Contacts of the strand formed by residues 222 - 229 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C TYR* 3.8 19.5 - - + +
155C MET* 3.8 16.8 - - + -
234C MET* 3.8 21.3 - - + -
184D ALA* 5.1 0.2 - - - -
185D PHE* 4.8 1.1 - - - -
210D THR* 3.2 4.3 - - - -
211D ALA 2.9 27.2 + - - +
213D LEU* 3.9 6.4 - - + +
220D GLU* 3.5 6.7 - - - +
221D ASP* 1.3 99.2 + - - +
223D GLY* 1.3 62.8 + - - +
239D VAL 3.2 7.2 - - - +
240D THR* 3.1 19.7 + - - +
242D LEU* 3.3 10.6 - - - +
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Residues in contact with GLY 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C MET* 3.5 1.0 - - - +
234C MET* 4.1 5.8 - - - -
185D PHE* 3.7 17.1 - - - -
209D TYR 3.1 13.9 - - - -
210D THR* 3.8 1.6 - - - -
222D THR* 1.3 80.7 - - - +
224D VAL* 1.3 65.5 + - - +
239D VAL* 2.8 35.6 + - - +
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C MET* 3.6 13.5 - - + -
226C ALA* 4.5 9.3 - - + +
234C MET* 3.8 6.3 - - + -
235C GLY* 3.4 48.2 - - - +
236C SER* 3.9 8.5 - - - -
185D PHE* 3.9 3.4 - - - -
207D TYR 4.1 0.2 - - - +
208D ALA* 3.1 4.7 - - - +
209D TYR* 2.9 36.6 + - + +
223D GLY* 1.3 79.4 - - - +
225D ALA* 1.3 71.5 + - - +
237D ILE 3.3 5.4 - - - +
238D ASN* 3.2 22.2 - - - +
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Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PHE* 4.4 0.6 - - + -
206D VAL* 4.9 1.3 - - + -
207D TYR 3.3 9.0 - - - +
208D ALA* 3.8 12.6 - - + -
224D VAL* 1.3 80.8 - - - +
226D ALA* 1.3 64.9 + - - +
227D LEU* 3.9 5.4 - - + +
236D SER* 3.0 7.3 - - - -
237D ILE* 2.9 50.6 + - + +
335D ILE* 4.0 21.3 - - + -
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Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C TYR* 4.7 4.5 - - + +
209C TYR* 3.6 23.1 - - + -
224C VAL* 4.1 13.9 - - + -
226C ALA* 4.1 22.1 - - + +
206D VAL* 3.3 6.6 - - - +
207D TYR* 2.7 38.3 + - + +
224D VAL 4.3 0.2 - - - -
225D ALA* 1.3 74.2 - - - +
227D LEU* 1.3 59.3 + - - +
235D GLY 3.5 6.1 - - - -
236D SER* 4.4 3.1 - - - +
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C TYR* 3.7 11.5 - - - -
156D VAL* 5.2 0.4 - - + +
196D LEU* 4.1 32.5 - - + -
203D VAL* 4.7 5.8 - - + -
205D SER 3.7 4.3 - - - -
206D VAL* 3.7 26.5 - - + -
225D ALA* 3.9 11.7 - - + +
226D ALA* 1.3 78.0 - - - +
228D ARG* 1.3 61.8 + - - +
229D TRP* 3.9 30.7 - - + -
234D MET* 3.4 4.6 - - - -
235D GLY 3.0 24.2 + - - +
236D SER* 3.7 33.2 - - - +
237D ILE* 4.1 3.8 - - + +
331D LEU* 4.7 3.4 - - + -
335D ILE* 5.4 1.1 - - + -
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Residues in contact with ARG 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLU* 5.4 5.7 + - - -
228B ARG* 5.9 3.2 - - - +
207C TYR* 5.5 0.6 + - - -
209C TYR* 3.6 47.7 - - + +
210C THR 4.7 10.3 + - - +
339C ALA 5.8 1.4 + - - -
203D VAL* 3.5 3.8 - - - +
204D GLU* 2.7 56.7 + - - +
205D SER* 3.1 16.3 + - - +
227D LEU* 1.3 75.2 - - - +
229D TRP* 1.3 65.6 + - - +
232D GLY* 5.2 6.1 - - - +
233D ALA 3.5 8.7 - - - +
234D MET* 4.5 9.6 - - + -
344D ARG* 4.6 13.9 - - - +
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Residues in contact with TRP 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D VAL* 3.6 28.5 - - + -
196D LEU* 3.2 46.0 + - + -
200D VAL* 3.7 21.9 - - + +
201D GLY 3.2 22.9 + - - -
202D PRO 3.4 11.2 - - - -
203D VAL* 3.7 10.7 - - + +
204D GLU* 3.9 3.4 - - - +
227D LEU* 3.9 24.9 - - + -
228D ARG* 1.3 89.1 - - - +
230D ARG* 1.3 65.9 + - - +
231D HIS* 3.1 24.7 - + + +
232D GLY* 2.9 10.7 + - - -
233D ALA* 2.9 34.7 + - + +
234D MET* 3.7 22.4 - - - -
235D GLY* 3.9 3.6 - - - -
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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