Contacts of the strand formed by residues 227 - 234 (chain D) in PDB entry 3FAA
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 GLU 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D THR* 3.4 13.6 - - - -
177D LEU* 2.6 43.6 + - + +
178D LYS* 3.5 34.1 - - + +
223D LYS* 3.2 3.7 - - - -
224D TRP* 3.0 37.8 + - - +
225D ARG* 2.5 31.7 - - - +
226D GLY* 1.3 72.8 - - - +
228D GLU* 1.3 62.4 + - - +
229D VAL* 3.9 1.4 - - - +
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Residues in contact with GLU 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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177D LEU* 4.3 5.0 - - - +
178D LYS* 5.1 3.2 + - - +
221D ARG* 3.2 35.5 + - + +
222D GLY 3.3 9.9 - - - +
223D LYS* 4.2 15.8 - - - -
226D GLY 3.6 2.1 + - - +
227D GLU* 1.3 70.9 - - - +
229D VAL* 1.3 71.3 + - - +
281D ASP* 5.6 0.3 - - - -
282D TYR* 3.3 43.6 + - + +
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Residues in contact with VAL 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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177D LEU* 3.5 26.7 - - + -
201D ILE* 6.4 0.9 - - + -
205D ILE* 4.5 7.6 - - + -
221D ARG* 3.6 4.2 - - - -
222D GLY* 2.7 42.3 + - - +
224D TRP* 4.4 13.2 - - + +
227D GLU 3.9 7.6 - - - +
228D GLU* 1.3 83.7 - - - +
230D ALA* 1.3 73.4 + - - +
231D VAL* 5.4 0.2 - - + -
263D ILE* 4.4 2.0 - - + -
279D VAL* 3.2 31.0 - - + -
280D SER 3.1 15.7 - - - +
282D TYR* 3.7 12.3 - - - +
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Residues in contact with ALA 230 (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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211D ILE* 5.7 0.4 - - + -
219D VAL* 4.7 2.2 - - + -
220D TRP 3.5 6.5 - - - +
229D VAL* 1.3 80.2 - - - +
231D VAL* 1.3 59.0 + - - +
279D VAL* 3.3 2.6 - - - -
280D SER* 2.7 38.0 + - - +
281D ASP 3.6 10.3 - - - +
282D TYR* 4.1 5.1 - - + +
601D 55F 3.3 48.5 - - + +
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Residues in contact with VAL 231 (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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205D ILE* 4.8 6.5 - - + -
207D LEU* 3.5 26.0 - - + -
218D GLU 3.6 0.7 - - - +
219D VAL* 3.6 1.1 - - - -
220D TRP* 3.0 43.2 + - + +
222D GLY* 4.4 9.9 - - - +
229D VAL 4.8 0.4 - - - +
230D ALA* 1.3 74.8 - - - +
232D LYS* 1.3 61.4 + - - +
233D ILE* 3.6 26.4 + - + +
277D TRP* 3.7 26.5 - - + -
278D LEU 3.2 8.1 - - - +
279D VAL* 3.8 13.9 - - + -
601D 55F 4.2 0.9 - - - -
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Residues in contact with LYS 232 (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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216D PHE* 3.3 45.1 - - + +
218D GLU 3.5 2.7 - - - -
219D VAL* 4.2 5.2 - - + +
231D VAL* 1.3 70.9 - - - +
233D ILE* 1.3 59.7 + - - +
234D PHE* 3.4 23.6 - - + -
245D GLU* 2.7 32.4 + - - +
277D TRP* 3.5 5.2 - - - -
278D LEU* 2.7 36.6 + - + +
351D ASP* 3.4 21.0 + - - -
601D 55F 3.5 49.0 + - + +
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Residues in contact with ILE 233 (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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207D LEU* 3.9 24.7 - - + -
216D PHE* 5.0 0.4 - - - -
217D GLY* 3.2 3.4 - - - -
218D GLU* 2.6 42.0 + - + +
220D TRP* 4.2 15.9 - - + +
231D VAL* 3.6 20.2 - - + +
232D LYS* 1.3 70.5 - - - +
234D PHE* 1.3 72.4 + - - +
275D GLN* 6.0 3.1 - - + -
276D LEU 3.7 2.9 - - - +
277D TRP* 3.5 38.8 - - + +
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Residues in contact with PHE 234 (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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216D PHE* 3.6 24.5 - - + +
217D GLY* 4.1 0.2 - - - -
232D LYS* 3.4 46.9 - - + -
233D ILE* 1.3 86.2 - - - +
235D SER* 1.3 67.0 + - - +
236D SER 3.8 1.4 + - - -
238D GLU 4.1 8.7 - - - +
241D SER* 4.1 11.0 - - - -
242D TRP* 3.8 43.5 - + + -
245D GLU* 3.8 6.5 - - - -
274D THR 5.1 1.9 - - - +
275D GLN* 5.2 0.9 - - - -
276D LEU* 3.1 29.3 + - + +
278D LEU* 3.3 35.4 - - + -
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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