Contacts of the helix formed by residues 247 - 255 (chain A) in PDB entry 1AKZ
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 SER 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLY* 1.3 68.5 - - - -
248A TYR* 1.3 67.2 + - - +
250A GLN* 3.2 8.5 + - - +
251A LYS* 3.0 51.5 + - - +
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Residues in contact with TYR 248 (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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143A GLY 4.2 5.2 - - - -
144A GLN* 3.5 55.9 - - + +
205A ALA* 3.4 34.6 - - + +
206A VAL* 4.6 3.4 - - + +
223A GLU* 3.6 22.9 + - - +
246A GLY 3.5 0.2 - - - -
247A SER* 1.3 79.3 - - - +
249A ALA* 1.3 61.2 + - - +
251A LYS* 3.3 9.7 + - + +
252A LYS* 2.9 37.2 + - + +
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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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142A LEU* 3.7 31.7 - - + +
143A GLY* 5.7 0.7 - - - -
244A LEU* 3.6 12.4 - - - +
245A TRP 3.6 33.6 + - - +
246A GLY 3.6 1.0 + - - -
247A SER 3.3 0.4 - - - -
248A TYR* 1.3 82.2 - - + +
250A GLN* 1.3 58.4 + - - +
252A LYS* 3.4 6.2 + - - +
253A GLY* 2.8 27.7 + - - -
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Residues in contact with GLN 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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244A LEU* 3.6 19.3 + - + +
246A GLY* 3.1 22.7 + - - +
247A SER* 3.7 7.6 - - - +
249A ALA* 1.3 75.9 - - - +
251A LYS* 1.3 60.8 + - + +
253A GLY 3.5 2.1 + - - -
254A SER* 3.2 22.0 + - - -
258A ARG* 5.8 0.3 + - - -
265A GLN* 3.5 31.2 + - - +
266A THR* 3.1 40.8 + - - +
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Residues in contact with LYS 251 (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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247A SER* 3.0 39.5 + - - +
248A TYR* 3.3 7.4 + - + +
250A GLN* 1.3 74.8 - - + +
252A LYS* 1.3 63.9 + - - +
254A SER* 2.7 29.2 + - - -
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Residues in contact with LYS 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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142A LEU* 4.2 25.4 - - + -
143A GLY 5.1 0.7 - - - +
203A LEU* 5.5 0.2 - - - -
204A ASN 5.6 0.2 - - - -
205A ALA* 3.8 26.0 - - + +
223A GLU* 3.6 10.7 + - - +
226A THR* 2.8 42.7 + - - -
227A ASP* 2.9 34.8 + - - +
230A VAL* 4.4 19.4 - - + +
248A TYR* 2.9 26.2 + - + +
249A ALA* 3.9 4.9 - - - +
251A LYS* 1.3 78.0 - - - +
253A GLY* 1.3 58.7 + - - +
254A SER 3.3 1.1 + - - -
255A ALA* 4.3 7.3 + - - +
256A ILE* 5.5 0.2 - - - +
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Residues in contact with GLY 253 (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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142A LEU* 4.3 3.3 - - - +
230A VAL* 5.5 0.7 - - - -
244A LEU* 3.9 15.3 - - - +
249A ALA 2.8 17.4 + - - -
250A GLN 3.7 3.6 - - - -
252A LYS* 1.3 75.1 - - - +
254A SER* 1.3 62.4 + - - +
255A ALA 3.1 4.4 + - - -
256A ILE* 3.2 40.2 + - - +
258A ARG* 4.6 5.2 + - - -
263A VAL* 5.4 0.2 - - - +
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Residues in contact with SER 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 GLN 3.2 10.3 + - - -
251A LYS* 2.7 22.9 + - - -
252A LYS 3.3 0.6 + - - -
253A GLY* 1.3 77.2 - - - +
255A ALA* 1.3 61.0 + - - +
256A ILE 3.4 4.4 + - - +
258A ARG* 5.0 12.5 + - - +
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Residues in contact with ALA 255 (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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230A VAL* 6.3 2.7 - - + -
234A ASN* 3.4 16.0 + - - +
252A LYS 4.3 6.2 + - - +
253A GLY* 3.1 1.8 - - - -
254A SER* 1.3 79.3 + - - +
256A ILE* 1.3 66.0 + - - +
257A ASP* 3.4 1.2 + - - +
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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