Contacts of the helix formed by residues 357 - 370 (chain A) in PDB entry 3U86
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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A SER* 3.7 11.3 - - - -
220A TRP* 2.8 49.3 + - - +
221A LEU* 3.4 13.5 + - - +
352A ASN 3.5 16.3 - - - +
353A TYR* 4.0 15.8 - - + -
354A CYS* 2.9 17.1 + - - +
356A GLU* 1.3 78.6 - - - +
358A GLU* 1.3 63.1 + - - +
359A GLU 3.0 5.1 + - - -
360A ILE* 3.1 19.1 + - + +
361A TYR* 3.2 10.7 + - - +
423A TRP* 4.5 3.1 - - - -
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Residues in contact with GLU 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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200A GLY* 5.7 2.3 - - - -
201A LYS* 5.3 13.2 + - - +
353A TYR* 4.8 8.1 - - - +
354A CYS 4.3 0.2 + - - -
355A ARG* 2.8 29.1 + - - +
356A GLU* 3.1 7.9 + - - +
357A ASP* 1.3 77.1 - - - +
359A GLU* 1.3 63.0 + - - +
361A TYR* 3.8 7.3 - - - +
362A LYS* 3.1 34.9 + - + +
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASP* 3.3 33.4 - - - +
220A TRP* 4.0 5.4 - - + -
319A TYR* 3.8 20.0 - - - +
356A GLU 4.8 1.2 + - - -
357A ASP 3.0 1.6 + - - -
358A GLU* 1.3 80.4 - - - +
360A ILE* 1.3 59.9 - - - +
362A LYS* 3.9 12.5 - - - +
363A GLU 3.6 7.4 + - - -
30B ARG* 2.8 50.1 + - + +
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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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220A TRP* 3.7 47.3 - - + +
318A ILE* 4.1 24.0 - - + -
319A TYR* 4.2 17.9 - - + +
322A MET* 4.8 2.0 - - - -
348A ILE* 4.8 2.9 - - + -
357A ASP* 3.1 13.7 + - + +
359A GLU* 1.3 76.8 - - - +
361A TYR* 1.3 69.6 + - - +
362A LYS 3.2 1.3 - - - -
363A GLU* 2.9 26.5 + - + +
364A PHE* 3.0 35.4 + - + -
423A TRP* 3.8 22.0 - - + -
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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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353A TYR* 3.6 49.4 - + + +
357A ASP 3.2 1.9 + - - +
358A GLU* 3.8 8.5 - - - +
360A ILE* 1.3 83.6 - - - +
362A LYS* 1.3 71.7 + - + +
363A GLU 3.2 0.2 + - - -
364A PHE* 3.2 3.2 + - - +
365A PHE* 3.0 43.4 + + - +
423A TRP* 3.9 18.4 - + - -
430A PRO 5.1 1.3 + - - -
431A VAL* 3.4 26.8 + - + -
433A HIS* 3.7 14.0 + - - -
436A TRP* 3.3 27.6 + + - -
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Residues in contact with LYS 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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201A LYS* 5.8 7.7 - - - +
358A GLU* 3.1 20.8 + - + +
359A GLU* 3.9 13.7 - - - +
361A TYR* 1.3 88.1 - - + +
363A GLU* 1.3 57.3 + - - +
365A PHE* 3.5 5.0 - - + +
366A GLU* 3.0 41.0 + - + +
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Residues in contact with GLU 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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319A TYR* 5.8 0.2 - - + -
322A MET* 3.6 35.8 - - + +
359A GLU 3.6 3.0 + - - +
360A ILE* 2.9 18.9 + - + +
362A LYS* 1.3 77.2 - - - +
364A PHE* 1.3 60.3 + - + +
366A GLU* 3.3 16.8 + - - +
367A VAL* 3.1 35.4 + - - +
30B ARG* 3.1 39.1 + - - +
37B PRO 5.0 0.5 - - - +
38B THR* 3.6 6.8 + - - -
39B ALA* 3.3 32.5 + - - +
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Residues in contact with PHE 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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318A ILE* 4.5 4.5 - - + -
322A MET* 5.2 4.9 - - - -
341A TRP* 6.4 0.7 - + - -
344A THR* 3.3 36.3 - - + -
345A ALA* 4.2 11.9 - - + -
348A ILE* 4.0 34.1 - - + -
360A ILE* 3.0 43.7 + - + -
361A TYR 3.8 4.7 - - - +
363A GLU* 1.3 76.6 - - + +
365A PHE* 1.3 55.2 + - - +
367A VAL* 3.8 5.2 - - + +
368A ALA* 2.8 37.6 + - - +
416A PHE* 3.9 23.7 - + - -
420A ILE* 4.3 12.8 - - + -
423A TRP* 3.9 18.4 - + + -
436A TRP* 4.0 13.9 - - + -
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Residues in contact with PHE 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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361A TYR* 3.0 34.0 + + + +
362A LYS* 3.5 10.5 - - + +
364A PHE* 1.3 76.5 - - - +
366A GLU* 1.3 64.3 + - + +
369A ASN* 2.9 69.9 + - + +
433A HIS* 3.6 33.7 - + - -
435A GLY* 5.6 2.7 - - - -
436A TRP* 3.6 24.2 - + + -
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Residues in contact with GLU 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 LYS* 3.0 27.8 + - + +
363A GLU* 3.3 16.5 + - - +
364A PHE 3.4 0.2 - - - -
365A PHE* 1.3 76.8 - - + +
367A VAL* 1.3 56.1 + - - +
370A ASP* 3.0 14.3 + - - +
371A VAL* 2.7 37.7 + - + +
38B THR* 2.6 29.6 + - - +
46B LYS* 3.7 36.8 + - + +
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Residues in contact with VAL 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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322A MET* 4.2 4.9 - - + -
341A TRP* 3.7 44.0 - - + +
363A GLU* 3.1 34.3 + - - +
364A PHE* 3.8 6.7 - - + +
366A GLU* 1.3 76.8 - - - +
368A ALA* 1.3 62.5 + - - +
371A VAL* 3.8 6.3 - - - -
372A ILE* 2.9 52.8 + - + +
416A PHE* 3.7 16.2 - - + -
39B ALA* 4.4 5.2 - - + -
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Residues in contact with ALA 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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364A PHE 2.8 23.5 + - - +
365A PHE 4.2 0.2 - - - +
367A VAL* 1.3 74.9 - - - +
369A ASN* 1.3 58.9 + - - +
372A ILE* 4.3 5.6 - - - +
373A PRO* 3.1 21.7 - - - +
416A PHE* 3.7 21.5 - - + -
417A TYR* 3.8 20.8 + - + +
436A TRP* 3.5 28.7 - - + -
439A PHE* 4.2 2.3 - - - +
443A SER* 4.9 0.5 + - - -
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Residues in contact with ASN 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 PHE* 2.9 70.6 + - + +
368A ALA* 1.3 81.3 - - - +
370A ASP* 1.3 56.7 + - + +
373A PRO* 3.2 14.6 - - - +
417A TYR* 5.2 0.5 + - - -
435A GLY 4.3 3.1 + - - -
436A TRP* 3.6 26.4 - - - +
439A PHE* 3.5 50.9 - - + +
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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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366A GLU* 3.0 20.0 + - + +
369A ASN* 1.3 80.1 - - + +
371A VAL* 1.3 59.7 + - + +
372A ILE 3.5 1.3 - - - -
373A PRO* 3.7 2.5 - - - -
374A ASN* 3.1 44.6 + - - +
46B LYS* 2.9 45.7 + - + +
47B LYS* 4.1 8.7 + - - -
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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