Contacts of the helix formed by residues 318 - 333 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER 3.8 0.7 - - - +
156B ILE* 3.5 24.4 - - + +
157B TYR 2.9 47.0 + - - +
158B PRO* 4.4 2.5 - - + +
161B ALA* 3.6 27.1 - - + +
162B VAL* 5.0 3.8 - - + -
254B ASP* 4.5 2.6 - - - +
282B VAL* 3.9 17.8 - - + +
283B LEU 4.9 1.3 - - - -
284B GLY* 4.2 2.3 - - - -
285B TYR 4.7 1.4 + - - -
288B ARG* 3.0 22.4 + - - -
317B ASP* 1.3 84.5 - - - +
319B ALA* 1.3 63.3 + - - +
321B LEU* 3.1 25.7 + - + +
322B LEU 4.4 0.3 + - - -
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Residues in contact with ALA 319 (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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158B PRO* 5.7 0.6 - - - +
161B ALA* 4.2 7.8 - - - +
317B ASP* 3.2 16.8 + - - +
318B GLU* 1.3 79.3 - - - +
320B ALA* 1.3 61.7 + - - +
321B LEU 3.2 0.9 + - - -
322B LEU* 3.5 18.2 + - - +
323B GLU 4.8 0.2 + - - -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.4 27.0 - - + +
316B SER* 4.1 13.9 - - - +
317B ASP* 3.0 14.0 + - - +
319B ALA* 1.3 76.9 - - - +
321B LEU* 1.3 65.0 + - - +
322B LEU 3.2 0.6 + - - -
323B GLU* 3.3 19.5 + - - +
324B LYS* 3.8 2.3 + - - +
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Residues in contact with LEU 321 (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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161B ALA 4.7 0.2 - - - +
162B VAL* 4.3 23.3 - - + -
165B PHE* 3.5 52.6 - - + -
252B VAL* 4.5 15.5 - - + -
280B ILE* 3.8 28.3 - - + -
282B VAL* 4.9 9.4 - - + -
315B VAL* 3.5 19.5 - - + +
317B ASP 3.5 4.2 + - - +
318B GLU* 3.1 21.1 + - + +
320B ALA* 1.3 76.5 - - - +
322B LEU* 1.3 63.7 + - - +
324B LYS* 2.9 16.8 + - + +
325B ALA 3.3 8.5 + - - -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA 5.2 2.6 + - - +
164B ASN* 4.1 25.6 - - + +
165B PHE* 4.6 5.2 - - - +
168B LYS* 3.9 34.8 - - + +
318B GLU 4.4 0.6 + - - -
319B ALA 3.5 13.4 + - - +
320B ALA 3.2 0.4 - - - -
321B LEU* 1.3 78.2 - - - +
323B GLU* 1.3 63.0 + - - +
325B ALA* 3.2 16.3 + - - +
326B GLY 4.1 1.7 + - - -
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Residues in contact with GLU 323 (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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319B ALA 4.8 0.2 + - - -
320B ALA* 3.3 11.9 + - + +
321B LEU 3.3 0.6 - - - -
322B LEU* 1.3 79.2 - - - +
324B LYS* 1.3 63.5 + - - +
325B ALA 3.3 0.7 + - - -
326B GLY* 3.6 8.7 + - - -
327B THR* 4.2 10.4 + - - +
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Residues in contact with LYS 324 (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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165B PHE* 4.7 5.6 - - + -
280B ILE* 5.7 3.8 - - + -
313B PHE* 4.2 23.0 - - + -
315B VAL* 4.3 20.4 - - + -
320B ALA 3.8 1.5 + - - +
321B LEU* 2.9 12.2 + - + +
323B GLU* 1.3 79.2 - - - +
325B ALA* 1.3 57.1 + - - +
327B THR* 3.3 10.5 + - - -
328B LEU* 2.9 30.7 + - + +
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Residues in contact with ALA 325 (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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165B PHE* 3.5 44.4 - - + +
168B LYS* 3.6 17.1 - - + +
169B PHE* 3.9 13.4 - - - +
321B LEU 3.3 3.6 + - - -
322B LEU 3.2 12.9 + - - +
323B GLU 3.2 1.2 - - - -
324B LYS* 1.3 76.7 - - - +
326B GLY* 1.3 56.6 + - - +
328B LEU* 3.6 3.3 - - - +
329B GLY* 2.9 27.5 + - - -
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Residues in contact with GLY 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 4.2 21.9 - - - +
322B LEU 4.1 2.0 + - - -
323B GLU 3.6 7.3 + - - -
324B LYS 3.3 1.0 - - - -
325B ALA* 1.3 76.4 - - - +
327B THR* 1.3 59.8 + - - +
329B GLY* 3.8 0.9 - - - -
330B GLU* 3.1 30.8 + - - +
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Residues in contact with THR 327 (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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313B PHE* 3.6 20.3 - - - -
323B GLU 4.3 10.8 - - - +
324B LYS* 3.3 10.5 + - - -
326B GLY* 1.3 74.6 - - - +
328B LEU* 1.3 65.8 + - - +
330B GLU* 3.5 21.3 - - - +
331B GLN* 3.1 26.5 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 4.1 13.5 - - + -
169B PHE* 3.8 23.6 - - + -
250B VAL* 4.1 13.0 - - + -
278B PHE* 3.7 35.9 - - + -
280B ILE* 4.0 27.6 - - + -
313B PHE* 4.7 13.9 - - + -
324B LYS* 2.9 17.1 + - + +
325B ALA* 3.6 5.6 - - - +
327B THR* 1.3 77.3 - - - +
329B GLY* 1.3 65.6 + - - +
331B GLN* 3.1 3.1 + - - -
332B ILE* 2.9 40.8 + - + +
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Residues in contact with GLY 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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168B LYS 6.0 0.2 - - - -
169B PHE* 4.0 23.1 - - - -
172B GLY* 4.6 10.1 - - - -
173B LEU* 3.7 11.1 - - - +
325B ALA 2.9 16.3 + - - -
326B GLY 3.8 1.3 - - - -
328B LEU* 1.3 77.0 - - - +
330B GLU* 1.3 57.0 + - - +
332B ILE* 3.0 2.4 + - - -
333B PHE* 2.9 29.5 + - - +
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Residues in contact with GLU 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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172B GLY 5.4 0.9 - - - -
326B GLY 3.1 15.4 + - - +
327B THR* 3.5 28.5 - - - +
329B GLY* 1.3 75.3 - - - +
331B GLN* 1.3 66.5 + - + +
332B ILE 3.4 0.2 + - - -
333B PHE* 3.6 7.1 + - - +
334B SER* 3.6 19.6 + - - -
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Residues in contact with GLN 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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278B PHE* 3.6 21.1 - - + -
310B ARG* 3.1 57.4 + - - +
311B TYR* 5.2 2.0 - - - -
313B PHE* 3.9 14.7 - - - -
327B THR 3.1 19.9 + - - +
328B LEU* 3.1 5.6 + - - +
330B GLU* 1.3 80.4 - - + +
332B ILE* 1.3 60.7 + - - +
334B SER* 4.0 10.2 - - - -
335B ILE* 4.0 14.0 - - - +
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Residues in contact with ILE 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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144B ILE* 3.2 20.3 - - + +
146B VAL* 4.1 21.1 - - + -
169B PHE* 3.7 24.2 - - + -
173B LEU* 4.0 16.2 - - + -
248B VAL* 4.1 8.7 - - + -
250B VAL* 3.8 16.8 - - + -
278B PHE* 3.9 26.7 - - + -
328B LEU* 2.9 31.8 + - + +
329B GLY 3.8 2.9 - - - +
331B GLN* 1.3 77.1 - - - +
333B PHE* 1.3 63.4 + - - +
334B SER 3.1 2.0 - - - -
335B ILE* 3.2 18.5 + - + +
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Residues in contact with PHE 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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141B PRO* 5.0 3.1 - - - +
142B SER* 3.5 24.5 + - - +
144B ILE* 5.0 2.0 - - - -
172B GLY 4.3 13.2 - - - +
173B LEU* 4.1 9.8 - - + +
174B ASP* 5.9 1.1 - - - +
180B THR* 5.8 1.1 - - - -
329B GLY 2.9 15.1 + - - +
330B GLU* 3.9 9.2 - - - +
332B ILE* 1.3 76.1 - - - +
334B SER* 1.3 57.6 + - - +
335B ILE 3.1 9.8 + - - +
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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