Contacts of the strand formed by residues 206 - 213 (chain E) in PDB entry 1IAS
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 VAL 206 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E THR 4.2 7.0 - - - +
205E ILE* 1.3 82.5 - - - +
207E LEU* 1.3 65.3 + - - +
208E GLN* 2.8 32.8 + - - +
223E LYS* 2.8 28.9 + - + +
225E ARG 6.2 1.1 - - - +
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Residues in contact with LEU 207 (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* 4.0 13.6 + - + -
206E VAL* 1.3 81.0 - - - +
208E GLN* 1.3 66.8 + - - +
220E TRP* 4.1 33.9 - - + -
221E ARG 4.1 1.8 - - - -
222E GLY* 4.1 1.6 - - - -
231E VAL* 4.0 21.5 - - + -
233E ILE* 3.6 24.7 - - + -
277E TRP* 3.9 28.3 - - + -
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Residues in contact with GLN 208 (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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20E SO4 4.0 4.2 + - - -
206E VAL* 2.8 34.2 + - - +
207E LEU* 1.3 78.8 + - - +
209E GLU* 1.3 69.2 + - + +
220E TRP* 4.5 4.4 - - - -
221E ARG* 2.8 56.0 + - - +
222E GLY* 3.8 10.5 - - - -
223E LYS* 3.6 36.3 + - + +
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Residues in contact with GLU 209 (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 GLN* 1.3 84.0 - - + +
210E SER* 1.3 70.6 + - - +
211E ILE* 4.4 2.6 - - - +
220E TRP* 3.3 15.1 - - - -
221E ARG* 2.3 73.1 + - - +
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Residues in contact with SER 210 (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 GLU* 1.3 90.5 - - - +
211E ILE* 1.3 60.1 + - - +
212E GLY* 3.7 10.2 + - - -
213E LYS* 5.1 1.6 - - - +
218E GLU* 2.9 27.0 + - - -
219E VAL 3.7 8.6 + - - -
220E TRP* 3.5 20.5 - - - -
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Residues in contact with ILE 211 (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 GLU* 4.4 2.2 - - - +
210E SER* 1.3 78.6 - - - +
212E GLY* 1.3 59.6 + - - +
219E VAL* 2.7 24.4 + - + +
220E TRP 3.7 4.9 - - - +
221E ARG* 3.3 43.1 - - + +
230E ALA* 5.4 1.1 - - + -
282E TYR* 3.4 25.4 - - + +
286E GLY* 5.6 10.1 - - - -
290E ASP* 5.6 1.9 - - - +
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Residues in contact with GLY 212 (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 4.3 + - - -
211E ILE* 1.3 83.5 - - - +
213E LYS* 1.3 69.0 + - - +
218E GLU* 3.3 5.5 - - - +
219E VAL* 2.8 32.5 + - - +
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Residues in contact with LYS 213 (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* 5.1 1.6 - - - +
212E GLY* 1.3 80.0 - - - +
214E GLY* 1.3 61.7 + - - +
216E PHE* 3.3 16.3 - - - -
217E GLY 3.4 9.4 - - - +
218E GLU* 3.4 33.0 + - + +
219E VAL* 5.5 0.2 - - - +
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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