Contacts of the strand formed by residues 217 - 224 (chain E) in PDB entry 3FAA
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213E LYS* 3.9 3.1 - - - +
214E GLY 3.3 22.5 + - - +
215E ARG 4.7 0.2 - - - -
216E PHE* 1.3 87.0 - - - +
218E GLU* 1.3 69.6 + - - +
233E ILE 3.5 10.8 - - - -
235E SER* 4.1 9.6 - - - -
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Residues in contact with GLU 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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210E SER* 3.1 17.3 + - - -
212E GLY 3.3 13.7 - - - +
213E LYS* 3.6 24.2 + - + +
216E PHE* 2.9 16.3 - - - -
217E GLY* 1.3 78.4 - - - +
219E VAL* 1.3 62.6 + - - +
220E TRP* 2.8 37.7 + - + +
233E ILE* 3.0 35.1 + - + +
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Residues in contact with VAL 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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210E SER* 3.7 1.4 + - - -
211E ILE* 3.1 31.0 + - + -
212E GLY* 3.0 22.7 + - - +
216E PHE* 3.7 22.7 - - + -
218E GLU* 1.3 74.3 - - - +
220E TRP* 1.3 75.7 + - - +
230E ALA* 4.7 2.2 - - + -
231E VAL 3.2 9.9 - - - +
232E LYS* 4.3 2.7 - - + +
601E 55F 3.7 61.7 - - + +
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Residues in contact with TRP 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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207E LEU* 3.9 29.8 - - + -
208E GLN 3.5 20.2 - - - -
209E GLU 2.9 26.9 - - - -
210E SER* 3.7 16.8 - - - -
211E ILE* 3.8 7.2 - - - +
218E GLU* 2.8 45.3 + - - +
219E VAL* 1.3 85.1 - - - +
221E ARG* 1.3 61.0 + - - +
230E ALA* 3.4 4.9 - - - -
231E VAL* 2.6 46.6 + - + +
233E ILE* 3.7 21.3 - - + +
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Residues in contact with ARG 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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207E LEU* 4.1 0.2 - - - -
208E GLN* 2.8 44.9 + - - +
209E GLU* 2.6 52.4 + - - +
211E ILE* 3.7 17.2 - - + +
220E TRP* 1.3 74.5 - - - +
222E GLY* 1.3 62.9 + - - +
223E LYS* 3.2 31.1 - - - +
228E GLU* 2.9 24.3 + - + +
229E VAL 3.4 5.8 - - - +
282E TYR* 3.5 35.5 + - + -
284E GLU* 5.0 3.2 + - - -
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Residues in contact with GLY 222 (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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205E ILE* 4.1 8.3 - - - -
206E VAL 3.3 13.7 - - - -
207E LEU* 3.9 8.3 - - - -
208E GLN* 3.6 1.8 - - - -
220E TRP 3.9 1.8 + - - -
221E ARG* 1.3 77.1 - - - +
223E LYS* 1.3 59.5 + - - +
228E GLU* 3.4 5.0 - - - +
229E VAL* 2.6 42.8 + - - +
231E VAL* 4.6 2.0 - - - +
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Residues in contact with LYS 223 (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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205E ILE* 3.6 3.4 - - - +
206E VAL* 2.7 43.0 + - + +
208E GLN* 3.2 21.0 + - + +
221E ARG* 3.2 27.2 - - - +
222E GLY* 1.3 78.6 - - - +
224E TRP* 1.3 58.9 + - - +
225E ARG 3.9 0.7 - - - -
226E GLY* 3.1 29.9 + - - +
227E GLU 3.4 2.9 - - - -
228E GLU* 4.0 17.7 - - + -
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Residues in contact with TRP 224 (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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171E ILE* 4.1 26.9 - - + -
175E THR 4.0 5.4 - - - -
176E THR 4.1 0.2 - - - -
177E LEU* 3.5 44.9 - - + -
180E LEU* 4.5 8.1 - - + -
200E THR* 5.9 0.4 - - + -
201E ILE* 3.6 35.7 + - + +
204E THR* 2.7 36.6 - - + +
205E ILE* 3.7 16.6 - - + -
223E LYS* 1.3 71.4 - - - +
225E ARG* 1.3 116.9 + - + +
226E GLY 3.1 0.3 + - - -
227E GLU* 2.9 33.0 + - - +
229E VAL* 4.8 5.7 - - + +
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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