Contacts of the strand formed by residues 214 - 221 (chain E) in PDB entry 3MY0
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 214 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210E LYS* 3.6 0.2 - - - -
211E GLY 2.9 33.9 + - - +
212E ARG 3.2 1.8 + - - -
213E TYR* 1.3 83.7 - - - +
215E GLU* 1.3 68.7 + - - +
230E ILE 3.4 9.6 - - - -
231E PHE 4.2 0.4 - - - -
232E SER* 3.7 14.8 - - - -
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Residues in contact with GLU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E CYS* 4.6 7.2 - - - -
209E GLY 3.5 13.9 - - - +
210E LYS* 4.3 10.5 - - + +
213E TYR* 3.9 3.9 - - - -
214E GLY* 1.3 79.5 - - - +
216E VAL* 1.3 64.3 + - - +
217E TRP* 3.1 32.9 + - + +
228E VAL 3.8 0.7 - - - +
229E LYS* 3.3 4.5 - - - +
230E ILE* 2.8 43.9 + - + +
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E CYS* 3.8 2.3 - - - -
208E VAL* 3.0 38.0 + - + +
209E GLY* 3.1 18.6 + - - +
213E TYR* 4.0 16.4 - - + +
215E GLU* 1.3 78.4 - - - +
217E TRP* 1.3 72.0 + - - +
227E ALA* 4.4 15.9 - - + -
228E VAL 3.6 6.3 - - - +
229E LYS* 3.8 23.6 - - + +
279E TYR* 5.9 1.3 - - + -
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Residues in contact with TRP 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E LEU* 3.7 44.0 - - + -
205E VAL 4.2 5.6 - - - -
206E GLU* 3.3 31.2 - - - -
207E CYS* 3.6 27.7 - - + +
208E VAL* 4.4 2.7 - - - -
215E GLU* 3.1 31.5 + - + +
216E VAL* 1.3 82.5 - - - +
218E ARG* 1.3 59.7 + - - +
227E ALA* 3.5 5.7 - - - -
228E VAL 2.9 36.2 + - - +
230E ILE* 3.7 24.8 - - + +
279E TYR* 4.8 0.3 - - - -
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Residues in contact with ARG 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E LEU* 3.9 1.2 - - - -
205E VAL* 2.9 46.9 + - + +
206E GLU* 2.6 41.2 + - + +
208E VAL* 4.3 7.8 - - + +
217E TRP* 1.3 73.0 - - - +
219E GLY* 1.3 67.8 + - - +
220E LEU* 5.2 7.6 - - + +
225E SER* 4.4 12.2 + - - +
226E VAL 3.7 2.2 - - - -
279E TYR* 3.2 55.7 + - + +
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Residues in contact with GLY 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E VAL* 4.2 5.2 - - - -
203E ALA 3.1 13.2 - - - -
204E LEU* 4.4 4.9 - - - -
205E VAL* 4.4 0.7 - - - -
217E TRP 3.8 1.2 + - - -
218E ARG* 1.3 75.4 - - - +
220E LEU* 1.3 64.0 - - - +
225E SER* 3.3 7.4 - - - -
226E VAL* 2.7 46.2 + - - -
228E VAL* 4.7 1.3 - - - +
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Residues in contact with LEU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLN 4.2 1.6 - - - +
202E VAL* 3.6 1.9 - - - -
203E ALA* 2.8 42.8 + - + +
205E VAL* 3.6 23.1 - - + +
218E ARG* 5.2 9.0 - - - +
219E GLY* 1.3 78.0 - - - +
221E TRP* 1.3 62.1 - - - +
222E HIS 4.2 0.4 - - - -
223E GLY* 4.8 13.7 - - - +
224E GLU 3.5 8.3 - - - +
225E SER* 4.1 15.9 - - - +
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Residues in contact with TRP 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E VAL* 3.7 36.0 - - + +
201E GLN* 3.4 35.9 + - + -
202E VAL* 3.8 27.6 - - + +
219E GLY 4.2 0.6 - - - -
220E LEU* 1.3 74.2 - - - +
222E HIS* 1.3 92.1 + + - +
223E GLY 3.3 0.6 - - - +
224E GLU* 2.9 73.8 + - - +
226E VAL* 4.3 17.9 - - + +
260E ILE* 5.6 8.5 - - + -
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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