Contacts of the helix formed by residues 326 - 341 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ILE* 1.3 73.3 - - - +
327A ASP* 1.3 65.9 + - - +
328A GLN* 3.0 21.4 + - - +
329A GLU* 2.9 49.0 + - + +
330A GLU* 2.9 19.9 + - + +
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 3.2 33.7 + - - -
286A HIS* 5.0 2.1 - - - +
289A TYR* 3.7 31.1 - - - +
290A GLN* 3.3 17.2 + - - +
293A SER* 3.9 9.2 - - - -
320A ILE 4.7 1.4 - - - +
321A THR* 4.5 11.3 + - - -
322A VAL 5.3 1.6 + - - +
325A ILE* 3.8 14.0 + - - +
326A ASP* 1.3 72.5 + - - +
328A GLN* 1.3 63.1 + - + +
330A GLU* 4.0 6.9 - - - +
331A LEU* 3.1 21.0 + - - +
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Residues in contact with GLN 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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293A SER* 3.8 31.9 + - - +
294A ASN 4.5 1.6 - - - +
295A MLY 3.7 48.6 - - + +
326A ASP* 2.9 18.9 + - - +
327A ASP* 1.3 80.3 - - + +
329A GLU* 1.3 61.3 + - - +
331A LEU* 3.7 7.2 + - - +
332A MET* 3.4 17.3 - - - +
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Residues in contact with GLU 329 (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 ASP* 2.9 35.6 + - + +
328A GLN* 1.3 77.4 - - - +
330A GLU* 1.3 75.3 + - + +
332A MET* 3.2 12.1 + - - +
333A ALA* 3.0 18.7 + - - +
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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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290A GLN* 3.5 20.2 - - + +
325A ILE* 4.4 16.4 - - + +
326A ASP* 2.9 26.5 + - - +
327A ASP* 3.9 4.9 - - - +
329A GLU* 1.3 83.4 - - - +
331A LEU* 1.3 51.9 - - - +
333A ALA* 2.7 16.0 + - - +
334A THR* 2.6 41.2 + - - +
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Residues in contact with LEU 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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290A GLN* 2.8 50.8 - - + +
291A ILE* 3.1 19.3 - - + +
293A SER* 3.8 6.1 - - - +
295A MLY 4.9 8.5 - - + +
296A MLY 3.8 30.7 - - + -
299A LEU* 4.2 9.2 - - + -
327A ASP 3.1 15.3 + - - +
328A GLN* 3.7 8.7 - - - +
329A GLU 3.3 0.2 - - - -
330A GLU* 1.3 74.3 - - - +
332A MET* 1.3 58.7 + - + +
334A THR* 3.3 3.3 - - + +
335A ASP* 2.8 28.6 + - - +
352A TYR* 4.0 17.0 + - + +
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Residues in contact with MET 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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295A MLY 3.0 54.7 - - + -
296A MLY 4.8 24.0 - - - -
328A GLN 3.4 12.3 - - - +
329A GLU* 3.4 9.0 - - - +
331A LEU* 1.3 75.3 - - - +
333A ALA* 1.3 57.2 + - - +
335A ASP* 3.8 5.6 - - - -
336A SER* 2.3 45.6 + - - +
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Residues in contact with ALA 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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227A PRO* 4.9 14.4 - - + +
329A GLU 3.0 9.4 + - - +
330A GLU* 2.7 26.6 + - + +
332A MET* 1.3 76.6 - - - +
334A THR* 1.3 65.4 + - - +
336A SER* 3.8 4.5 - - - -
337A ALA* 2.8 26.0 + - - +
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Residues in contact with THR 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 PRO 3.8 17.4 + - - +
228A LEU* 4.2 19.0 - - + +
231A ALA* 3.8 9.1 - - + +
287A ILE* 4.5 11.2 - - + -
290A GLN* 2.4 33.2 + - - +
330A GLU* 2.6 15.8 + - - +
331A LEU* 3.3 6.1 - - + +
333A ALA* 1.3 75.4 - - - +
335A ASP* 1.3 68.2 + - - +
337A ALA* 3.0 15.3 + - - +
338A ILE* 3.0 17.9 + - + +
352A TYR* 4.9 4.9 - - + +
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Residues in contact with ASP 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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296A MLY 2.8 47.1 + - - +
331A LEU 2.8 19.9 + - - +
332A MET* 3.3 5.4 - - - +
334A THR* 1.3 76.5 - - - +
336A SER* 1.3 58.9 + - - +
338A ILE* 2.9 32.3 + - - +
339A ASP* 3.2 5.9 - - - +
348A MLY 2.5 35.0 + - - -
352A TYR* 2.7 25.3 + - - +
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Residues in contact with SER 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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214A MET* 4.7 18.1 - - - +
215A GLN* 2.2 36.7 + - - +
296A MLY 5.4 2.5 - - - -
332A MET* 2.3 35.1 + - - +
333A ALA* 3.9 4.9 + - - -
335A ASP* 1.3 74.1 + - - +
337A ALA* 1.3 53.0 + - - +
339A ASP* 3.4 8.4 - - - +
340A ILE* 3.1 6.1 + - - +
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Residues in contact with ALA 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 SER* 3.7 35.4 - - - +
227A PRO* 4.8 4.7 - - + -
228A LEU* 4.6 10.8 - - + +
333A ALA 2.8 20.2 + - - +
334A THR* 3.0 8.3 + - - +
336A SER* 1.3 73.2 - - - +
338A ILE* 1.3 56.5 + - - +
340A ILE* 3.2 2.9 + - - +
341A LEU* 2.7 43.9 + - + +
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Residues in contact with ILE 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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228A LEU* 3.5 27.6 - - + -
232A PHE* 5.5 0.7 - - + -
334A THR* 3.0 19.6 + - + +
335A ASP* 2.9 16.0 + - - +
337A ALA* 1.3 75.8 - - - +
339A ASP* 1.3 67.8 + - - +
341A LEU* 3.0 13.2 + - - -
342A GLY 3.3 6.1 + - - -
343A PHE* 3.3 37.5 + - + +
348A MLY 3.6 33.0 - - + -
351A ILE* 4.7 23.8 - - + -
352A TYR* 4.7 10.5 - - + +
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Residues in contact with ASP 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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215A GLN* 1.4 64.4 - - - +
296A MLY 5.5 0.7 - - - -
335A ASP* 3.2 14.4 - - - +
336A SER* 3.4 5.5 - - - +
338A ILE* 1.3 76.6 - - - +
340A ILE* 1.3 48.5 + - - -
342A GLY* 2.5 28.9 + - - -
343A PHE 4.0 10.1 + - - +
345A ALA* 6.0 0.3 - - - -
348A MLY 2.8 47.0 + - - +
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Residues in contact with ILE 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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213A LYS 3.3 9.0 - - - +
214A MET* 2.8 33.2 - - + +
215A GLN* 1.0 199.6 - - + +
216A GLY 4.0 4.6 + - - +
217A THR 4.2 11.2 - - - +
221A GLN* 3.6 23.7 - - + +
224A SER* 3.8 19.7 - - - +
336A SER* 3.5 13.7 - - - +
337A ALA 3.6 6.1 - - - +
339A ASP 1.3 25.7 - - - +
341A LEU* 1.3 59.3 - - - +
342A GLY* 3.0 5.5 + - - -
448A GLN* 5.1 0.3 - - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 3.4 35.7 - - + +
224A SER* 3.4 35.7 - - - +
225A ALA* 3.6 5.8 - - - +
228A LEU* 4.5 11.7 - - + -
337A ALA* 2.7 27.3 + - + +
338A ILE 3.3 4.9 - - - +
339A ASP 2.9 0.4 - - - -
340A ILE* 1.3 80.9 - - - +
342A GLY* 1.3 49.9 + - - +
343A PHE* 3.4 21.0 - - + -
444A ARG 5.0 0.9 - - - +
445A ILE* 3.9 28.1 - - + +
448A GLN* 2.6 37.7 + - + +
449A 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