Contacts of the helix formed by residues 356 - 374 (chain A) in PDB entry 5CEO
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 SER 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A HIS* 6.1 0.4 - - - -
289A GLU* 5.6 5.6 - - - -
290A LYS* 3.9 10.6 - - - +
293A ILE* 3.9 5.2 - - - -
355A PRO* 1.3 77.0 - - - +
357A PHE* 1.3 59.0 + - - +
358A ARG* 3.4 11.7 + - - +
359A GLN* 3.2 32.2 + - - +
360A ILE* 3.0 25.5 + - - +
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Residues in contact with PHE 357 (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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221A ALA* 3.7 29.2 - - + +
224A MET* 3.4 33.4 - - + -
225A ASN* 3.7 16.1 + - + +
228A HIS* 3.4 39.5 + + - +
237A LEU* 4.1 1.3 - - + -
292A ASP* 3.7 26.7 - - + -
293A ILE* 3.6 16.5 - - + +
296A PHE* 3.6 34.8 - + + -
356A SER* 1.3 72.6 - - - +
358A ARG* 1.4 55.6 + - - +
360A ILE* 3.4 16.4 + - + +
361A LEU* 2.9 33.5 + - - +
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Residues in contact with ARG 358 (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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225A ASN* 3.8 21.5 + - - +
356A SER* 3.2 10.4 + - - +
357A PHE* 1.4 73.6 - - - +
359A GLN* 1.4 68.0 + - + +
361A LEU* 3.3 14.4 + - + +
362A LEU* 3.2 21.9 + - - +
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Residues in contact with GLN 359 (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 LYS* 5.4 0.9 + - - -
355A PRO* 3.9 16.8 - - + +
356A SER* 3.2 34.1 + - - +
358A ARG* 1.4 79.2 - - + +
360A ILE* 1.3 63.7 + - - +
362A LEU* 3.2 10.3 + - + +
363A HIS* 3.0 44.7 + - + +
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Residues in contact with ILE 360 (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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221A ALA* 3.9 7.2 - - + -
293A ILE* 3.8 32.1 - - + -
296A PHE* 3.5 28.9 - - + -
342A LEU* 4.0 25.7 - - + +
346A CYS* 3.9 21.1 - - - -
355A PRO* 4.1 7.6 - - + -
356A SER 3.0 13.7 + - - +
357A PHE* 3.6 21.8 - - + +
359A GLN* 1.3 73.3 - - - +
361A LEU* 1.4 55.9 + - - +
363A HIS 3.7 0.5 - - - -
364A LEU* 2.8 46.6 + - + +
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Residues in contact with LEU 361 (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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218A MET* 3.4 36.0 - - + +
221A ALA* 3.8 8.5 - - + -
222A GLY* 3.7 27.4 - - - +
225A ASN* 3.8 31.4 - - + +
357A PHE 2.9 20.2 + - - +
358A ARG* 3.4 12.1 - - + +
359A GLN 3.3 0.4 - - - -
360A ILE* 1.4 75.2 - - - +
362A LEU* 1.4 61.9 + - - +
364A LEU* 4.6 0.9 - - - -
365A ASP* 3.2 24.1 + - - +
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Residues in contact with LEU 362 (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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358A ARG* 3.2 15.9 + - - +
359A GLN* 3.2 12.4 + - + +
361A LEU* 1.4 74.9 - - - +
363A HIS* 1.3 82.2 + - + +
365A ASP* 3.2 9.7 + - + +
366A ILE* 3.1 51.2 + - + +
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Residues in contact with HIS 363 (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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338A GLY* 5.4 4.8 - - - +
341A ILE* 6.5 1.3 - - + -
342A LEU* 4.3 22.4 - - + +
345A GLN* 4.7 14.5 + - - +
355A PRO* 5.8 2.0 - - + -
359A GLN* 3.0 41.3 + - + +
360A ILE 4.2 1.3 - - - +
362A LEU* 1.3 97.8 - - + +
364A LEU* 1.3 58.1 + - - +
366A ILE* 3.6 15.0 + - + +
367A ALA* 3.1 27.9 + - - +
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Residues in contact with LEU 364 (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 VAL* 5.6 1.8 - - + +
217A SER* 3.4 49.6 - - - +
218A MET* 3.9 20.7 - - + +
221A ALA* 4.1 4.0 - - + -
296A PHE* 3.8 5.2 - - + -
300A LEU* 4.3 4.3 - - + -
339A PHE* 3.8 26.9 - - + -
342A LEU* 3.8 18.6 - - + +
360A ILE* 2.8 38.1 + - + +
361A LEU 4.0 2.5 - - - +
363A HIS* 1.3 70.1 - - - +
365A ASP* 1.3 60.5 + - - +
367A ALA* 3.4 4.3 + - - +
368A SER* 2.8 29.8 + - - -
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Residues in contact with ASP 365 (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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218A MET* 4.1 17.9 - - + +
361A LEU 3.2 16.9 + - - +
362A LEU* 3.2 7.6 + - + +
364A LEU* 1.3 76.0 - - - +
366A ILE* 1.4 65.4 + - + +
368A SER* 2.6 26.9 + - - -
369A ALA* 3.7 4.0 + - - +
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Residues in contact with ILE 366 (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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362A LEU* 3.1 41.9 + - + +
363A HIS* 4.0 19.3 - - + +
364A LEU 3.4 0.2 - - - -
365A ASP* 1.4 77.2 - - + +
367A ALA* 1.4 62.3 + - - +
368A SER 3.4 0.7 + - - -
369A ALA* 3.4 20.9 - - - +
370A ASP* 4.3 1.9 + - - +
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Residues in contact with ALA 367 (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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336A PRO* 5.7 0.8 - - + +
338A GLY* 4.1 22.0 - - - -
339A PHE* 3.7 30.4 - - + -
342A LEU* 6.3 0.9 - - + -
363A HIS 3.1 18.6 + - - +
364A LEU* 3.4 6.5 + - - +
366A ILE* 1.4 77.5 - - - +
368A SER* 1.4 59.4 + - - +
370A ASP* 3.4 14.7 + - - +
371A VAL* 3.4 17.3 + - - +
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Residues in contact with SER 368 (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 VAL* 3.8 29.6 - - - -
218A MET* 5.2 0.7 - - - -
339A PHE* 5.2 0.4 - - - -
364A LEU 2.8 16.9 + - - -
365A ASP* 2.6 26.7 + - - -
367A ALA* 1.4 73.3 - - - +
369A ALA* 1.4 65.4 + - - +
371A VAL* 3.8 9.4 - - - -
372A LEU* 3.1 38.6 + - - +
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Residues in contact with ALA 369 (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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365A ASP 4.6 2.9 - - - +
366A ILE* 3.4 15.8 + - - +
368A SER* 1.4 81.1 + - - +
370A ASP* 1.3 62.0 + - - +
372A LEU* 4.5 3.1 - - - +
373A SER* 3.7 16.6 + - - -
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Residues in contact with ASP 370 (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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336A PRO* 3.7 27.1 - - + +
366A ILE 5.3 1.1 - - - +
367A ALA* 3.4 10.6 + - - +
368A SER 3.3 0.8 - - - -
369A ALA* 1.3 77.8 - - - +
371A VAL* 1.4 65.9 + - - +
373A SER* 2.7 25.2 + - - -
374A THR* 3.3 13.6 + - - -
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Residues in contact with VAL 371 (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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210A PRO* 3.2 21.1 - - + +
213A LEU* 4.2 9.0 - - + -
214A VAL* 4.0 13.0 - - + -
336A PRO* 3.6 24.2 - - + -
339A PHE* 3.6 32.1 - - + -
367A ALA 3.4 15.0 - - - +
368A SER* 3.7 11.9 - - - +
370A ASP* 1.4 78.3 - - - +
372A LEU* 1.3 62.9 - - - +
374A THR* 3.2 21.9 + - - +
379A TYR* 4.2 19.3 - - + -
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Residues in contact with LEU 372 (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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210A PRO* 3.8 7.9 - - + +
211A SER* 3.6 42.6 - - - +
214A VAL* 4.1 16.4 - - + -
368A SER* 3.1 39.2 + - - +
369A ALA* 4.5 3.6 - - - +
371A VAL* 1.3 74.5 - - - +
373A SER* 1.4 59.3 + - - +
374A THR 3.5 5.7 + - - +
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Residues in contact with SER 373 (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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369A ALA 3.7 11.7 + - - -
370A ASP* 2.7 22.2 + - - -
372A LEU* 1.4 74.1 - - - +
374A THR* 1.3 62.8 + - - +
375A PRO* 3.5 8.5 - - - +
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Residues in contact with THR 374 (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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210A PRO* 3.9 9.2 - - - +
370A ASP* 3.3 19.1 + - - -
371A VAL* 3.2 21.5 + - - +
372A LEU 3.9 5.2 - - - +
373A SER* 1.3 75.4 + - - +
375A PRO* 1.4 74.3 - - + +
376A GLN* 3.7 1.0 + - - +
378A THR* 4.1 10.8 - - + -
379A TYR* 3.8 37.5 - - + +
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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