Contacts of the helix formed by residues 215 - 225 (chain A) in PDB entry 3REO
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLY 3.3 3.7 + - - -
213A GLY 3.1 4.9 - - - -
214A THR* 1.3 79.4 - - - +
216A ALA* 1.3 67.1 + - - +
217A VAL 3.3 2.0 - - - -
218A ALA* 3.2 3.7 + - - +
219A SER* 2.8 25.5 + - - -
232A ASN* 3.4 28.9 - - - -
245A PHE* 3.7 10.1 - - - -
250A HIS* 4.1 2.5 - - - -
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Residues in contact with ALA 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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184A SER* 3.4 33.9 - - - +
187A SER* 5.5 0.7 - - - -
188A THR* 3.9 17.9 - - - +
212A GLY 4.5 1.4 + - - -
214A THR* 3.5 3.5 + - - +
215A GLY* 1.3 76.4 - - - +
217A VAL* 1.3 64.7 + - + +
219A SER* 2.8 23.1 + - - -
220A MET* 3.0 18.2 + - - +
245A PHE* 4.2 6.4 - - + -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 3.8 24.0 - - - +
191A MET* 3.7 37.0 - - + -
209A ASP* 3.3 15.0 - - - +
212A GLY 5.0 4.3 + - - +
215A GLY* 3.3 1.0 - - - -
216A ALA* 1.3 77.5 - - + +
218A ALA* 1.3 64.5 + - - +
220A MET* 3.1 15.5 + - - +
221A ILE* 3.1 21.0 + - + +
266A PHE* 3.5 28.3 - - + -
268A LYS* 4.6 7.9 - - + -
370A SAH 5.1 7.2 - - - +
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Residues in contact with ALA 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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207A ILE* 6.2 0.4 - - + -
209A ASP* 3.9 14.5 + - + -
215A GLY 3.2 8.0 + - - +
217A VAL* 1.3 79.9 - - - +
219A SER* 1.3 62.1 + - - +
221A ILE* 3.4 9.7 + - - +
222A VAL* 3.1 27.9 + - - +
230A ALA* 4.2 12.2 - - + +
231A ILE 4.8 0.2 - - - +
232A ASN* 4.2 19.3 - - + +
248A VAL* 3.7 24.0 - - + -
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Residues in contact with SER 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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215A GLY 2.8 14.1 + - - -
216A ALA* 2.8 22.5 + - - -
218A ALA* 1.3 77.0 - - - +
220A MET* 1.3 60.8 + - - +
222A VAL* 3.6 2.9 + - - +
223A ALA* 2.9 29.5 + - - +
245A PHE* 3.5 41.3 - - - -
248A VAL* 3.7 8.9 - - - +
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Residues in contact with MET 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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187A SER 4.7 0.2 - - - +
188A THR* 3.5 40.8 - - + +
191A MET* 3.9 12.3 - - + -
192A LYS* 3.5 40.4 - - + +
195A LEU* 3.8 17.6 - - + +
216A ALA* 3.0 18.1 + - + +
217A VAL* 3.1 7.1 + - - +
219A SER* 1.3 78.3 - - - +
221A ILE* 1.3 59.0 + - - +
223A ALA* 3.5 7.7 + - - +
224A LYS* 3.1 27.0 + - - +
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Residues in contact with ILE 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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191A MET* 4.5 7.2 - - + -
195A LEU* 4.5 6.7 - - + -
201A PHE* 3.7 45.8 - - + -
207A ILE* 4.3 23.6 - - + -
209A ASP* 5.6 1.3 - - + +
217A VAL* 3.1 31.6 + - + +
218A ALA* 3.7 10.5 - - - +
220A MET* 1.3 76.4 - - - +
222A VAL* 1.3 53.1 + - + +
224A LYS* 3.0 3.4 + - - -
225A TYR* 2.7 38.6 + - + +
228A ILE* 4.0 24.9 - - + -
266A PHE* 4.7 7.4 - - + -
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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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218A ALA 3.1 18.0 + - - +
219A SER* 4.1 3.4 - - - +
221A ILE* 1.3 73.4 - - + +
223A ALA* 1.3 65.1 + - - +
225A TYR 3.8 6.7 - - - -
226A PRO* 3.1 33.6 - - + +
228A ILE* 3.7 24.5 - - + +
230A ALA* 3.4 26.7 - - + -
246A SER 3.6 23.6 - - - +
247A GLY* 3.8 12.6 - - - +
248A VAL* 4.1 4.9 - - + -
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Residues in contact with ALA 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 SER 2.9 19.6 + - - +
220A MET* 3.7 8.7 - - - +
222A VAL* 1.3 76.7 - - - +
224A LYS* 1.3 61.9 + - - +
226A PRO* 4.1 6.6 - - - +
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Residues in contact with LYS 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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195A LEU* 3.0 45.0 + - + +
196A GLU* 4.4 5.1 - - - +
220A MET 3.1 14.9 + - - +
221A ILE 3.0 6.2 + - - +
223A ALA* 1.3 80.8 - - - +
225A TYR* 1.3 98.1 + - + +
226A PRO* 3.4 8.2 - - - +
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Residues in contact with TYR 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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195A LEU* 4.7 5.0 + - + +
198A TYR 4.1 15.1 + - - -
199A ASN* 4.7 6.9 + - - -
201A PHE* 3.7 34.2 - + + +
202A GLU* 3.7 36.0 + - + +
221A ILE* 2.7 22.7 + - + +
222A VAL* 3.2 8.3 - - - +
224A LYS* 1.3 111.8 - - + +
226A PRO* 1.3 58.7 - - - +
227A SER* 2.9 7.6 - - - -
228A ILE* 2.8 46.2 + - + +
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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