Contacts of the helix formed by residues 223 - 230 (chain C) in PDB entry 3B4M
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 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C ALA* 3.8 21.3 - - + +
172C ARG* 3.7 38.7 - - + +
221C SER 3.9 7.7 + - - -
222C ASP* 1.3 76.4 + - + +
224C GLU* 1.3 64.7 + - + +
225C SER 3.1 2.1 + - - -
226C VAL* 3.4 19.4 + - - +
227C ARG* 4.2 3.6 + - - +
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Residues in contact with GLU 224 (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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222C ASP* 3.8 25.8 - - + +
223C LYS* 1.3 81.8 - - + +
225C SER* 1.3 70.4 + - - +
227C ARG* 3.2 19.9 + - - +
228C THR* 3.1 13.5 + - - +
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Residues in contact with SER 225 (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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195C CYS* 3.0 21.3 + - - +
196C GLY* 3.5 10.4 - - - -
197C SER 4.6 1.0 + - - -
220C PHE* 3.6 25.2 - - - +
222C ASP* 3.0 21.6 + - - +
224C GLU* 1.3 85.5 + - - +
226C VAL* 1.3 53.7 + - - +
228C THR* 3.1 12.0 + - - -
229C SER* 2.8 36.4 + - - -
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Residues in contact with VAL 226 (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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171C ALA 4.6 4.5 - - - +
172C ARG* 3.4 39.0 - - - +
173C SER 4.0 7.0 - - - +
174C ILE* 3.8 17.2 - - + +
220C PHE* 3.9 3.1 - - + -
223C LYS* 3.4 14.5 + - - +
224C GLU 3.2 0.2 - - - -
225C SER* 1.3 76.5 - - - +
227C ARG* 1.3 67.0 + - + +
229C SER* 2.5 25.6 + - - -
230C LEU* 3.0 11.5 + - + +
246C PRO* 4.2 28.7 - - + -
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Residues in contact with ARG 227 (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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223C LYS 5.2 3.1 - - - +
224C GLU* 3.2 13.6 + - - +
226C VAL* 1.3 77.3 - - + +
228C THR* 1.3 67.1 + - - +
230C LEU* 3.5 30.8 - - + +
231C ALA* 4.2 1.9 + - - +
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Residues in contact with THR 228 (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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194C GLY 5.0 3.4 - - - +
195C CYS* 3.7 26.5 + - - +
224C GLU* 3.1 15.8 + - - +
225C SER* 3.1 12.0 + - - -
227C ARG* 1.3 77.1 - - - +
229C SER* 1.3 63.5 + - - +
231C ALA* 3.3 22.0 + - - +
232C LEU* 5.4 0.3 - - - +
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Residues in contact with SER 229 (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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174C ILE* 3.2 36.4 - - - +
192C PHE* 4.1 3.4 - - - -
195C CYS* 3.6 18.6 - - - +
220C PHE* 3.3 13.3 - - - -
225C SER 2.8 17.2 + - - -
226C VAL* 2.5 22.7 + - - -
228C THR* 1.3 68.0 - - - +
230C LEU* 1.3 49.5 + - - +
231C ALA 2.8 5.3 + - - -
232C LEU* 2.7 35.9 + - - +
244C VAL* 3.9 6.5 - - - +
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Residues in contact with LEU 230 (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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174C ILE* 5.0 0.7 - - + -
226C VAL* 3.0 21.4 + - + +
227C ARG* 3.5 26.9 - - + +
228C THR 3.4 0.2 - - - -
229C SER* 1.3 74.6 + - - +
231C ALA* 1.3 60.0 + - - +
232C LEU 3.2 0.4 - - - -
233C ASP* 3.3 21.0 + - - +
244C VAL* 3.9 14.3 - - + +
245C ILE* 3.7 15.9 - - - -
246C PRO* 3.6 39.7 - - + -
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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