16.3 + - - -
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Residues in contact with ILE 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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144A ILE* 4.0 30.6 - - + +
146A VAL* 4.3 19.5 - - + -
169A PHE* 3.6 36.1 - - + -
173A LEU* 4.5 15.7 - - + -
180A THR* 5.5 1.8 - - + +
248A VAL* 4.4 9.4 - - + -
250A VAL* 4.6 5.2 - - + -
278A PHE* 4.3 20.9 - - + -
328A LEU* 3.0 11.7 + - + +
329A GLY* 2.9 9.1 + - - +
331A GLN* 1.3 76.7 - - - +
333A PHE* 1.3 57.6 + - + +
335A ILE* 2.6 39.4 - - - +
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Residues in contact with PHE 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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144A ILE* 6.5 0.4 - - + -
172A GLY 3.7 23.8 - - - -
173A LEU* 4.6 7.2 - - + -
174A ASP* 4.4 25.1 - - + -
180A THR* 5.4 4.3 - - - -
329A GLY 3.0 14.6 + - - +
330A GLU* 3.4 21.1 - - + +
332A ILE* 1.3 83.9 - - + +
334A SER* 1.3 62.4 + - - +
335A ILE* 3.0 10.4 + - - +
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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