Contacts of the helix formed by residues 292 - 303 (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 LYS 292 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D GLU* 3.2 36.2 + - - -
59D SER 3.3 23.3 - - - +
172D GLU* 4.4 3.2 + - - -
248D ALA* 3.4 23.1 - - + +
249D LEU* 3.6 3.3 - - - +
250D SER* 3.4 17.4 + - - +
251D ASP* 5.5 1.6 + - - -
291D ASN* 1.3 75.2 + - - +
293D LYS* 1.3 62.3 + - - +
294D ASP* 3.3 7.4 - - - -
295D LEU* 3.8 24.7 - - + +
296D PHE* 3.0 25.6 + - - +
346D THR 3.7 1.2 + - - -
476D GDP 3.0 53.4 + - + -
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Residues in contact with LYS 293 (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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249D LEU* 3.9 17.0 - - + -
290D LEU 4.6 1.3 - - - +
291D ASN 3.4 1.4 - - - -
292D LYS* 1.3 74.9 - - - +
294D ASP* 1.3 69.3 + - - +
296D PHE* 3.2 1.9 + - - +
297D GLU* 2.8 49.5 + - - +
318D TYR* 3.9 24.7 - - + +
345D PHE* 3.6 17.7 - - + +
346D THR 3.3 11.5 + - - +
347D CYS* 3.1 27.9 - - + +
350D ASP* 5.1 4.4 - - - +
353D ASN* 3.5 31.7 + - - +
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Residues in contact with ASP 294 (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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292D LYS 3.6 0.7 - - - -
293D LYS* 1.3 85.7 + - + +
295D LEU* 1.3 75.1 + - - +
297D GLU* 3.2 22.0 + - - +
298D GLU* 3.2 24.3 - - - +
347D CYS* 3.1 30.3 - - - -
349D THR* 4.7 1.4 + - - -
476D GDP 3.5 29.8 + - - -
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Residues in contact with LEU 295 (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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172D GLU* 4.0 27.1 - - + -
250D SER* 3.3 19.7 - - - +
292D LYS* 3.7 31.4 + - + +
293D LYS 3.3 0.2 - - - -
294D ASP* 1.3 88.9 + - - +
296D PHE* 1.3 65.2 + - - +
298D GLU* 3.2 7.0 + - - +
299D LYS* 2.9 22.2 + - + +
476D GDP 3.8 26.5 - - + +
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Residues in contact with PHE 296 (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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249D LEU* 3.7 30.7 - - + -
250D SER* 3.6 8.0 - - - +
252D TYR* 3.5 35.0 - + - -
292D LYS 3.0 20.8 + - - +
293D LYS 3.2 3.8 + - - +
295D LEU* 1.3 78.2 - - - +
297D GLU* 1.3 60.9 + - - +
299D LYS* 3.0 11.2 + - - +
300D ILE* 3.0 45.1 + - + +
305D LEU* 5.2 1.8 - - + -
318D TYR* 3.7 31.0 - + - -
321D ALA* 3.8 15.3 - - + -
322D ALA* 4.1 17.0 - - + -
325D ILE* 4.0 19.1 - - + -
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Residues in contact with GLU 297 (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* 2.8 39.9 + - - +
294D ASP* 3.3 18.1 - - - +
295D LEU 3.2 0.2 - - - -
296D PHE* 1.3 72.7 - - - +
298D GLU* 1.3 69.1 + - - +
300D ILE* 3.1 30.0 - - - +
301D LYS* 4.0 9.0 - - - +
318D TYR* 3.4 38.0 - - + -
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Residues in contact with GLU 298 (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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294D ASP* 3.2 19.9 + - - +
295D LEU* 3.2 8.3 + - - +
297D GLU* 1.3 90.3 - - - +
299D LYS* 1.3 64.2 + - - +
300D ILE 3.6 0.2 - - - -
301D LYS* 3.2 47.1 + - + +
302D LYS* 4.4 1.2 + - - +
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Residues in contact with LYS 299 (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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165D ARG* 5.2 17.0 - - - +
166D ARG* 5.9 2.5 - - - -
250D SER* 3.7 30.4 + - - -
252D TYR* 3.5 24.0 + - + +
253D ASP* 3.1 32.8 + - - +
254D GLN* 4.6 11.5 - - - +
295D LEU* 2.9 17.8 + - + +
296D PHE* 3.0 12.1 + - - +
298D GLU* 1.3 74.8 - - - +
300D ILE* 1.3 60.5 + - - +
301D LYS 2.7 11.0 + - - -
302D LYS* 3.2 12.0 + - - +
303D SER* 3.4 15.8 + - - +
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Residues in contact with ILE 300 (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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252D TYR* 3.5 10.9 + - + +
296D PHE* 3.0 45.2 + - + +
297D GLU* 3.1 19.7 - - - +
299D LYS* 1.3 71.5 - - - +
301D LYS* 1.3 64.1 + - + +
302D LYS 4.3 0.9 - - - +
303D SER 3.9 8.9 - - - +
304D PRO* 4.8 0.5 - - - +
305D LEU* 5.1 7.6 - - + +
316D ASN* 4.1 34.6 - - + +
317D THR* 3.7 2.7 - - - -
318D TYR* 3.0 46.4 - - + +
321D ALA* 4.2 13.2 - - + -
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Residues in contact with LYS 301 (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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297D GLU 4.0 6.5 + - - +
298D GLU* 3.2 55.4 + - + +
299D LYS 2.7 1.4 + - - -
300D ILE* 1.3 84.2 - - + +
302D LYS* 1.3 61.5 + - + +
316D ASN* 5.6 0.8 - - - +
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Residues in contact with LYS 302 (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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306A THR* 6.1 1.5 - - - -
310A PRO* 3.3 52.4 - - + +
163D ASP 4.8 13.4 + - - -
164D ARG* 6.1 0.8 - - - +
166D ARG* 5.0 15.2 - - - +
298D GLU 4.4 0.8 + - - +
299D LYS 3.2 3.9 + - - +
300D ILE 4.4 0.2 - - - +
301D LYS* 1.3 83.0 - - + +
303D SER* 1.3 79.0 + - - +
304D PRO* 3.0 15.8 - - - +
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Residues in contact with SER 303 (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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166D ARG* 4.5 4.6 + - - +
252D TYR* 2.6 29.2 + - - -
253D ASP* 3.6 25.9 + - - +
299D LYS* 3.4 13.4 + - - +
300D ILE* 3.9 4.5 - - - -
302D LYS* 1.3 95.6 + - - +
304D PRO* 1.3 60.9 - - - +
307D ILE* 3.1 29.3 - - - +
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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