Contacts of the strand formed by residues 193 - 201 (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 ARG 193 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.7 33.8 + - - +
188E LYS* 4.0 27.4 - - - +
189E VAL 4.2 12.1 + - - +
190E GLY* 6.0 0.2 - - - -
191E ALA 3.8 13.2 - - - +
192E GLU* 1.3 72.8 - - - +
194E ASN* 1.3 63.1 + - - +
195E VAL* 3.8 13.4 + - + +
210E LEU 3.5 1.4 - - - +
211E THR* 3.1 6.1 - - - -
212E ILE* 2.8 46.7 + - + +
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Residues in contact with ASN 194 (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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192E GLU* 3.4 16.3 + - - +
193E ARG* 1.3 72.0 - - - +
195E VAL* 1.3 62.0 + - - +
209E ILE* 5.6 2.0 - - + -
210E LEU 3.5 3.6 - - - +
211E THR* 3.3 23.8 - - + +
326E LEU* 3.9 31.9 - - + +
330E GLN* 2.8 37.0 + - - +
331E ILE* 3.8 25.7 - - + +
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Residues in contact with VAL 195 (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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180E ALA* 4.7 4.0 - - + -
185E LEU* 3.6 26.7 - - + -
193E ARG* 4.2 14.1 - - + +
194E ASN* 1.3 78.4 - - - +
196E LEU* 1.3 64.1 + - - +
197E ILE* 3.6 27.5 + - + -
208E SER 3.6 1.0 - - - +
209E ILE* 3.2 9.0 - - - +
210E LEU* 2.6 51.5 + - + +
212E ILE* 3.7 27.4 - - + -
331E ILE* 4.9 1.3 - - - -
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Residues in contact with LEU 196 (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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195E VAL* 1.3 74.3 - - - +
197E ILE* 1.3 64.3 + - - +
198E PHE* 3.8 31.9 + - + +
207E VAL* 3.6 28.0 - - + -
208E SER 3.5 2.0 - - - +
209E ILE* 3.8 23.1 - - + +
317E VAL* 4.3 19.5 - - + -
321E LEU* 5.3 2.5 - - + -
331E ILE* 4.1 26.9 - - + +
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Residues in contact with ILE 197 (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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175E GLU 5.6 0.2 - - - -
176E PRO* 3.4 52.0 - - + +
179E ALA* 4.2 14.6 - - + -
180E ALA* 4.2 12.6 - - + +
185E LEU* 5.2 1.6 - - + -
195E VAL* 3.6 25.4 - - + -
196E LEU* 1.3 73.5 - - - +
198E PHE* 1.3 64.7 + - - +
199E ASP* 4.8 10.1 - - + +
206E ASP 3.6 1.9 - - - +
207E VAL* 3.3 8.3 - - - +
208E SER* 2.8 40.8 + - - +
210E LEU* 4.3 8.1 - - + -
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Residues in contact with PHE 198 (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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196E LEU* 3.8 17.3 + - + +
197E ILE* 1.3 73.5 - - - +
199E ASP* 1.3 58.3 + - - +
200E LEU* 3.9 21.6 + - + -
205E PHE* 3.6 26.2 - + - -
206E ASP 4.1 1.8 - - - -
207E VAL* 4.2 2.7 - - + -
313E THR* 3.6 31.6 - - + -
314E LEU* 5.1 5.8 - - + -
317E VAL* 3.8 26.5 - - + -
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Residues in contact with ASP 199 (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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175E GLU* 4.5 18.0 - - - +
197E ILE* 4.8 11.9 - - + +
198E PHE* 1.3 69.6 - - - +
200E LEU* 1.3 62.0 + - - +
201E GLY* 3.8 16.8 + - - +
204E THR* 3.8 1.8 - - - +
205E PHE* 3.4 5.8 - - - -
206E ASP* 2.8 60.3 + - + +
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Residues in contact with LEU 200 (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 PHE* 3.9 20.5 + - + -
199E ASP* 1.3 74.0 + - - +
201E GLY* 1.3 58.8 + - - +
204E THR 4.0 0.2 - - - -
205E PHE* 3.7 33.0 - - + -
228E LEU* 4.0 27.1 - - + +
229E GLY* 4.5 5.8 - - - -
233E PHE* 4.2 23.1 - - + -
310E PHE* 6.0 1.6 - - + -
313E THR* 4.1 19.7 - - + -
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Residues in contact with GLY 201 (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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199E ASP* 3.8 11.2 + - - +
200E LEU* 1.3 75.7 - - - +
202E GLY* 1.3 65.8 + - - +
203E GLY 3.4 2.5 - - - -
204E THR* 3.2 22.0 + - - +
228E LEU 5.4 0.2 + - - -
229E GLY* 5.6 4.0 - - - -
230E GLY 6.0 1.8 - - - -
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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