Contacts of the helix formed by residues 246 - 258 (chain A) in PDB entry 1WLZ
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 HIS 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ALA* 2.8 27.6 + - + +
243A VAL 3.6 2.7 - - - -
245A SER* 1.3 94.4 + - - +
247A TYR* 1.3 59.6 + - - +
248A HIS 3.4 2.4 + - - -
249A ALA* 3.4 7.4 + - + +
250A ILE* 2.9 35.1 + - + +
277A ARG* 3.6 37.7 + - - +
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Residues in contact with TYR 247 (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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243A VAL* 2.9 26.2 + - + +
244A THR* 3.8 9.8 + - - +
245A SER 3.6 1.8 - - - -
246A HIS* 1.3 77.5 - - - +
248A HIS* 1.3 78.1 + + + +
250A ILE* 4.1 3.3 - - - +
251A THR* 2.9 49.8 + - + +
307A LEU* 3.9 30.3 - - + +
308A SER* 5.3 0.3 + - - -
311A SER* 3.5 33.4 + - - -
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Residues in contact with HIS 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 HIS 3.4 1.0 - - - -
247A TYR* 1.3 94.6 - + + +
249A ALA* 1.3 63.5 + - - +
251A THR* 3.5 3.6 + - - -
252A GLN* 3.2 28.3 + - + +
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Residues in contact with ALA 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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246A HIS* 3.4 10.5 + - + +
248A HIS* 1.3 76.1 - - - +
250A ILE* 1.3 66.1 + - - +
252A GLN* 3.2 7.5 + - - +
253A GLU* 3.0 27.6 + - - +
277A ARG* 3.6 25.4 - - - +
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Residues in contact with ILE 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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239A LEU* 6.4 0.4 - - + -
242A ALA* 3.6 28.0 - - + +
243A VAL* 3.9 16.2 - - + -
246A HIS* 2.9 22.4 + - + +
247A TYR* 4.1 3.6 - - - +
249A ALA* 1.3 72.8 - - - +
251A THR* 1.3 67.7 + - - +
253A GLU* 3.1 11.5 + - - +
254A PHE* 3.1 46.9 + - + -
273A ILE* 4.5 12.3 - - + -
277A ARG* 3.9 36.8 - - + +
306A PHE* 5.1 4.7 - - + -
307A LEU* 4.5 6.7 - - + -
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Residues in contact with THR 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 TYR* 2.9 46.8 + - + +
248A HIS* 3.8 4.9 - - - -
250A ILE* 1.3 77.9 - - - +
252A GLN* 1.3 69.8 + - - +
254A PHE* 3.3 13.8 + - + +
255A GLU* 3.0 35.1 + - + +
303A TYR* 5.2 1.1 - - + -
307A LEU* 3.7 22.5 - - + +
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Residues in contact with GLN 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 HIS 3.2 14.6 + - - +
249A ALA* 3.7 9.4 - - - +
250A ILE 3.2 0.8 - - - -
251A THR* 1.3 82.9 - - - +
253A GLU* 1.3 61.0 + - - +
255A GLU* 3.5 23.7 - - - +
256A ASN* 2.9 43.9 + - - +
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Residues in contact with GLU 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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249A ALA* 3.0 15.6 + - + +
250A ILE* 3.1 18.2 + - - +
252A GLN* 1.3 76.2 - - - +
254A PHE* 1.3 63.1 + - - +
256A ASN* 3.4 6.2 + - - +
257A PHE* 3.0 37.8 + - + -
273A ILE* 3.7 30.4 - - + +
276A ARG* 4.6 11.7 - - - +
277A ARG* 3.1 39.9 + - - +
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Residues in contact with PHE 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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250A ILE* 3.1 40.8 + - + -
251A THR 3.4 5.4 - - - +
253A GLU* 1.3 77.6 - - - +
255A GLU* 1.3 56.7 + - - +
257A PHE* 3.1 2.0 + - - -
258A ASP* 2.8 32.7 + - - +
265A ILE* 3.3 40.5 - - + +
270A PHE* 4.2 6.1 - + - -
273A ILE* 3.7 12.3 - - + -
301A LEU* 3.7 15.7 - - + -
303A TYR* 3.7 34.3 - + + -
306A PHE* 3.7 27.1 - + - -
307A LEU* 3.7 29.8 - - + -
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Residues in contact with GLU 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 THR* 3.0 26.6 + - + +
252A GLN* 3.3 33.2 + - - +
254A PHE* 1.3 76.9 - - - +
256A ASN* 1.3 65.0 + - - +
258A ASP 3.3 9.2 + - - +
261A LYS* 3.1 48.5 + - - +
263A ASN* 5.1 2.3 - - - +
303A TYR* 3.4 25.8 + - - -
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Residues in contact with ASN 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 GLN* 2.9 29.5 + - - +
253A GLU* 3.8 6.1 - - - +
255A GLU* 1.3 78.3 + - - +
257A PHE* 1.3 67.0 + - + +
259A THR* 3.7 16.1 + - - +
261A LYS* 5.1 2.8 + - - +
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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 GLU* 3.0 29.9 + - + +
254A PHE 3.1 0.2 + - - -
256A ASN* 1.3 77.3 - - + +
258A ASP* 1.3 57.1 + - - +
259A THR* 2.9 18.0 + - - +
264A THR 5.0 0.2 - - - +
265A ILE* 3.6 13.9 - - + -
269A GLU* 3.5 49.5 - - + +
272A ALA* 4.8 2.9 - - + -
273A ILE* 3.9 32.5 - - + -
300A ARG* 5.1 3.5 + - - -
280C ILE* 3.4 33.4 - - + -
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Residues in contact with ASP 258 (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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254A PHE 2.8 17.0 + - - +
255A GLU 3.6 6.3 - - - +
256A ASN 3.2 0.2 - - - -
257A PHE* 1.3 73.9 - - - +
259A THR* 1.3 57.2 + - - +
260A MET* 3.9 1.7 + - - +
261A LYS* 2.9 45.1 + - + +
262A THR* 2.8 24.8 + - - -
263A ASN* 2.7 19.7 + - - +
264A THR 3.4 25.8 - - - +
265A ILE* 4.0 0.2 - - - +
300A ARG* 4.9 2.6 + - - +
303A TYR* 2.7 25.4 + - + +
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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