Contacts of the helix formed by residues 350 - 368 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLN* 3.7 0.9 - - - -
194A GLN* 5.0 5.2 - - - +
347A CYS* 2.7 30.4 + - + +
349A THR* 1.3 72.9 + - - +
351A THR* 1.3 63.4 + - - +
352A LYS* 3.0 19.4 + - - +
353A ASN* 2.9 28.9 + - + -
354A VAL* 3.0 25.1 + - - +
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Residues in contact with THR 351 (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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67A GLN* 3.1 28.8 + - - +
70A ILE* 4.7 7.9 - - + +
71A ILE* 3.6 23.8 - - + -
193A GLN* 3.9 25.6 + - - +
197A LEU* 4.2 3.5 - - - +
349A THR 3.5 3.1 + - - -
350A ASP* 1.3 71.5 + - - +
352A LYS* 1.3 68.4 + - + +
354A VAL* 2.9 5.5 + - - +
355A GLN* 2.9 25.7 + - - +
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Residues in contact with LYS 352 (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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350A ASP* 3.0 11.6 + - - +
351A THR* 1.3 78.0 - - + +
353A ASN* 1.3 62.1 + - - +
355A GLN* 3.4 10.9 + - - +
356A PHE* 3.1 22.9 + - - +
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Residues in contact with ASN 353 (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 LYS* 5.5 3.9 - - - +
345A PHE 4.3 6.6 + - - -
346A THR* 3.3 6.9 - - - -
347A CYS* 2.7 37.9 + - + +
350A ASP* 2.9 26.9 + - + +
352A LYS* 1.3 73.4 - - - +
354A VAL* 1.3 66.6 + - - +
356A PHE* 3.2 9.2 + - - +
357A VAL* 3.0 41.0 + - - +
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Residues in contact with VAL 354 (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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64A PHE* 4.3 20.0 - - + -
67A GLN* 3.5 28.9 - - + -
68A MET* 3.6 18.2 - - + -
71A ILE* 4.9 1.8 - - + -
346A THR* 5.6 1.6 - - - -
347A CYS 3.8 3.6 - - - +
348A ALA* 3.4 33.7 - - - +
350A ASP 3.0 15.9 - - - +
351A THR* 2.9 7.3 + - + +
353A ASN* 1.3 77.7 - - - +
355A GLN* 1.3 56.1 + - - +
357A VAL* 4.2 4.4 - - - +
358A PHE* 3.0 29.5 + - + +
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Residues in contact with GLN 355 (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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71A ILE* 4.3 39.7 - - + +
72A HIS* 5.6 3.3 + - - +
351A THR* 2.9 18.7 + - - +
352A LYS* 3.8 9.3 - - - +
353A ASN 3.2 0.2 - - - -
354A VAL* 1.3 74.5 - - - +
356A PHE* 1.3 66.2 + - - +
358A PHE* 4.3 1.5 - - - +
359A ASP* 3.4 23.5 + - - +
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Residues in contact with PHE 356 (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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344A HIS* 5.8 5.4 - + - -
352A LYS 3.1 16.2 + - - +
353A ASN* 3.2 9.6 + - - +
355A GLN* 1.3 77.9 - - - +
357A VAL* 1.3 75.7 + - + +
359A ASP* 3.2 16.1 + - + +
360A ALA* 3.3 18.1 + - + +
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Residues in contact with VAL 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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289A PHE* 3.3 35.2 - - + -
344A HIS* 3.8 22.2 - - + +
345A PHE 4.5 3.6 - - - +
346A THR* 3.5 22.4 - - + -
353A ASN* 3.0 35.3 + - - +
354A VAL* 4.2 3.1 - - - +
356A PHE* 1.3 84.7 - - + +
358A PHE* 1.3 60.3 + - - +
360A ALA* 3.3 8.5 + - - +
361A VAL* 3.1 20.6 + - - +
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Residues in contact with PHE 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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51A LEU* 4.7 9.4 - - + -
68A MET* 4.0 23.3 - - + -
71A ILE* 4.8 0.4 - - + -
72A HIS* 3.4 36.1 - + - -
211A PHE* 4.2 14.6 - + - -
213A PHE* 3.6 21.5 - + - -
218A PHE* 4.3 14.4 - + - -
220A MET* 3.9 20.9 - - + -
244A ILE* 4.8 9.2 - - + -
289A PHE* 5.4 4.9 - + + -
354A VAL* 3.0 21.0 + - + +
355A GLN* 4.3 4.0 - - - +
356A PHE 3.3 0.2 - - - -
357A VAL* 1.3 76.4 - - - +
359A ASP* 1.3 59.6 + - - +
361A VAL* 3.3 14.8 + - + +
362A THR* 2.9 39.7 + - - -
365A ILE* 6.1 0.2 - - + -
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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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213A PHE* 3.8 18.0 - - + -
214A LYS* 2.7 38.8 + - - -
355A GLN* 3.4 15.7 + - - +
356A PHE* 3.2 12.2 + - + +
358A PHE* 1.3 79.4 - - - +
360A ALA* 1.3 61.2 + - - +
362A THR* 3.7 2.9 + - - -
363A ASP* 3.2 26.5 + - - +
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Residues in contact with ALA 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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344A HIS* 4.1 25.0 + - + +
356A PHE* 3.3 15.5 + - + +
357A VAL* 3.3 9.6 + - - +
358A PHE 3.2 0.2 - - - -
359A ASP* 1.3 78.1 - - - +
361A VAL* 1.3 59.2 + - - +
363A ASP* 3.9 10.0 + - - +
364A VAL* 3.2 27.5 + - - +
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Residues in contact with VAL 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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51A LEU* 5.2 0.4 - - + -
244A ILE* 4.5 10.3 - - + -
287A ILE* 3.4 36.6 - - + -
289A PHE* 3.6 32.1 - - + -
344A HIS* 4.6 5.4 - - + -
357A VAL* 3.1 16.8 - - + +
358A PHE* 3.5 17.9 - - + +
359A ASP 3.2 0.4 - - - -
360A ALA* 1.3 78.2 - - - +
362A THR* 1.3 59.2 + - - +
364A VAL* 3.3 8.5 + - - +
365A ILE* 3.1 34.4 + - + +
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Residues in contact with THR 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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213A PHE* 3.3 23.8 - - + -
214A LYS* 3.5 28.7 - - + -
216A LEU* 4.4 5.2 - - + -
218A PHE* 4.0 19.8 - - + -
358A PHE* 2.9 26.0 + - - -
359A ASP 4.0 4.3 - - - -
360A ALA 3.4 0.2 - - - -
361A VAL* 1.3 75.4 - - - +
363A ASP* 1.3 63.7 + - - +
364A VAL 3.1 0.7 - - - -
365A ILE* 3.3 8.8 + - - +
366A ILE* 3.1 32.7 + - + +
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Residues in contact with ASP 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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214A LYS* 2.8 27.0 + - - +
359A ASP* 3.2 17.7 + - - +
360A ALA* 4.1 9.1 - - - +
361A VAL 3.3 0.4 - - - -
362A THR* 1.3 77.1 - - - +
364A VAL* 1.3 59.8 + - + +
366A ILE* 4.0 8.8 - - - +
367A LYS* 3.0 39.5 + - + +
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Residues in contact with VAL 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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285A SER* 5.0 5.2 - - - -
287A ILE* 5.5 4.7 - - + -
342A TYR* 3.5 58.3 - - + +
344A HIS* 6.2 1.1 - - - +
360A ALA 3.2 18.2 - - - +
361A VAL* 3.3 11.2 + - + +
362A THR 3.1 0.6 - - - -
363A ASP* 1.3 77.6 - - + +
365A ILE* 1.3 68.6 + - + +
367A LYS* 3.3 8.0 + - + -
368A ASN* 3.1 28.4 + - - +
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Residues in contact with ILE 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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49A VAL* 4.4 14.4 - - + -
51A LEU* 4.5 5.2 - - + -
216A LEU* 5.1 5.8 - - + -
218A PHE* 4.1 25.1 - - + -
241A THR* 3.8 27.6 - - + +
242A ALA* 4.0 24.9 - - + -
285A SER* 4.7 10.1 - - - +
287A ILE* 4.9 2.9 - - + -
358A PHE* 6.1 0.2 - - + -
361A VAL* 3.1 28.7 + - + +
362A THR* 3.3 11.4 + - + +
364A VAL* 1.3 78.2 - - + +
366A ILE* 1.3 62.1 + - + +
368A ASN 3.5 0.5 + - - -
369A ASN* 3.2 26.5 + - + +
370A LEU* 4.4 1.7 - - + +
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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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214A LYS* 4.7 15.3 - - + +
216A LEU* 3.9 23.6 - - + -
362A THR* 3.1 31.1 + - + +
363A ASP* 4.0 11.0 - - - +
365A ILE* 1.3 74.9 - - - +
367A LYS* 1.3 69.9 + - + +
370A LEU* 3.0 51.3 + - + +
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Residues in contact with LYS 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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363A ASP* 3.0 27.6 + - + +
364A VAL* 3.3 8.3 + - + +
366A ILE* 1.3 80.2 - - + +
368A ASN* 1.3 65.4 + - - +
369A ASN 3.3 0.7 - - - -
370A LEU 5.6 0.4 - - - -
371A LYS* 3.5 28.3 - - + +
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Residues in contact with ASN 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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285A SER* 3.9 24.1 + - - +
342A TYR* 2.6 35.9 + - - -
364A VAL* 3.1 21.5 + - - +
365A ILE 3.5 2.2 + - - +
366A ILE 3.2 0.2 - - - -
367A LYS* 1.3 83.5 - - - +
369A ASN* 1.3 68.6 + - - +
371A LYS* 5.5 0.7 - - - -
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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