Contacts of the strand formed by residues 203 - 211 (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 VAL 203 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196E LEU* 4.6 5.6 - - + +
197E ASP* 4.4 5.1 + - + +
201E GLY 4.0 2.9 - - - +
202E PRO* 1.3 71.9 - - - +
204E GLU* 1.3 63.9 + - - +
205E SER 3.6 21.8 - - - +
206E VAL* 4.0 15.7 - - + -
227E LEU* 4.7 8.3 - - + -
228E ARG 3.7 8.1 - - - +
229E TRP* 3.7 30.1 - - + +
230E ARG* 3.5 14.9 + - - -
331E LEU* 4.0 27.4 - - + -
347E LEU* 3.4 24.8 - - + +
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Residues in contact with GLU 204 (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* 1.3 72.5 - - - +
205E SER* 1.3 70.1 + - - +
228E ARG* 2.6 62.7 + - - +
229E TRP 4.1 2.3 - - - +
230E ARG* 3.7 40.7 - - + +
344E ARG* 5.2 0.7 + - - -
346E PRO* 3.4 4.8 - - + +
347E LEU* 2.9 26.3 + - - +
228G ARG* 5.6 3.5 + - - -
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Residues in contact with SER 205 (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 3.8 - - - +
204E GLU* 1.3 97.9 + - - +
206E VAL* 1.3 70.7 + - - +
227E LEU* 3.6 0.3 - - - -
228E ARG* 3.2 24.4 + - - +
344E ARG* 3.2 20.5 - - - -
345E ILE 3.3 14.4 - - - -
346E PRO* 3.7 10.3 - - - -
347E LEU* 4.5 1.8 - - - +
209F TYR* 2.8 25.3 + - - -
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Residues in contact with VAL 206 (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* 4.0 3.4 - - + -
205E SER* 1.3 81.7 - - - +
207E TYR* 1.3 66.9 + - - +
225E ALA* 4.9 0.7 - - + -
226E ALA 3.3 10.8 - - - +
227E LEU* 3.6 23.6 - - + -
331E LEU* 3.7 22.9 - - + -
334E ALA* 3.7 40.6 - - + +
335E ILE* 3.9 14.1 - - + +
338E SER* 3.8 2.2 + - - -
344E ARG* 3.4 4.7 - - - +
345E ILE* 2.8 32.8 + - + +
347E LEU* 5.5 0.7 - - + -
209F TYR* 3.4 5.6 - - - -
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Residues in contact with TYR 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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206E VAL* 1.3 76.2 - - - +
208E ALA* 1.3 78.8 + - - +
209E TYR* 3.7 28.7 - + - -
225E ALA* 3.2 2.5 - - - -
226E ALA* 2.7 36.5 + - + +
338E SER* 3.2 6.5 - - - -
342E GLY* 3.5 18.7 - - - -
343E VAL* 3.5 37.5 - - - -
344E ARG 3.7 1.6 - - - -
207F TYR* 3.3 61.5 - + + -
209F TYR* 3.8 0.6 + - - +
226F ALA* 4.6 4.1 - - + +
228F ARG* 5.6 0.2 + - - -
344F ARG* 3.4 31.1 + - + -
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Residues in contact with ALA 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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207E TYR* 1.3 92.1 + - - +
209E TYR* 1.3 67.5 + - - +
210E THR* 4.9 1.1 - - + -
224E VAL 3.0 14.1 - - - +
225E ALA* 3.9 5.4 - - + -
335E ILE* 3.5 44.0 - - + +
338E SER* 3.1 8.9 + - - -
339E ALA* 3.4 18.6 + - + +
226F ALA* 5.6 0.2 - - - -
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Residues in contact with TYR 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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207E TYR* 3.7 22.4 - + - -
208E ALA* 1.3 77.9 - - - +
210E THR* 1.3 65.3 + - - +
223E GLY* 3.1 2.4 - - - -
224E VAL* 2.8 34.3 + - + +
339E ALA* 4.4 4.3 - - - +
205F SER* 2.8 25.5 + - - -
206F VAL 3.4 21.5 - - - -
207F TYR 4.6 0.2 - - - -
226F ALA* 3.8 16.4 - - + -
227F LEU 3.6 39.7 - - - -
228F ARG* 3.5 46.9 - - + +
234F MET* 3.5 19.8 - - + +
344F ARG* 3.7 4.9 - - - +
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Residues in contact with THR 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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178E TRP* 5.6 4.5 - - - -
185E PHE* 3.9 25.6 - - + -
208E ALA* 4.9 0.9 - - + -
209E TYR* 1.3 80.8 - - - +
211E ALA* 1.3 67.4 + - - +
220E GLU* 3.5 25.9 + - + +
222E THR 3.3 7.6 - - - -
335E ILE* 4.7 6.1 - - + -
336E TYR* 4.6 8.4 - - + -
339E ALA* 3.6 28.6 + - + +
228F ARG* 5.3 6.2 + - - -
234F MET* 3.6 5.5 - - - +
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Residues in contact with ALA 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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210E THR* 1.3 82.3 - - - +
212E THR* 1.3 64.4 + - - +
213E LEU* 3.6 16.8 - - + -
220E GLU* 3.3 4.8 - - - -
221E ASP* 3.2 22.7 + - - +
222E THR* 3.0 11.4 + - - +
228F ARG* 6.3 1.8 - - - -
232F GLY 5.1 0.9 - - - +
234F MET* 3.9 16.8 - - + +
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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