Contacts of the strand formed by residues 220 - 229 (chain B) in PDB entry 3RIE
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 LEU 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B ASN* 3.6 12.0 - - - +
190B TYR 3.3 16.4 - - - +
191B ASP 4.1 1.1 - - - +
193B ILE* 3.8 25.6 - - + +
216B ILE* 3.1 22.3 + - + +
217B TYR 3.6 6.1 - - - +
218B ASN 3.3 4.7 - - - +
219B ALA* 1.3 81.9 - - - +
221B LYS* 1.3 70.3 + - - +
224B GLY* 3.8 8.3 - - - +
225B TYR 3.2 43.1 - - - +
226B CYS 4.0 1.3 - - - +
251B PHE* 3.7 31.4 - - + -
276B LYS* 3.1 15.1 + - - -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN* 5.8 3.1 - - - +
188B ASN* 3.0 39.4 + - - +
189B THR* 3.9 16.6 - - - +
190B TYR 2.9 17.9 + - - +
191B ASP* 3.6 22.7 - - - +
219B ALA 3.9 0.6 + - - -
220B LEU* 1.3 73.9 - - - +
222B PRO* 1.3 77.6 - - + +
223B ASN* 3.1 14.4 - - - +
224B GLY 2.9 12.2 + - - +
276B LYS* 3.0 13.0 + - - -
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Residues in contact with PRO 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ASN* 3.2 17.7 - - - +
221B LYS* 1.3 92.3 - - + +
223B ASN* 1.3 60.7 + - + +
224B GLY 3.5 0.2 - - - -
276B LYS* 3.2 30.9 - - + +
277B THR* 5.1 0.5 - - - +
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Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ASP* 4.7 5.3 + - - +
221B LYS* 3.8 14.0 - - - +
222B PRO* 1.3 77.2 - - + +
224B GLY* 1.3 64.9 + - - +
225B TYR* 3.5 21.7 + - - -
276B LYS* 4.4 0.4 - - - -
277B THR* 4.0 23.5 - - + +
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Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR 4.3 2.7 - - - -
191B ASP* 3.2 19.3 - - - -
220B LEU* 3.8 16.4 - - - +
221B LYS 2.9 15.6 + - - -
222B PRO 3.5 0.2 - - - -
223B ASN* 1.3 83.5 + - - +
225B TYR* 1.3 60.5 + - - -
275B SER* 4.3 0.3 - - - -
276B LYS* 3.5 28.2 + - - +
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Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PRO* 4.6 11.2 - - + -
113B VAL* 3.7 18.9 + - + +
114B SER* 3.9 37.7 - - - -
191B ASP 3.1 8.9 + - - +
192B VAL* 3.2 6.6 - - + +
193B ILE 2.9 23.4 + - - -
220B LEU* 3.2 6.7 - - - +
223B ASN 3.5 16.8 + - - -
224B GLY* 1.3 77.0 - - - -
226B CYS* 1.3 60.4 + - - +
274B CYS 3.4 4.0 - - - +
275B SER* 3.3 37.5 - - - -
277B THR* 3.4 23.3 + - + +
279B THR* 4.6 3.6 + - - -
280B GLY 4.3 3.5 + - - -
281B LEU* 3.7 27.1 - - + -
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Residues in contact with CYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ILE* 3.2 13.0 - - + +
195B VAL* 3.9 17.9 - - - -
213B TYR* 4.6 13.7 - - - -
216B ILE* 3.6 35.4 - - + -
220B LEU* 4.0 3.5 - - + +
225B TYR* 1.3 75.7 - - - +
227B VAL* 1.3 77.2 + - - +
228B ALA* 4.6 1.1 - - - -
272B LEU 3.7 0.7 - - - +
274B CYS* 2.8 47.0 + - + +
281B LEU* 4.2 0.2 - - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B MET* 3.3 28.5 - - - +
109B VAL* 4.9 1.1 - - + -
110B PRO* 3.8 30.5 - - + +
193B ILE 3.1 6.6 + - - +
194B ILE* 3.4 22.2 - - + -
195B VAL 2.8 31.0 + - - +
226B CYS* 1.3 81.9 - - - +
228B ALA* 1.3 55.1 + - - +
271B ILE* 3.5 17.5 - - + -
272B LEU 3.1 4.3 - - - -
273B CYS* 4.1 11.0 - - - -
281B LEU* 3.9 16.4 - - + -
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B MET* 4.3 4.5 - - - -
195B VAL* 3.6 24.7 - - + -
213B TYR* 3.2 28.9 - - + +
226B CYS* 4.7 2.5 - - - -
227B VAL* 1.3 76.3 - - - +
229B GLN* 1.3 70.5 + - - +
230B CYS* 3.6 1.0 - - - +
271B ILE* 3.5 1.6 - - - +
272B LEU* 2.8 37.1 + - + +
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 3.3 37.2 - - + +
106B MET* 3.7 6.9 - - + +
195B VAL* 3.1 14.7 + - - +
197B SER* 3.1 38.5 + - - +
198B SER 3.7 11.1 + - - -
199B ASP* 4.5 7.4 + - - +
208B PHE* 3.8 20.8 - - - -
213B TYR* 5.4 0.5 + - - -
228B ALA* 1.3 76.1 - - - +
230B CYS* 1.3 63.9 + - - +
231B GLU 4.3 3.5 + - - -
269B ILE* 3.5 19.4 - - + +
270B GLY 3.6 6.5 - - - -
501B JFQ 3.8 9.9 - - + +
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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