Contacts of the helix formed by residues 251 - 255 (chain C) in PDB entry 6ACQ
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 ASP 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B SER* 5.8 1.4 - - - -
253B LYS 5.8 0.2 + - - -
255B ARG* 2.9 36.3 + - - -
246C TYR* 3.2 12.8 + - - -
249C THR* 3.1 17.8 + - - +
250C GLY* 1.3 77.7 - - - +
252C SER* 1.3 63.3 + - - +
253C LYS* 2.9 32.2 + - - +
254C TYR* 3.1 20.8 + - + -
252E SER* 4.1 4.9 + - - -
255E ARG* 4.2 19.1 + - - +
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TYR* 5.7 0.2 - - - -
250A GLY 2.9 21.3 + - - -
251A ASP* 4.0 2.5 + - - -
252A SER* 3.9 18.6 + - - -
251B ASP* 5.8 1.1 - - - -
246C TYR* 3.6 16.4 + - - -
251C ASP* 1.3 74.4 + - - +
253C LYS* 1.3 63.7 + - - +
254C TYR 3.0 0.4 - - - -
255C ARG* 2.9 38.7 + - - -
252E SER* 3.8 13.5 + - - -
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ASN* 4.3 17.0 - - - +
197B GLU* 3.1 31.0 + - - +
251B ASP* 5.9 0.2 + - - -
253B LYS* 3.2 70.1 + - + +
255B ARG* 4.2 14.4 + - - +
196C ASN* 5.7 0.2 + - - -
242C MET* 5.3 0.5 - - - +
251C ASP* 2.9 27.3 + - - +
252C SER* 1.3 78.2 - - - +
254C TYR* 1.3 84.5 + - + +
255C ARG* 3.6 3.5 + - - +
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 2.6 41.7 + - - -
189C ARG* 3.4 15.8 + - - -
193C PRO* 4.3 13.7 - - + -
242C MET* 3.3 20.3 - - + +
245C LEU* 3.7 35.2 - - + -
246C TYR* 3.6 14.0 - - - +
249C THR* 3.4 38.4 - - + -
251C ASP* 3.1 13.7 + - + +
252C SER 3.0 1.4 - - - -
253C LYS* 1.3 103.9 + - + +
255C ARG* 1.3 66.2 + - - +
256C PRO* 3.3 6.6 - - - +
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Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A THR 3.4 24.8 + - - +
250A GLY* 3.4 28.5 - - - +
251A ASP* 4.2 15.2 + - - +
251B ASP* 3.0 33.5 + - - -
253B LYS* 4.4 15.4 + - - +
196C ASN* 3.3 14.4 + - - -
246C TYR* 4.2 8.7 - - + -
251C ASP 4.4 0.6 + - - -
252C SER* 2.9 34.7 + - - +
253C LYS 3.4 2.7 - - - +
254C TYR* 1.3 77.3 - - - +
256C PRO* 1.3 72.4 - - + +
257C HIS* 4.5 0.8 - - - -
255F ARG* 4.0 15.6 - - - +
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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