Contacts of the helix formed by residues 350 - 369 (chain D) in PDB entry 1SHZ
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 350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D GLN* 3.9 1.6 - - - -
194D GLN* 5.2 0.4 - - - -
293D LYS* 5.1 3.6 - - - +
347D CYS* 2.8 33.2 + - + +
349D THR* 1.3 69.7 + - - +
351D THR* 1.3 68.0 + - - +
352D LYS* 3.3 12.7 + - - +
353D ASN* 3.0 38.8 + - + +
354D VAL* 3.4 11.6 + - - +
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Residues in contact with THR 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLN* 3.3 29.8 + - - +
70D ILE* 4.8 9.7 - - + +
71D ILE* 4.3 19.0 - - + +
194D GLN* 5.4 1.3 + - - -
197D LEU* 4.0 10.7 - - - +
349D THR 3.5 3.5 + - - -
350D ASP* 1.3 72.5 - - - +
352D LYS* 1.3 63.9 + - - +
354D VAL* 3.4 2.1 + - - +
355D GLN* 3.2 25.6 + - + +
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Residues in contact with LYS 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ASP* 3.2 9.9 + - - +
351D THR* 1.3 81.5 - - - +
353D ASN* 1.3 64.0 + - - +
355D GLN* 3.5 26.9 + - - +
356D PHE* 3.4 18.5 + - - +
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Residues in contact with ASN 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D LYS* 3.5 18.5 - - - +
345D PHE 3.6 4.5 + - - +
346D THR* 3.3 12.0 - - - -
347D CYS 3.1 27.7 + - - +
350D ASP* 3.0 25.8 + - + +
352D LYS* 1.3 76.2 - - - +
354D VAL* 1.3 58.6 + - - +
356D PHE* 3.2 12.9 + - - +
357D VAL* 2.9 40.3 + - - +
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 3.7 17.4 - - + -
67D GLN* 3.8 15.5 - - + +
68D MET* 3.5 31.4 - - + -
71D ILE* 3.9 2.9 - - + -
346D THR* 5.6 4.5 - - - -
347D CYS 4.3 3.4 - - - +
348D ALA* 3.7 38.6 - - - +
350D ASP 3.4 7.5 + - - +
351D THR 3.9 6.5 - - - +
352D LYS 3.4 0.6 - - - -
353D ASN* 1.3 73.5 - - - +
355D GLN* 1.3 61.7 + - - +
357D VAL* 4.1 5.3 - - - +
358D PHE* 2.8 29.5 + - - +
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Residues in contact with GLN 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ILE* 3.9 30.5 - - + +
72D HIS* 6.0 1.7 - - + +
351D THR* 3.2 19.1 + - + +
352D LYS* 3.7 29.8 + - - +
354D VAL* 1.3 77.4 - - - +
356D PHE* 1.3 62.3 + - - +
358D PHE* 4.2 3.5 - - - +
359D ASP* 3.3 23.6 + - + +
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Residues in contact with PHE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D HIS* 5.0 9.0 - + - -
352D LYS 3.4 9.4 + - - +
353D ASN* 3.2 16.0 + - - +
355D GLN* 1.3 81.0 - - - +
357D VAL* 1.3 78.7 + - + +
359D ASP* 3.4 9.1 + - - +
360D ALA* 3.1 34.9 + - + +
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Residues in contact with VAL 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 5.6 0.9 - - + -
289D PHE* 3.2 41.7 - - + -
344D HIS* 4.2 16.6 - - + +
345D PHE 5.2 2.7 - - - +
346D THR* 4.0 16.2 - - + -
353D ASN* 2.9 26.7 + - - +
354D VAL* 4.1 5.2 - - - +
356D PHE* 1.3 96.4 - - + +
358D PHE* 1.3 65.8 + - - +
360D ALA* 3.3 6.0 + - - +
361D VAL* 3.0 23.5 + - + +
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Residues in contact with PHE 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 4.4 10.3 - - + -
64D PHE* 3.4 26.5 - + + -
68D MET* 3.8 13.7 - - + -
72D HIS* 3.3 28.9 - + + -
211D PHE* 3.4 26.2 - + - -
213D PHE* 3.4 30.1 - + - -
218D PHE* 4.2 6.1 - + - -
220D MET* 4.0 15.7 - - + -
244D ILE* 5.2 3.8 - - + -
289D PHE* 5.6 0.4 - - - -
354D VAL 2.8 22.1 + - - +
355D GLN* 4.2 4.7 - - - +
357D VAL* 1.3 74.6 - - - +
359D ASP* 1.3 57.9 + - - +
361D VAL* 3.2 6.9 + - + -
362D THR* 2.9 45.3 + - + +
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Residues in contact with ASP 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D PHE* 3.9 13.1 - - + -
214D LYS* 2.7 30.2 + - - -
355D GLN 3.3 17.6 + - - +
356D PHE* 3.5 8.0 - - - +
357D VAL 3.3 0.4 - - - -
358D PHE* 1.3 80.7 - - - +
360D ALA* 1.3 61.0 + - - +
362D THR* 2.6 19.2 + - - -
363D ASP* 3.2 22.7 + - - +
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Residues in contact with ALA 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D HIS* 4.0 23.1 - - + +
356D PHE* 3.1 24.9 + - + +
357D VAL* 3.6 10.5 - - - +
358D PHE 3.2 0.4 - - - -
359D ASP* 1.3 77.8 + - - +
361D VAL* 1.3 64.3 + - - +
363D ASP* 3.3 16.3 + - - +
364D VAL* 3.3 16.9 + - - +
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Residues in contact with VAL 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 5.6 3.4 - - + -
244D ILE* 4.7 14.4 - - + -
287D ILE* 3.5 40.2 - - + -
289D PHE* 3.7 31.0 - - + -
342D TYR* 6.3 0.2 - - + -
344D HIS* 4.0 10.3 - - + -
357D VAL 3.0 16.9 + - - +
358D PHE* 3.8 7.6 - - + +
360D ALA* 1.3 76.5 - - - +
362D THR* 1.3 63.2 + - + +
364D VAL* 3.2 8.5 + - + +
365D ILE* 3.1 26.5 + - + +
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Residues in contact with THR 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D PHE* 3.5 11.4 - - + -
214D LYS* 3.4 12.2 + - - -
216D LEU* 5.6 1.3 - - - -
218D PHE* 3.4 32.8 - - + -
358D PHE* 2.9 40.1 + - + +
359D ASP* 2.6 27.4 + - - -
361D VAL* 1.3 74.2 - - + +
363D ASP* 1.3 57.9 + - - -
365D ILE* 3.3 9.1 + - - +
366D ILE* 3.0 35.8 + - - +
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Residues in contact with ASP 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LYS* 2.7 28.8 + - - -
359D ASP* 3.2 20.8 + - - +
360D ALA* 3.3 10.2 + - - +
361D VAL 3.3 0.4 - - - -
362D THR* 1.3 77.0 - - - +
364D VAL* 1.3 61.2 + - - +
366D ILE* 3.5 13.9 + - - +
367D LYS* 3.2 25.2 + - - +
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Residues in contact with VAL 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D SER* 4.4 5.2 - - - +
287D ILE* 5.0 2.0 - - + -
342D TYR* 3.4 58.6 - - + +
344D HIS* 6.2 1.8 - - - +
360D ALA 3.3 11.4 + - - +
361D VAL* 3.2 14.1 + - + +
362D THR 3.2 0.6 - - - -
363D ASP* 1.3 78.0 - - - +
365D ILE* 1.3 67.4 + - + +
367D LYS* 3.3 6.1 + - - +
368D ASN* 2.8 30.5 + - - +
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Residues in contact with ILE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 4.4 22.7 - - + -
51D LEU* 4.9 4.3 - - + -
216D LEU* 4.7 9.2 - - + -
218D PHE* 5.4 4.5 - - + -
241D THR* 4.4 22.7 - - + -
242D ALA* 3.5 33.0 - - + -
285D SER* 4.1 16.8 - - - +
287D ILE* 4.3 1.1 - - + -
361D VAL* 3.1 37.2 + - + +
362D THR* 3.6 10.8 - - - +
363D ASP 3.3 0.2 - - - -
364D VAL* 1.3 74.9 - - + +
366D ILE* 1.3 66.7 + - - +
367D LYS 2.9 5.6 + - - -
368D ASN 4.5 0.2 - - - +
369D ASN* 3.0 32.1 + - + +
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Residues in contact with ILE 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LYS* 3.8 32.8 - - + +
216D LEU* 3.8 26.9 - - + -
362D THR* 3.0 21.3 + - - +
363D ASP* 3.8 15.7 - - - +
364D VAL 3.4 0.2 - - - -
365D ILE* 1.3 75.9 - - - +
367D LYS* 1.3 55.4 + - - +
369D ASN* 2.6 25.4 + - - +
370D LEU* 3.6 11.4 - - + +
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Residues in contact with LYS 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D ASP 3.2 16.3 + - - +
364D VAL* 3.6 5.8 - - - +
365D ILE 2.9 2.2 + - - -
366D ILE* 1.3 78.8 - - - +
368D ASN* 1.3 67.4 + - - +
369D ASN 3.1 5.6 + - - -
370D LEU* 3.2 24.2 + - - +
371D LYS* 4.7 2.8 - - - -
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Residues in contact with ASN 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D SER* 3.7 20.3 + - - +
340D GLU* 6.1 0.2 - - - +
342D TYR* 3.1 31.7 + - - -
364D VAL* 2.8 22.3 + - - +
365D ILE 4.6 0.2 - - - +
367D LYS* 1.3 76.4 - - - +
369D ASN* 1.3 59.0 + - - +
370D LEU 3.2 0.4 - - - -
371D LYS* 3.0 52.2 + - - +
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Residues in contact with ASN 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D THR* 5.6 7.9 - - + -
365D ILE* 3.0 19.0 + - + +
366D ILE* 2.6 38.4 + - - +
367D LYS 3.1 0.4 - - - -
368D ASN* 1.3 78.3 - - - +
370D LEU* 1.3 86.9 + - - +
371D LYS* 3.3 6.1 + - - +
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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
------------------------------------------------------------
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