Contacts of the helix formed by residues 214 - 231 (chain A) in PDB entry 2R4S
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 ILE 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A CYS* 3.5 27.1 - - - -
129A VAL* 5.6 3.4 - - + -
210A VAL* 3.3 23.6 - - + +
213A VAL* 1.3 82.7 - - + +
215A MET* 1.3 58.5 + - - +
216A VAL 3.0 2.7 - - - -
217A PHE* 2.8 26.9 + - - +
218A VAL* 2.8 31.1 + - + +
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Residues in contact with MET 215 (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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121A ILE* 4.5 12.1 - - + -
124A LEU* 3.1 62.8 - - + +
125A CYS* 3.7 9.4 - - - +
128A ALA* 3.7 10.5 - - + +
129A VAL* 6.2 0.2 - - - -
211A PRO 2.8 24.1 + - - +
212A LEU* 4.0 6.7 - - + -
213A VAL 3.7 0.2 - - - -
214A ILE* 1.3 83.4 - - - +
216A VAL* 1.3 70.5 + - + +
218A VAL* 4.7 2.2 - - - -
219A TYR* 3.3 25.2 + - - +
279A MET* 3.9 28.7 - - + +
282A PHE* 5.8 2.0 - - + -
283A THR* 6.2 0.9 - - - -
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Residues in contact with VAL 216 (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* 3.2 41.0 + - + +
214A ILE 3.0 1.6 - - - -
215A MET* 1.3 88.4 - - - +
217A PHE* 1.3 77.5 + - + +
219A TYR* 4.4 5.0 - - - +
220A SER* 3.1 23.7 + - - -
283A THR* 5.9 2.7 - - - +
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Residues in contact with PHE 217 (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 5.3 0.2 - - - -
213A VAL* 3.1 25.6 - - + +
214A ILE* 2.8 8.3 + - - +
216A VAL* 1.3 97.3 - - + +
218A VAL* 1.3 59.2 + - + +
219A TYR 3.0 1.6 - - - -
220A SER* 3.4 11.1 - - - -
221A ARG* 2.8 30.1 + - - +
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Residues in contact with VAL 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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128A ALA* 2.8 42.4 - - + +
129A VAL* 3.4 25.6 - - + -
132A TYR* 3.7 15.5 - - + -
214A ILE* 2.8 30.7 + - + +
215A MET* 4.7 0.4 - - - +
217A PHE* 1.3 77.0 - - + +
219A TYR* 1.3 56.9 + - - +
221A ARG* 3.8 3.2 - - - +
222A VAL* 3.0 23.6 + - - +
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Residues in contact with TYR 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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128A ALA* 4.2 12.3 - - + -
131A ARG* 6.5 1.3 - - + -
215A MET* 3.3 20.9 + - - +
216A VAL* 4.4 4.3 - - - +
217A PHE 3.0 0.2 - - - -
218A VAL* 1.3 79.5 - - - +
220A SER* 1.3 68.4 + - - +
222A VAL* 2.9 16.9 + - + -
223A PHE* 2.7 54.3 + + + +
272A LEU* 2.7 37.2 + - + -
276A GLY* 2.8 28.8 - - - -
279A MET* 4.1 31.9 - - + -
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Residues in contact with SER 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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216A VAL* 3.1 21.5 + - - -
217A PHE* 3.2 16.3 + - - -
219A TYR* 1.3 79.9 - - - +
221A ARG* 1.3 67.0 + - - +
223A PHE* 3.4 5.6 + - - +
224A GLN* 2.9 39.4 + - - +
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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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132A TYR* 3.2 38.7 + - + -
217A PHE 2.8 21.1 + - - +
218A VAL* 3.8 7.2 - - - +
220A SER* 1.3 76.0 - - - +
222A VAL* 1.3 51.8 + - - +
224A GLN* 3.0 5.2 + - - +
225A GLU* 2.8 54.5 + - + +
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Residues in contact with VAL 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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128A ALA 4.2 3.6 - - - +
131A ARG* 5.1 4.7 - - + +
132A TYR* 3.4 39.7 - - + +
135A ILE* 3.7 30.5 - - + -
218A VAL 3.0 18.6 - - - +
219A TYR* 2.9 19.1 + - + +
221A ARG* 1.3 76.0 - - - +
223A PHE* 1.3 57.6 + - - +
224A GLN 2.5 17.5 + - - -
225A GLU* 4.6 2.5 - - - +
226A ALA* 2.9 23.9 + - - +
272A LEU* 4.1 18.4 - - + -
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Residues in contact with PHE 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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219A TYR* 2.7 46.8 + + + +
220A SER* 4.0 5.2 - - - +
222A VAL* 1.3 75.0 - - - +
224A GLN* 1.3 76.1 + - + +
226A ALA* 4.1 7.3 - - - +
227A LYS* 3.7 32.9 + - + +
269A HIS* 5.0 18.5 - + - -
272A LEU* 4.7 12.8 - - + -
273A LYS* 5.7 3.8 - - + -
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Residues in contact with GLN 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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220A SER* 2.9 32.9 + - - +
221A ARG* 3.2 9.0 - - - +
222A VAL 2.5 5.7 + - - -
223A PHE* 1.3 89.6 - - - +
225A GLU* 1.3 54.3 + - - +
226A ALA 2.8 4.3 - - - -
227A LYS* 2.7 39.4 + - - +
228A ARG* 3.6 5.4 + - - +
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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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132A TYR* 6.4 0.9 - - - -
135A ILE* 4.9 15.2 - - + +
136A THR* 5.3 9.4 + - - -
221A ARG* 2.8 40.8 + - + +
222A VAL* 3.7 2.5 - - - +
224A GLN* 1.3 71.6 - - - +
226A ALA* 1.3 56.5 + - - +
227A LYS 3.2 2.6 + - - -
228A ARG* 4.2 21.9 - - + +
229A GLN* 4.0 17.3 + - - +
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Residues in contact with ALA 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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135A ILE* 3.8 25.6 - - + -
222A VAL 2.9 18.0 + - - +
223A PHE* 4.1 8.3 - - + +
224A GLN 2.8 1.0 + - - -
225A GLU* 1.3 77.9 - - - +
227A LYS* 1.3 59.8 + - - +
229A GLN* 4.3 3.4 - - - -
230A LEU* 3.3 12.6 + - - +
264A PHE* 3.2 35.9 - - + -
269A HIS* 4.0 6.2 + - + +
272A LEU* 4.3 6.1 - - + -
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Residues in contact with LYS 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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223A PHE* 3.7 28.9 - - + +
224A GLN* 2.7 18.0 + - - +
226A ALA* 1.3 79.6 - - - +
228A ARG* 1.3 65.9 + - + +
229A GLN 3.1 2.3 + - - -
230A LEU* 3.1 28.5 + - + +
231A GLN* 3.6 5.5 + - - +
269A HIS* 3.2 32.8 + - + -
57H ASN* 5.7 4.0 - - - +
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Residues in contact with ARG 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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224A GLN 3.6 6.8 + - - +
225A GLU* 4.5 20.4 - - + +
227A LYS* 1.3 80.5 - - + +
229A GLN* 1.3 63.0 + - - +
231A GLN 3.8 1.0 + - - -
232A LYS* 3.2 23.4 + - + +
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Residues in contact with GLN 229 (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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135A ILE* 5.0 12.6 - - - +
225A GLU 4.0 15.0 + - - +
226A ALA* 4.5 4.0 - - - +
227A LYS 3.1 0.4 - - - -
228A ARG* 1.3 75.7 - - - +
230A LEU* 1.3 54.7 + - - +
231A GLN 2.4 20.6 + - - -
232A LYS* 2.5 20.7 + - + +
233A ILE* 3.5 9.6 + - + +
264A PHE* 3.0 52.3 + - + +
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Residues in contact with LEU 230 (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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226A ALA 3.3 11.9 + - - +
227A LYS* 3.1 28.4 + - + +
229A GLN* 1.3 76.9 - - - +
231A GLN* 1.3 67.3 + - + +
233A ILE* 2.9 23.8 - - - +
264A PHE* 3.4 27.6 - - + -
265A CYS 3.8 3.1 - - - +
266A LEU* 3.8 26.5 - - + +
269A HIS* 3.2 48.0 - - + +
57H ASN* 6.0 0.9 - - - +
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Residues in contact with GLN 231 (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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227A LYS 3.6 6.7 + - - +
228A ARG 4.1 2.0 - - - +
229A GLN 2.4 10.7 + - - -
230A LEU* 1.3 86.3 - - + +
232A LYS* 1.3 55.5 + - - +
233A ILE* 2.5 26.9 + - - +
234A ASP 5.1 0.4 - - - -
235A LYS* 3.2 54.5 - - + +
239A ARG* 4.0 11.5 - - - +
33H TYR* 4.4 7.5 + - - -
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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