Contacts of the helix formed by residues 317 - 331 (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 THR 317 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ILE* 3.7 6.7 - - - +
315D SER* 3.2 13.0 + - - -
316D ASN* 1.3 78.1 + - - +
318D TYR* 1.3 75.7 + - + +
319D GLU* 3.2 3.9 + - + +
320D GLU* 3.0 30.2 - - - +
321D ALA* 3.1 21.9 + - - +
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Residues in contact with TYR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D LEU* 5.1 0.4 - - + -
293D LYS* 3.9 20.3 - - + +
296D PHE* 3.7 26.5 - + - -
297D GLU* 3.4 41.1 - - + -
300D ILE* 3.0 20.3 - - + +
317D THR* 1.3 78.7 - - + +
319D GLU* 1.3 82.1 + - + +
322D ALA* 3.1 36.2 + - + +
345D PHE* 3.6 25.4 - + - +
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Residues in contact with GLU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D THR* 3.3 3.8 - - + +
318D TYR* 1.3 94.9 - - + +
320D GLU* 1.3 81.2 + - - +
322D ALA* 4.0 1.6 - - - +
323D ALA* 3.2 18.9 + - - +
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Residues in contact with GLU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D TYR* 3.7 10.5 - - - +
314D GLY* 5.7 0.7 - - - -
315D SER* 3.0 32.8 + - - +
317D THR* 3.0 40.9 - - - +
319D GLU* 1.3 89.4 - - - +
321D ALA* 1.3 63.3 + - - +
323D ALA* 2.9 19.3 + - - +
324D TYR* 3.1 5.7 + - - +
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Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D PHE* 3.8 18.2 - - + -
300D ILE* 4.2 9.0 - - + -
305D LEU* 3.5 25.6 - - + -
312D TYR* 3.3 15.0 + - + +
315D SER 4.5 3.4 - - - +
316D ASN* 5.3 0.2 - - - -
317D THR 3.1 16.0 + - - +
320D GLU* 1.3 74.7 - - - +
322D ALA* 1.3 55.7 + - - +
324D TYR* 2.7 25.6 + - - +
325D ILE* 3.0 15.2 + - - +
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D LEU* 5.3 2.0 - - + -
290D LEU* 4.7 0.3 - - - +
296D PHE* 4.1 12.8 - - + -
318D TYR* 3.1 36.6 + - + +
319D GLU 4.0 1.8 - - - +
321D ALA* 1.3 77.5 - - - +
323D ALA* 1.3 60.9 + - - +
325D ILE* 3.6 8.3 + - - +
326D GLN* 3.2 23.7 + - - +
345D PHE* 3.4 32.0 - - + -
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Residues in contact with ALA 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D GLU* 3.2 13.6 + - - +
320D GLU* 2.9 15.8 + - - +
322D ALA* 1.3 77.5 - - - +
324D TYR* 1.3 56.1 + - - +
326D GLN* 3.4 13.4 + - - +
327D CYS* 2.9 27.8 + - - +
345D PHE* 5.1 0.2 - - - -
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Residues in contact with TYR 324 (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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305D LEU* 4.2 9.2 - - + -
309D TYR* 4.1 24.0 - + - +
311D GLU* 4.2 21.0 + - - +
312D TYR* 3.5 55.3 - + + -
320D GLU 3.1 3.0 + - - +
321D ALA* 2.7 19.0 + - - +
323D ALA* 1.3 73.4 - - - +
325D ILE* 1.3 57.5 + - - -
327D CYS* 3.2 13.2 + - + +
328D GLN* 2.9 61.9 + - + +
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Residues in contact with ILE 325 (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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247D VAL* 6.1 0.7 - - + -
249D LEU* 4.1 24.0 - - + -
265D MET* 3.3 36.6 - - + -
290D LEU* 5.0 4.9 - - + -
296D PHE* 4.0 28.9 - - + -
305D LEU* 4.1 14.4 - - + -
309D TYR* 4.1 15.5 - - + +
321D ALA 3.0 8.8 + - - +
322D ALA* 4.1 5.6 - - - +
324D TYR* 1.3 73.4 - - - +
326D GLN* 1.3 66.6 + - - +
328D GLN* 3.4 6.7 + - - +
329D PHE* 3.2 40.8 + - + -
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Residues in contact with GLN 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU* 5.4 0.6 - - - +
290D LEU* 4.1 14.3 - - + +
322D ALA 3.2 17.8 + - - +
323D ALA* 3.5 9.5 - - - +
325D ILE* 1.3 76.4 - - - +
327D CYS* 1.3 62.6 + - - +
329D PHE* 3.4 5.3 + - - +
330D GLU* 3.2 37.1 + - - +
343D THR* 3.0 43.1 + - + +
345D PHE* 3.2 24.9 - - - -
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Residues in contact with CYS 327 (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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323D ALA 2.9 15.0 + - - +
324D TYR* 3.2 19.0 + - + +
326D GLN* 1.3 79.1 - - - +
328D GLN* 1.3 72.6 + - - +
330D GLU* 3.4 4.9 + - - +
331D ASP* 3.2 25.6 + - - +
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Residues in contact with GLN 328 (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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269D MET* 3.8 30.6 - - + +
309D TYR* 4.4 19.2 - - + +
324D TYR* 2.9 57.3 + - + +
325D ILE* 3.8 7.4 - - - +
326D GLN 3.4 0.2 - - - -
327D CYS* 1.3 84.1 + - - +
329D PHE* 1.3 62.1 + - + +
331D ASP* 4.1 13.2 + - - +
332D LEU* 3.5 19.4 - - - +
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Residues in contact with PHE 329 (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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247D VAL* 4.0 23.1 - - + -
265D MET* 4.4 10.5 - - - -
268D SER* 3.6 43.3 - - - -
269D MET* 3.8 25.1 - - + -
272D PHE* 3.2 48.8 - + + -
288D LEU* 3.8 26.9 - - + -
290D LEU* 5.2 4.3 - - + -
309D TYR* 4.5 1.6 - - - -
325D ILE* 3.2 41.6 + - + +
326D GLN* 3.8 4.0 - - - +
327D CYS 3.2 1.0 - - - -
328D GLN* 1.3 78.1 - - + +
330D GLU* 1.3 64.1 + - - +
331D ASP 3.1 1.8 - - - -
332D LEU* 3.3 14.4 + - + +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU* 5.2 1.8 - - + -
326D GLN* 3.2 30.9 + - + +
327D CYS* 3.4 4.4 + - - +
329D PHE* 1.3 75.5 - - + +
331D ASP* 1.3 63.9 + - - +
333D ASN* 3.4 20.1 - - - +
336D LYS* 4.6 6.8 - - - +
340D GLU* 4.9 3.6 - - - +
341D ILE* 3.5 41.6 + - + +
343D THR* 3.3 24.7 + - - +
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Residues in contact with ASP 331 (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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327D CYS* 3.2 19.1 + - - +
328D GLN* 4.1 12.5 + - - +
329D PHE 3.1 0.8 - - - -
330D GLU* 1.3 74.4 - - - +
332D LEU* 1.3 62.6 + - - +
333D ASN 2.7 24.5 + - - +
336D LYS* 4.4 17.2 + - - +
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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