Contacts of the strand formed by residues 216 - 225 (chain E) in PDB entry 5AQP
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 216 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E THR 3.2 7.4 - - - +
212E ILE* 3.2 4.3 - - - +
213E GLU* 3.0 34.0 + - + +
214E ASP 3.2 2.7 - - - +
215E GLY* 1.3 79.2 - - - +
217E PHE* 1.3 62.8 + - - +
218E GLU* 3.9 0.8 + - + -
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Residues in contact with PHE 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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177E THR* 3.7 41.1 - - + +
180E ALA* 4.1 15.9 - - + -
181E ILE* 3.9 21.5 - - + -
186E ASP* 3.6 26.0 - - + -
210E LEU* 4.7 9.9 - - + -
211E THR 3.7 2.7 - - - -
212E ILE* 3.6 36.8 - - + -
215E GLY* 4.0 15.3 - - - -
216E ILE* 1.3 74.0 - - - +
218E GLU* 1.3 60.9 + - - +
219E VAL* 4.1 3.0 + - + +
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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 LEU* 3.2 7.5 - - - -
211E THR* 2.9 50.6 + - - +
216E ILE* 3.9 1.1 + - + +
217E PHE* 1.3 72.5 - - - +
219E VAL* 1.3 70.1 + - - +
220E LYS* 3.3 9.2 + - - +
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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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148E ALA* 4.2 14.1 - - + +
174E ASN* 3.5 28.3 - - - +
177E THR* 5.1 0.9 - - - +
208E SER* 5.3 1.1 - - - -
210E LEU* 3.3 25.8 - - + -
217E PHE 4.1 3.6 + - - +
218E GLU* 1.3 75.3 - - - +
220E LYS* 1.3 59.3 + - - +
221E SER* 4.1 8.5 - - - +
222E THR* 3.7 29.8 - - + -
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Residues in contact with LYS 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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209E ILE* 2.9 19.1 + - + +
211E THR* 4.7 13.2 - - + -
218E GLU* 3.3 14.2 + - - +
219E VAL* 1.3 73.7 - - - +
221E SER* 1.4 62.5 + - - +
323E ASP* 4.1 11.3 - - - +
324E ALA* 3.8 23.2 - - + +
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Residues in contact with SER 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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208E SER* 3.4 3.3 - - - -
209E ILE* 3.0 40.2 + - - +
219E VAL* 3.6 3.7 - - - +
220E LYS* 1.4 80.3 - - - +
222E THR* 1.3 68.1 + - - +
320E ALA* 2.7 38.2 + - - -
323E ASP* 3.8 19.7 - - - -
324E ALA* 3.5 3.2 - - - +
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Residues in contact with THR 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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148E ALA* 3.9 25.4 - - + +
149E TYR* 4.1 22.5 - - + +
207E VAL 3.4 7.0 - - - -
208E SER* 4.2 7.9 - - - +
219E VAL* 3.7 21.3 - - + -
221E SER* 1.3 81.5 - - - +
223E ALA* 1.3 61.6 + - - +
319E LYS* 5.6 0.7 - - - +
320E ALA* 5.1 0.6 - - - -
323E ASP* 4.8 8.0 - - - +
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Residues in contact with ALA 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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206E ASP* 3.6 5.9 - - - +
207E VAL* 2.8 30.7 + - + +
222E THR* 1.3 76.8 - - - +
224E GLY* 1.3 59.5 + - - +
316E PRO* 3.4 27.1 - - + +
319E LYS* 4.2 17.0 - - + -
320E ALA* 4.1 15.9 - - + +
323E ASP* 5.8 0.2 - - - +
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Residues in contact with GLY 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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205E PHE* 3.2 16.2 - - - -
207E VAL 4.6 0.4 - - - -
223E ALA* 1.3 79.1 - - - +
225E ASP* 1.3 59.8 + - - +
226E THR* 4.3 1.8 - - - -
316E PRO* 4.1 20.3 - - - +
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Residues in contact with ASP 225 (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 PHE* 2.8 46.3 + - + +
224E GLY* 1.3 71.6 - - - +
226E THR* 1.3 55.5 + - - +
227E HIS* 3.1 25.9 + - - +
228E LEU* 3.5 27.6 + - + +
316E PRO* 6.0 1.1 - - + -
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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