Contacts of the helix formed by residues 326 - 341 (chain J) in PDB entry 1O1F
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 326 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325J ILE* 1.3 73.2 - - - +
327J ASP* 1.3 65.0 + - - +
328J GLN* 3.0 21.9 + - - +
329J GLU* 2.9 50.6 + - + +
330J GLU* 2.9 19.7 + - + +
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Residues in contact with ASP 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283J ARG* 3.2 32.0 + - - -
286J HIS* 5.0 2.6 - - - +
289J TYR* 3.7 31.7 - - - +
290J GLN* 3.3 16.6 + - - +
293J SER* 3.9 10.0 + - - -
320J ILE 4.7 1.6 - - - +
321J THR* 4.5 11.6 + - - -
322J VAL 5.3 1.4 + - - +
325J ILE* 3.8 14.2 + - - +
326J ASP* 1.3 73.3 + - - +
328J GLN* 1.3 61.9 + - + +
330J GLU* 4.0 6.9 - - - +
331J LEU* 3.1 21.3 + - - +
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Residues in contact with GLN 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293J SER* 3.8 32.1 + - - +
294J ASN 4.5 1.0 - - - +
295J MLY 3.7 49.1 + - + +
326J ASP* 2.9 19.2 + - - +
327J ASP* 1.3 81.5 - - + +
329J GLU* 1.3 60.4 + - - +
331J LEU* 3.7 6.9 + - - +
332J MET* 3.4 17.3 - - - +
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Residues in contact with GLU 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295J MLY 5.7 0.4 - - - -
326J ASP* 2.9 35.7 + - + +
328J GLN* 1.3 76.9 - - - +
330J GLU* 1.3 74.4 - - + +
332J MET* 3.2 12.1 + - - +
333J ALA* 3.0 18.5 + - - +
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Residues in contact with GLU 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J GLN* 3.5 20.4 - - + +
325J ILE* 4.4 16.3 - - + +
326J ASP* 2.9 27.0 + - - +
327J ASP* 3.9 4.3 - - - +
329J GLU* 1.3 83.3 - - - +
331J LEU* 1.3 52.6 + - - +
333J ALA* 2.7 15.8 + - + +
334J THR* 2.6 40.9 + - - +
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Residues in contact with LEU 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J GLN* 2.8 51.1 - - + +
291J ILE* 3.1 18.8 - - + +
293J SER* 3.8 6.7 - - - +
295J MLY 4.9 8.3 - - + +
296J MLY 3.8 31.4 - - + +
299J LEU* 4.2 8.5 - - + -
327J ASP 3.1 15.3 + - - +
328J GLN* 3.7 8.3 - - - +
329J GLU 3.3 0.2 - - - -
330J GLU* 1.3 73.9 - - - +
332J MET* 1.3 60.2 + - + +
334J THR* 3.3 3.0 - - + +
335J ASP* 2.8 28.6 + - - +
352J TYR* 4.0 17.7 + - + +
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Residues in contact with MET 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295J MLY 3.0 54.3 - - + -
296J MLY 4.8 23.6 - - - -
328J GLN 3.4 13.0 - - - +
329J GLU* 3.4 9.2 - - - +
330J GLU 3.0 0.2 - - - -
331J LEU* 1.3 76.0 - - - +
333J ALA* 1.3 56.4 + - - +
335J ASP* 3.3 6.5 - - - +
336J SER* 2.3 45.0 + - - +
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Residues in contact with ALA 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J PRO* 4.9 14.4 - - + +
329J GLU 3.0 9.6 + - - +
330J GLU* 2.7 26.4 + - - +
332J MET* 1.3 75.4 - - - +
334J THR* 1.3 65.3 + - - +
336J SER* 3.8 4.1 - - - -
337J ALA* 2.8 26.3 + - - +
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Residues in contact with THR 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J PRO 3.8 18.2 + - - +
228J LEU* 4.2 17.9 - - + +
231J ALA* 3.8 8.8 - - + +
287J ILE* 4.5 11.0 - - + -
290J GLN* 2.4 33.4 + - - +
330J GLU* 2.6 16.2 + - - +
331J LEU* 3.3 6.5 - - + +
333J ALA* 1.3 73.8 - - - +
335J ASP* 1.3 69.2 + - - +
337J ALA* 3.0 15.7 + - - +
338J ILE* 3.0 18.8 + - + +
352J TYR* 4.9 4.9 - - + +
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Residues in contact with ASP 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J MLY 2.8 45.8 + - - +
331J LEU* 2.8 15.5 + - + +
332J MET* 3.3 5.8 - - - +
334J THR* 1.3 79.8 - - - +
336J SER* 1.3 57.7 + - - +
338J ILE* 2.9 31.6 + - - +
339J ASP* 3.2 6.8 - - - +
348J MLY 2.5 36.3 + - - -
352J TYR* 2.7 25.6 + - - +
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Residues in contact with SER 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J MET* 4.7 18.3 - - - +
215J GLN* 2.2 36.4 + - - +
296J MLY 5.2 3.5 - - - -
332J MET* 2.3 35.7 + - - +
333J ALA* 3.9 4.3 - - - -
335J ASP* 1.3 75.1 - - - +
337J ALA* 1.3 53.3 + - - +
339J ASP* 3.4 8.0 - - - +
340J ILE* 3.1 5.8 + - - +
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Residues in contact with ALA 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J SER* 3.7 34.3 - - - +
227J PRO* 4.8 4.7 - - + -
228J LEU* 4.6 10.8 - - + +
333J ALA 2.8 20.4 + - - +
334J THR* 3.1 7.9 - - - +
336J SER* 1.3 73.6 - - - +
338J ILE* 1.3 57.0 + - - +
340J ILE* 3.2 2.9 + - - +
341J LEU* 2.7 44.3 + - + +
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Residues in contact with ILE 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J LEU* 3.5 26.2 - - + -
232J PHE* 5.5 0.7 - - + -
287J ILE* 6.4 0.2 - - + -
334J THR* 3.0 19.6 + - + +
335J ASP* 2.9 15.8 + - - +
337J ALA* 1.3 76.7 - - - +
339J ASP* 1.3 65.2 + - - +
341J LEU* 3.0 12.7 + - - -
342J GLY 3.3 6.9 + - - -
343J PHE* 3.3 38.2 + - + -
348J MLY 3.6 34.5 - - + -
351J ILE* 4.7 23.8 - - + -
352J TYR* 4.7 10.8 - - + +
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Residues in contact with ASP 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J GLN* 1.4 64.5 - - - +
296J MLY 5.5 0.5 - - - -
335J ASP* 3.2 14.1 - - - +
336J SER* 3.4 5.8 - - - +
338J ILE* 1.3 77.7 - - - +
340J ILE* 1.3 48.2 + - - -
342J GLY* 2.5 28.9 + - - -
343J PHE 4.0 9.3 + - - +
345J ALA* 6.0 0.2 - - - -
348J MLY 2.8 48.8 + - - +
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Residues in contact with ILE 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J LYS 3.3 9.6 - - - +
214J MET* 2.8 32.8 - - + +
215J GLN* 1.0 198.6 - - + +
216J GLY 3.9 4.6 + - - +
217J THR 4.1 11.0 - - - +
221J GLN* 3.6 23.6 - - - +
224J SER* 3.8 19.7 - - - +
336J SER* 3.5 13.2 - - - +
337J ALA* 3.6 6.1 - - - +
339J ASP 1.3 25.9 - - - +
341J LEU* 1.3 60.0 + - - +
342J GLY* 3.0 5.2 + - - -
448J GLN* 5.1 0.3 - - - +
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Residues in contact with LEU 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221J GLN* 3.4 35.4 - - + +
224J SER* 3.4 35.2 - - - +
225J ALA* 3.6 6.1 - - - +
228J LEU* 4.5 12.3 - - + -
337J ALA* 2.7 26.2 + - + +
338J ILE 3.3 4.7 - - - +
339J ASP 2.9 0.2 - - - -
340J ILE* 1.3 80.7 - - - +
342J GLY* 1.3 49.1 + - - +
343J PHE* 3.4 20.6 + - + -
444J ARG 5.0 1.0 - - - +
445J ILE* 3.9 28.1 - - + +
448J GLN* 2.6 37.2 + - + +
449J LEU* 4.5 5.4 - - + -
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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