Contacts of the helix formed by residues 218 - 224 (chain C) in PDB entry 1U8R
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 PRO 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C LEU* 5.7 0.9 - - + -
204C GLY* 4.3 2.9 - - - -
216C THR 4.1 5.4 - - - +
217C LEU* 1.3 87.1 - - + +
219C HIS* 1.3 67.5 + - - +
220C GLU* 3.2 18.6 + - + +
221C MET* 3.3 21.5 + - + -
222C ALA* 2.9 20.1 + - - +
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Residues in contact with HIS 219 (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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155C THR* 3.8 15.5 - - + +
202C GLY 4.5 5.5 + - - +
203C GLY* 3.5 32.0 + - - +
204C GLY* 4.0 5.3 - - - +
218C PRO* 1.3 72.4 - - - +
220C GLU* 1.3 65.8 + - - +
222C ALA* 3.3 6.2 + - - +
223C HIS* 3.0 34.4 + + - -
3003C CO 1.8 31.8 + - - -
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Residues in contact with GLU 220 (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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21C GLU* 4.7 1.6 - - - +
33C ARG* 5.1 3.8 + - - +
173C HIS* 3.4 32.8 + - - +
218C PRO* 4.2 13.4 - - + +
219C HIS* 1.3 81.5 - - - +
221C MET* 1.3 87.0 + - + +
223C HIS* 2.9 28.3 + - - +
224C ALA* 3.6 1.7 + - - +
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Residues in contact with MET 221 (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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173C HIS* 3.7 25.8 - - + +
174C VAL* 3.2 52.5 - - + +
177C ASP* 5.2 8.7 - - + +
180C LEU* 3.5 17.5 - - + -
217C LEU* 4.0 12.6 - - + -
218C PRO* 3.3 30.0 + - + +
220C GLU* 1.3 93.1 - - + +
222C ALA* 1.3 53.9 + - - +
224C ALA* 2.7 33.1 + - - +
225C VAL* 3.8 6.4 + - + +
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Residues in contact with ALA 222 (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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153C ARG* 4.0 2.4 - - - +
154C LEU* 3.6 34.6 - - + +
155C THR* 3.7 12.8 - - + -
203C GLY 5.3 0.9 - - - +
205C VAL* 4.3 20.9 - - + +
217C LEU* 4.3 6.0 - - + +
218C PRO 2.9 14.1 + - - +
219C HIS* 3.3 13.9 - - - +
221C MET* 1.3 76.6 - - - +
223C HIS* 1.3 61.3 + - - +
224C ALA 2.8 1.6 + - - -
225C VAL 3.1 12.7 + - - +
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Residues in contact with HIS 223 (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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21C GLU* 3.1 31.9 + - + +
22C GLY 4.0 14.4 - - - -
23C VAL* 3.7 21.9 - - + +
153C ARG* 2.9 29.9 + - - +
155C THR* 3.4 24.9 + - + +
171C THR* 5.8 0.2 - - - +
219C HIS* 3.0 34.4 + + - -
220C GLU* 2.9 15.0 + - - +
222C ALA* 1.3 75.8 - - - +
224C ALA* 1.3 56.5 + - - +
226C LYS* 5.8 0.3 - - - +
3003C CO 1.9 32.4 + - - -
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Residues in contact with ALA 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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21C GLU* 4.1 5.8 - - + -
170C LEU* 3.9 2.3 - - - -
171C THR* 2.8 44.9 + - - +
173C HIS* 4.0 25.8 - - + -
174C VAL* 4.1 13.2 - - + +
220C GLU 4.5 0.2 - - - +
221C MET 2.7 14.0 + - - +
223C HIS* 1.3 79.8 - - - +
225C VAL* 1.3 63.2 + - - +
226C LYS* 4.3 1.1 - - - -
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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