Contacts of the strand formed by residues 220 - 228 (chain L) in PDB entry 1DU3
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 ILE 220 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G LEU* 4.3 6.3 - - + -
61G LEU* 4.0 23.1 - - + -
132J ARG* 3.9 21.5 - - - +
270J HIS* 5.9 2.7 - - - +
271J GLU* 5.9 0.7 - - - +
211L TYR* 3.5 3.1 - - - -
212L LYS* 2.9 47.8 + - + +
214L THR* 4.1 21.5 - - + -
216L TYR* 4.0 26.2 - - + -
218L ASP 3.9 4.7 - - - +
219L PRO* 1.3 80.1 - - - +
221L LEU* 1.3 72.8 + - - +
222L LEU* 3.5 6.0 - - + +
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Residues in contact with LEU 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J ARG* 5.3 3.4 - - - +
133J SER* 4.4 12.6 - - - +
134J ASN 5.7 1.6 - - - +
270J HIS* 4.5 4.3 + - - -
271J GLU* 3.9 44.4 + - + +
147L LEU* 5.5 4.3 - - + -
209L TYR* 3.3 45.8 - - + -
210L ILE 4.1 0.9 - - - +
211L TYR* 3.3 32.8 - - + +
220L ILE* 1.3 81.9 - - - +
222L LEU* 1.3 63.3 + - - +
223L MET 3.6 14.1 - - - +
224L LYS* 4.2 13.5 - - + -
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Residues in contact with LEU 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J GLY 5.8 2.5 - - - +
161J HIS* 6.3 1.3 - - + -
270J HIS* 4.6 3.6 - - - +
271J GLU* 3.6 21.1 - - - +
274J PHE* 5.6 0.2 - - - -
184L ILE* 4.3 8.7 - - + -
210L ILE* 2.8 25.9 + - + +
211L TYR 4.6 0.2 - - - +
212L LYS* 3.6 44.0 - - + -
220L ILE* 3.5 12.1 - - + +
221L LEU* 1.3 82.9 - - - +
223L MET* 1.3 67.6 + - + +
248L PHE* 3.6 54.5 - - + -
250L LEU* 4.7 1.3 - - + -
256L ILE* 4.2 13.9 - - + -
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Residues in contact with MET 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J GLU* 3.8 6.7 - - - -
274J PHE* 4.0 18.6 - - + -
184L ILE* 3.4 31.0 - - + +
210L ILE* 3.1 36.3 + - + -
221L LEU* 3.6 8.9 - - - +
222L LEU* 1.3 91.5 - - + +
224L LYS* 1.3 67.7 + - - +
244L GLN* 3.4 20.0 - - + +
245L GLY* 3.3 32.1 - - - +
246L GLY* 3.4 3.8 - - - +
248L PHE* 3.1 35.2 - - + -
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Residues in contact with LYS 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLU* 2.8 44.0 + - - +
133J SER* 3.6 33.1 + - - -
187J GLN* 3.1 10.9 + - - -
189J TYR* 3.8 12.9 - - + -
191J ARG* 5.4 0.6 - - - +
241J SER* 4.4 1.6 + - - -
267J ASP* 4.6 6.1 + - - -
269J ASP* 4.9 2.2 + - - -
271J GLU* 3.6 14.3 + - - +
272J ALA* 4.0 24.1 - - - +
207L VAL* 4.8 2.7 - - + -
208L GLN 3.0 12.6 - - - +
209L TYR* 3.9 18.6 - - + -
221L LEU* 4.2 7.2 - - + -
223L MET* 1.3 77.6 - - - +
225L SER* 1.3 59.5 + - - +
244L GLN* 2.7 12.2 + - - +
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Residues in contact with SER 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J GLN* 4.2 6.3 - - - -
189J TYR* 6.5 0.2 - - - -
241J SER* 3.4 13.5 - - - -
206L MET 4.1 0.2 - - - +
207L VAL* 3.2 4.3 - - - -
208L GLN 2.9 29.1 + - - -
224L LYS* 1.3 76.2 - - - +
226L ALA* 1.3 59.5 + - - +
227L ARG* 2.6 26.6 + - - -
242L ILE* 2.9 22.4 - - - +
243L TYR 4.6 1.4 + - - -
244L GLN* 3.1 19.0 + - - -
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Residues in contact with ALA 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLU* 4.2 3.4 - - + -
189J TYR* 3.5 26.4 - - + +
239J LEU* 3.3 19.4 - - + +
241J SER* 2.9 18.1 + - - -
206L MET 3.3 9.0 - - - +
207L VAL* 3.8 19.1 - - + -
224L LYS* 6.1 0.2 - - + -
225L SER* 1.3 75.0 + - - +
227L ARG* 1.3 86.9 + - - +
242L ILE* 5.0 0.2 - - - -
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Residues in contact with ARG 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J ARG* 4.3 16.5 - - - +
239J LEU* 3.2 16.8 - - - +
240J TYR* 4.8 7.9 - - - +
241J SER* 3.4 26.0 + - - +
243J TYR* 5.8 1.4 - - - +
227K ARG* 4.8 12.3 - - - +
205L GLN* 3.5 4.7 - - - -
206L MET* 2.8 35.6 + - + +
225L SER* 2.6 30.1 + - - -
226L ALA* 1.3 99.8 + - - +
228L ASN* 1.3 61.8 + - - +
229L SER 4.3 0.2 - - - -
240L TYR* 4.3 25.6 - - + -
241L SER 4.3 5.7 + - - -
242L ILE* 3.6 38.3 - - + +
243L TYR 4.6 7.3 + - - +
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Residues in contact with ASN 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J CYS* 5.3 0.7 - - - +
237J TYR* 3.9 12.5 - - + +
238J GLY* 3.5 2.2 - - - -
239J LEU* 3.4 36.8 + - + +
240J TYR* 3.4 29.0 + - - -
203L ASP* 6.5 0.4 - - + -
204L LYS 3.2 9.2 - - - +
206L MET* 3.7 2.5 - - - -
227L ARG* 1.3 76.7 - - - +
229L SER* 1.3 77.8 + - - +
230L CYS* 3.6 1.6 + - - -
231L TRP* 2.8 34.0 + - + +
240L TYR* 4.0 9.5 - - - -
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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