Contacts of the helix formed by residues 357 - 368 (chain A) in PDB entry 1U54
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 PRO 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A LEU* 4.1 26.5 - - + -
324A PHE* 4.8 4.7 - - + -
355A ASP 4.1 0.4 - - - +
356A CYS* 1.3 90.5 - - - +
358A GLN* 1.3 66.1 + - - +
359A ASP* 3.1 16.5 + - - +
360A ILE* 3.1 31.2 + - + -
361A TYR* 3.2 7.6 + - - +
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Residues in contact with GLN 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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352A ARG* 4.3 15.8 + - - +
356A CYS 3.2 4.6 + - - -
357A PRO* 1.3 69.5 - - - +
359A ASP* 1.3 51.8 + - - +
361A TYR* 2.9 25.6 + - - +
362A ASN* 2.8 62.5 + - - +
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Residues in contact with ASP 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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357A PRO* 3.2 13.5 - - - +
358A GLN* 1.3 77.1 - - - +
360A ILE* 1.3 78.4 + - - +
362A ASN* 3.3 19.2 + - + +
363A VAL* 3.3 19.6 + - - +
387A GLU 3.8 7.1 - - - +
388A ALA* 3.2 35.4 - - - +
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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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226A LEU* 5.3 3.1 - - + +
230A SER* 3.5 25.1 - - - +
320A LEU* 4.4 7.7 - - + +
324A PHE* 3.6 29.6 - - + -
356A CYS* 3.5 18.6 - - - -
357A PRO* 3.1 27.4 + - + +
359A ASP* 1.3 78.1 + - - +
361A TYR* 1.3 67.1 + - - +
362A ASN 3.0 2.7 + - - -
363A VAL* 3.3 17.3 + - - +
364A MET* 3.4 12.9 + - + +
385A LEU* 5.2 12.1 - - + +
388A ALA* 3.8 32.1 - - + +
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Residues in contact with TYR 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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349A ARG* 5.2 3.1 - - - +
350A LEU 3.0 22.7 + - - -
351A PRO* 4.1 2.3 - - - +
352A ARG* 3.4 54.8 + - + -
353A PRO* 4.0 2.0 - - + -
356A CYS* 3.7 10.3 - - - -
357A PRO 3.2 7.2 + - - +
358A GLN* 2.9 28.3 + - - +
360A ILE* 1.3 76.9 - - - +
362A ASN* 1.3 59.1 + - - +
364A MET* 2.8 47.1 - - - +
365A VAL* 2.8 37.2 + - + +
368A TRP* 4.3 6.1 - + - -
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Residues in contact with ASN 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 GLN* 2.8 47.6 + - - +
359A ASP* 3.5 14.9 - - - +
360A ILE 3.0 0.8 - - - -
361A TYR* 1.3 78.2 - - - +
363A VAL* 1.3 67.2 + - - +
364A MET 3.0 0.7 - - - -
365A VAL* 3.1 14.4 + - + +
366A GLN* 3.0 28.9 + - - +
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Residues in contact with VAL 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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316A PHE* 4.7 1.6 - - + -
320A LEU* 4.2 9.6 - - + -
359A ASP 3.3 16.6 - - - +
360A ILE* 3.5 10.8 - - + +
362A ASN* 1.3 76.3 - - - +
364A MET* 1.3 62.6 + - - +
366A GLN* 3.3 12.9 + - - +
367A CYS* 3.1 27.7 + - - -
381A LEU* 3.4 31.0 - - + +
384A PHE* 3.9 24.5 - - + +
385A LEU* 3.8 33.4 - - + +
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Residues in contact with MET 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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317A GLY* 3.5 19.5 - - - +
320A LEU* 4.0 21.9 - - + +
321A TRP* 3.7 42.6 - - - +
324A PHE* 4.5 7.6 - - + -
353A PRO* 4.5 4.3 - - + -
356A CYS* 4.4 22.0 - - - -
360A ILE* 3.4 3.0 + - + +
361A TYR* 2.8 40.1 + - + +
363A VAL* 1.3 80.2 - - - +
365A VAL* 1.3 59.8 + - - +
367A CYS* 2.9 24.7 + - - +
368A TRP* 3.4 21.5 + - + -
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Residues in contact with VAL 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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349A ARG* 5.4 6.5 - - + -
361A TYR* 2.8 51.0 + - + +
362A ASN* 3.1 16.4 + - + +
364A MET* 1.3 75.8 - - - +
366A GLN* 1.3 65.9 + - + +
368A TRP* 3.2 23.6 + - + +
369A ALA* 3.4 8.3 + - - -
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Residues in contact with GLN 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 ASN* 3.0 17.3 + - - +
363A VAL* 3.4 10.6 - - - +
365A VAL* 1.3 77.3 - - + +
367A CYS* 1.3 68.4 + - - +
368A TRP 2.8 2.0 - - - -
369A ALA* 2.6 26.2 + - + +
374A ASP 4.8 7.2 + - - +
375A ARG* 3.9 4.3 - - - +
376A PRO* 4.0 23.1 - - + +
384A PHE* 3.5 38.9 - - - -
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Residues in contact with CYS 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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313A THR* 3.1 36.3 - - - +
314A TRP* 3.6 7.8 - - - -
316A PHE* 3.8 16.2 - - - -
317A GLY* 3.4 24.0 - - - -
320A LEU* 5.5 0.2 - - - -
363A VAL* 3.1 23.0 + - - -
364A MET* 2.9 11.3 + - - +
366A GLN* 1.3 77.9 - - - +
368A TRP* 1.3 58.8 + - + +
375A ARG* 3.1 26.5 - - - -
376A PRO* 4.4 1.5 - - - +
381A LEU* 3.9 17.0 - - - -
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Residues in contact with TRP 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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314A TRP* 3.1 57.9 + + + -
317A GLY* 3.6 23.1 - - - -
318A VAL* 3.6 19.7 - - + +
321A TRP* 4.2 5.6 - + + -
349A ARG* 3.2 46.3 + - + +
350A LEU* 4.0 40.6 - - + -
361A TYR* 4.3 9.9 - + - -
364A MET* 3.4 39.7 + - + -
365A VAL* 3.2 16.0 + - + +
366A GLN 2.7 2.0 + - - -
367A CYS* 1.3 82.3 - - - +
369A ALA* 1.3 68.0 + - - -
370A HIS 2.7 4.3 + - - -
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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