Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 1Z00
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 ASN 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A THR* 3.6 9.0 - - - -
243A LYS* 5.1 9.7 + - - +
244A SER 3.3 8.0 + - - +
245A VAL* 1.3 78.0 + - - +
247A LYS* 1.4 92.4 + - - +
248A THR* 3.1 14.3 + - - +
249A ASP* 2.9 21.3 + - - +
250A SER* 3.0 10.6 + - - -
281A LYS* 5.3 0.6 - - - +
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A THR* 4.8 11.9 - - + -
240A THR* 4.0 4.4 - - + +
246A ASN* 1.4 103.1 + - - +
248A THR* 1.3 78.1 + - - +
250A SER* 3.1 11.9 + - - -
251A GLN* 3.0 30.3 + - - +
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Residues in contact with THR 248 (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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246A ASN* 4.0 10.5 + - - +
247A LYS* 1.3 91.0 + - + +
249A ASP* 1.3 53.4 + - - +
251A GLN* 3.0 32.5 - - - +
252A THR* 2.7 23.8 + - - +
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Residues in contact with ASP 249 (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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245A VAL* 3.2 31.6 - - + +
246A ASN 2.9 13.8 + - - +
248A THR* 1.3 77.8 - - - +
250A SER* 1.3 60.5 + - - +
252A THR* 3.0 10.7 + - - +
253A LEU* 2.8 57.2 + - - +
276A GLY 5.0 0.8 - - - +
277A LEU* 3.1 35.2 - - + +
281A LYS* 5.1 4.0 - - + +
285A LEU* 4.1 0.2 - - - +
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Residues in contact with SER 250 (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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236A THR* 3.5 27.2 + - - +
239A LEU* 3.5 21.7 - - - +
240A THR* 3.0 22.9 - - - +
245A VAL* 4.6 0.4 - - - +
246A ASN 3.0 14.8 + - - -
247A LYS* 3.2 9.5 - - - -
249A ASP* 1.3 76.2 - - - +
251A GLN* 1.3 57.7 + - - +
253A LEU 3.3 0.2 + - - -
254A LEU* 2.9 36.7 + - - +
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Residues in contact with GLN 251 (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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247A LYS* 3.0 17.4 + - - +
248A THR* 3.0 40.5 + - - +
250A SER* 1.3 75.5 - - - +
252A THR* 1.3 63.9 + - - +
254A LEU* 3.3 12.0 + - + +
255A THR* 3.1 26.1 + - - +
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Residues in contact with THR 252 (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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248A THR* 2.7 20.9 + - - +
249A ASP* 3.0 23.8 + - - +
251A GLN* 1.3 79.6 - - - +
253A LEU* 1.3 56.3 + - + +
255A THR* 3.1 10.3 - - - +
256A THR* 2.7 31.5 + - - -
274A CYS* 4.1 11.4 - - + -
275A PRO* 4.0 26.7 - - + -
276A GLY 4.3 19.5 + - - +
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Residues in contact with LEU 253 (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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239A LEU* 3.9 16.2 - - + -
249A ASP* 2.8 48.4 + - - +
252A THR* 1.3 72.1 - - + +
254A LEU* 1.3 60.4 + - - +
256A THR* 4.0 0.9 - - - -
257A PHE* 2.8 49.2 + - + +
258A GLY 3.6 2.4 + - - -
263A LEU* 3.6 26.1 - - + +
271A LEU* 4.2 4.0 - - + -
274A CYS* 3.6 28.9 - - + -
277A LEU* 3.9 10.1 - - + -
285A LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 254 (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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232A VAL* 4.3 21.1 - - + -
235A VAL* 3.9 11.4 - - + -
236A THR* 4.7 9.2 - - - +
239A LEU* 3.8 17.9 - - + -
250A SER 2.9 29.6 + - - +
251A GLN* 3.4 12.6 - - - +
252A THR 3.2 0.4 - - - -
253A LEU* 1.3 76.5 - - - +
255A THR* 1.3 58.1 + - - +
258A GLY* 3.0 27.9 + - - -
263A LEU* 5.3 0.4 - - + -
894B PHE* 3.3 43.0 - - + -
895B ALA* 3.9 6.8 - - + +
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Residues in contact with THR 255 (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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251A GLN 3.1 10.7 + - - +
252A THR* 3.1 20.0 - - - +
254A LEU* 1.3 78.8 - - - +
256A THR* 1.3 66.2 + - - +
257A PHE 4.9 1.0 - - - -
258A GLY* 5.4 0.2 - - - -
275A PRO* 4.8 9.2 - - + -
895B ALA* 5.4 4.0 - - - +
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Residues in contact with THR 256 (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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252A THR 2.7 22.1 + - - -
253A LEU 3.2 2.9 + - - -
255A THR* 1.3 81.9 - - - +
257A PHE* 1.3 76.8 + - + +
273A LEU* 4.8 8.7 - - + -
274A CYS* 3.5 29.8 - - + -
275A PRO* 3.1 24.8 - - + +
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Residues in contact with PHE 257 (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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253A LEU* 2.8 28.6 + - + -
254A LEU 4.0 0.2 - - - -
255A THR 4.9 0.7 - - - -
256A THR* 1.3 81.6 - - + +
258A GLY* 1.3 61.8 + - - +
259A SER 3.3 1.6 + - - -
262A GLN* 3.7 40.5 - - + +
263A LEU* 3.5 26.2 - - + -
266A ALA* 3.4 7.4 - - + -
270A ASP* 3.3 46.4 - - - -
271A LEU* 3.5 29.6 - - + -
274A CYS* 3.5 21.1 - - - -
893B SER* 5.4 0.9 - - - -
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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