Contacts of the helix formed by residues 217 - 228 (chain A) in PDB entry 4R8U
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 GLY 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LEU* 2.7 35.9 + - - +
214A LYS 4.3 1.8 + - - -
215A ARG 4.0 0.2 - - - -
216A PHE* 1.3 72.5 - - - +
218A LYS* 1.3 54.8 + - - -
220A GLY* 2.8 28.2 + - - -
221A ARG 3.5 3.5 + - - -
27V T 4.5 4.3 - - - -
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Residues in contact with LYS 218 (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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213A LEU* 5.2 1.3 - - - -
217A GLY* 1.3 71.0 - - - -
219A PHE* 1.3 60.7 + - - +
221A ARG* 3.4 10.6 + - + +
222A ILE* 3.0 43.9 + - + +
26V C 3.9 40.6 + - - +
27V T 3.3 33.8 + - - +
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Residues in contact with PHE 219 (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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184A GLY* 3.4 23.3 - - - -
185A VAL* 3.7 24.5 - - + -
189A SER* 3.7 26.0 - - - -
193A LEU* 4.7 1.3 - - + -
216A PHE* 3.3 38.8 + + + +
217A GLY 2.9 0.4 + - - -
218A LYS* 1.3 78.7 - - - +
220A GLY* 1.3 59.0 + - - +
222A ILE* 3.3 12.8 + - + +
223A LEU* 3.0 47.1 + - + +
26V C 5.6 0.4 + - - -
27V T 4.7 0.6 + - - -
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Residues in contact with GLY 220 (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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212A LEU* 3.5 34.5 - - - +
213A LEU* 4.5 1.8 - - - -
216A PHE* 3.4 12.3 - - - +
217A GLY 2.8 13.7 + - - -
219A PHE* 1.3 74.9 - - - +
221A ARG* 1.3 57.7 + - - +
223A LEU* 3.5 7.6 - - - +
224A TRP* 3.1 26.9 + - - +
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Residues in contact with ARG 221 (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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209A LEU* 3.8 34.8 - - + +
213A LEU* 3.6 44.8 - - + +
217A GLY 3.5 3.2 + - - -
218A LYS* 3.4 11.7 + - - +
219A PHE 3.2 0.6 - - - -
220A GLY* 1.3 75.0 - - - +
222A ILE* 1.3 73.6 + - + +
224A TRP* 3.4 3.0 + - - +
225A GLU* 3.0 46.3 + - + +
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Residues in contact with ILE 222 (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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182A ILE* 5.8 1.8 - - + -
183A PRO 5.8 4.0 - - - +
218A LYS* 3.0 39.8 + - + +
219A PHE* 3.3 17.0 + - + +
221A ARG* 1.3 83.1 - - + +
223A LEU* 1.3 59.2 + - - +
225A GLU* 3.2 9.8 + - - +
226A ARG* 2.9 73.2 + - + +
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Residues in contact with LEU 223 (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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179A LEU* 4.2 25.8 - - + -
182A ILE* 4.6 6.5 - - + -
185A VAL* 4.4 17.3 - - + -
193A LEU* 3.7 37.0 - - + -
204A VAL* 4.3 7.9 - - + -
212A LEU* 4.7 13.2 - - + -
216A PHE* 5.0 1.3 - - + -
219A PHE* 3.0 34.4 + - + +
220A GLY* 3.5 11.7 - - - +
222A ILE* 1.3 79.3 - - - +
224A TRP* 1.3 63.6 + - - +
226A ARG* 3.4 3.5 + - - +
227A SER* 3.0 30.6 + - - +
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Residues in contact with TRP 224 (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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204A VAL* 4.1 16.7 + - - +
205A GLN 5.2 1.8 + - - -
207A CYS 3.8 22.9 + - - -
209A LEU* 3.8 46.6 - - + +
212A LEU* 4.1 11.2 - - + +
220A GLY 3.1 14.0 + - - +
221A ARG* 3.4 4.0 + - + +
223A LEU* 1.3 78.8 - - - +
225A GLU* 1.3 76.7 + - + +
227A SER* 3.6 2.9 + - - -
228A GLN* 3.1 60.8 + - + +
230A ILE* 4.4 14.6 - - + -
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Residues in contact with GLU 225 (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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221A ARG* 3.0 44.3 + - + +
222A ILE* 3.2 8.9 + - - +
224A TRP* 1.3 92.6 - - + +
226A ARG* 1.3 73.0 + - - +
228A GLN* 2.7 24.9 + - - +
230A ILE* 2.9 47.8 + - + +
231A ASP* 5.4 0.5 - - - -
232A GLU* 5.5 3.4 + - - +
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Residues in contact with ARG 226 (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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148A PHE* 3.3 51.6 - - + +
174A LEU* 3.5 5.1 - - - +
182A ILE* 4.1 24.4 - - + +
183A PRO 6.0 0.4 + - - -
201A CYS* 4.9 1.3 - - - -
222A ILE* 2.9 57.5 + - + +
223A LEU* 3.9 4.0 - - - +
225A GLU* 1.3 93.8 + - - +
227A SER* 1.3 54.7 + - - +
229A GLY* 2.7 21.1 + - - -
230A ILE 2.9 23.7 + - - -
231A ASP* 3.8 15.5 + - - +
232A GLU 5.1 0.6 - - - +
233A ARG* 3.3 35.6 - - - +
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Residues in contact with SER 227 (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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174A LEU* 3.5 7.4 - - - +
179A LEU* 4.2 3.1 - - - +
182A ILE* 4.8 0.3 - - - +
201A CYS* 3.8 30.2 - - - +
204A VAL* 3.2 36.1 - - - +
205A GLN* 2.8 33.5 + - - -
223A LEU* 3.0 19.7 + - - +
224A TRP 3.7 4.7 - - - -
225A GLU 3.1 0.2 - - - -
226A ARG* 1.3 75.7 - - - +
228A GLN* 1.3 57.8 + - - +
229A GLY 3.2 0.4 - - - -
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Residues in contact with GLN 228 (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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170A VAL* 4.9 2.3 - - - +
174A LEU* 3.6 9.2 - - - +
205A GLN* 4.6 25.2 + - - +
224A TRP* 3.1 56.0 + - + +
225A GLU 2.7 12.2 + - - +
227A SER* 1.3 74.1 - - - +
229A GLY* 1.3 60.4 + - - +
230A ILE* 3.6 25.8 + - + +
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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