Contacts of the strand formed by residues 222 - 229 (chain E) in PDB entry 3Q2K
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 THR 222 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184E ALA* 5.3 0.2 - - - -
185E PHE* 4.8 0.2 - - - -
210E THR* 3.3 4.2 - - - -
211E ALA 3.0 25.4 + - - +
213E LEU* 3.7 6.7 - - + +
220E GLU* 3.5 6.7 - - - +
221E ASP* 1.3 93.8 + - - +
223E GLY* 1.3 62.1 + - - +
239E VAL* 3.2 6.3 - - - -
240E THR* 2.5 23.9 + - - +
242E LEU* 3.4 10.0 - - - +
154F TYR* 3.8 14.5 - - - +
155F MET* 3.7 19.1 - - + -
234F MET* 3.3 23.6 - - + +
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Residues in contact with GLY 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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185E PHE* 3.6 18.1 - - - -
209E TYR 3.1 13.2 - - - -
210E THR* 3.8 0.7 - - - -
222E THR* 1.3 79.0 - - - +
224E VAL* 1.3 69.0 + - - +
239E VAL* 2.8 33.8 + - - +
155F MET* 3.4 1.3 - - - +
234F MET* 4.1 6.1 - - - -
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Residues in contact with VAL 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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185E PHE* 3.8 5.4 - - - -
207E TYR 4.2 0.2 - - - +
208E ALA* 3.0 4.5 - - - +
209E TYR* 2.8 37.1 + - + +
223E GLY* 1.3 81.3 - - - +
225E ALA* 1.3 73.2 + - - +
237E ILE 3.2 7.0 - - - +
238E ASN* 3.5 26.0 - - - +
155F MET* 4.0 9.4 - - + -
226F ALA* 4.1 12.8 - - + -
234F MET* 4.2 5.6 - - + -
235F GLY* 3.6 41.1 - - - +
236F SER* 4.0 8.3 - - - -
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Residues in contact with ALA 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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185E PHE* 4.8 0.7 - - + -
206E VAL* 4.9 0.9 - - + -
207E TYR 3.2 10.3 - - - +
208E ALA* 3.9 11.7 - - + -
224E VAL* 1.3 82.8 - - - +
226E ALA* 1.3 64.1 + - - +
227E LEU* 3.9 7.4 - - + +
236E SER* 3.0 6.2 - - - -
237E ILE* 2.8 47.7 + - + -
335E ILE* 4.1 20.2 - - + -
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Residues in contact with ALA 226 (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 VAL* 3.3 4.7 - - - +
207E TYR* 2.7 37.1 + - + +
224E VAL* 4.5 1.6 - - - +
225E ALA* 1.3 74.7 - - - +
227E LEU* 1.3 60.9 + - - +
235E GLY 3.4 6.1 - - - -
236E SER* 4.4 2.0 - - - +
207F TYR* 5.0 3.8 - - + +
209F TYR* 3.6 21.7 - - + -
224F VAL* 4.0 17.7 - - + +
226F ALA* 4.1 19.7 - - + +
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Residues in contact with LEU 227 (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* 4.1 26.9 - - + -
203E VAL* 4.7 8.1 - - + -
205E SER 3.6 7.6 - - - +
206E VAL* 3.6 26.0 - - + -
225E ALA* 3.9 13.7 - - + +
226E ALA* 1.3 79.7 - - - +
228E ARG* 1.3 59.7 + - - +
229E TRP* 4.1 27.1 - - + -
234E MET* 3.3 8.8 - - - +
235E GLY 2.8 47.6 + - - +
236E SER* 3.8 15.9 - - - +
237E ILE* 4.2 3.4 - - + +
331E LEU* 4.6 5.4 - - + -
335E ILE* 5.3 1.3 - - + -
209F TYR* 3.7 8.3 - - - -
224F VAL* 5.5 0.2 - - - +
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Residues in contact with ARG 228 (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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203E VAL* 3.6 3.5 - - - +
204E GLU* 2.6 64.5 + - - +
205E SER* 3.2 15.3 + - - +
227E LEU* 1.3 74.8 - - - +
229E TRP* 1.3 67.4 + - - +
232E GLY* 4.9 6.3 - - - +
233E ALA 3.5 8.7 - - - +
234E MET* 4.5 9.9 - - + +
344E ARG* 4.3 13.7 - - - +
207F TYR* 5.4 0.6 + - - -
209F TYR* 3.4 47.3 - - + +
210F THR 5.3 5.3 + - - -
339F ALA 5.8 1.4 + - - -
204G GLU* 5.9 0.8 + - - -
228G ARG* 6.0 1.6 - - - +
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Residues in contact with TRP 229 (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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156E VAL* 3.8 30.1 - - + -
196E LEU* 2.9 46.9 + - + -
200E VAL* 3.3 25.7 - - + +
201E GLY* 2.8 34.7 + - - -
202E PRO 3.4 14.8 - - - -
203E VAL* 3.7 10.2 - - + +
204E GLU* 3.9 2.4 - - - +
227E LEU* 4.1 16.2 - - + -
228E ARG* 1.3 82.7 - - - +
230E ARG* 1.3 56.9 + - - +
231E HIS* 3.5 26.0 - + + +
232E GLY* 2.7 26.5 + - - -
233E ALA* 3.0 25.9 + - + +
234E MET* 4.0 15.3 - - - -
235E GLY 4.0 3.4 - - - -
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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