Contacts of the strand formed by residues 210 - 219 (chain B) in PDB entry 5BOU
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 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 5.9 0.2 - - + -
47B ALA 3.5 15.7 - - - +
48B GLU* 4.3 2.5 - - - -
49B ARG* 3.5 15.1 + - - -
58B GLN* 4.0 2.4 - - - +
193B LEU* 4.0 9.9 - - + -
196B LEU* 3.8 24.9 - - + -
205B LEU* 3.9 30.3 - - + -
206B THR 3.7 15.3 - - - +
207B TYR 3.3 12.0 + - - +
208B ASP 3.5 0.8 + - - -
209B ARG* 1.3 84.4 - - - +
211B GLU* 1.3 66.2 + - - +
212B PHE* 5.7 2.2 - - + -
234B ILE* 3.5 25.3 - - + +
238B LEU* 3.8 31.4 - - + -
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Residues in contact with GLU 211 (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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46B ALA* 3.7 1.2 - - - -
47B ALA 2.8 35.3 + - - +
49B ARG* 3.5 41.9 - - + +
61B SER 4.9 0.4 - - - +
62B THR* 4.1 9.1 - - - +
63B GLU* 3.0 30.7 + - - +
64B LYS* 3.1 21.2 + - + +
65B LEU* 3.1 36.2 + - + +
210B LEU* 1.3 74.0 - - - +
212B PHE* 1.3 64.0 + - - +
228B ILE* 5.9 1.6 - - - +
234B ILE* 4.2 3.1 - - - -
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Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.6 24.0 - - + -
45B LEU 3.5 2.7 - - - -
46B ALA* 3.6 26.7 - - + -
65B LEU* 3.4 5.3 - - - +
189B ILE* 3.7 39.5 - - + -
192B ALA* 4.8 0.2 - - + -
193B LEU* 3.6 33.7 - - + -
210B LEU* 5.7 3.4 - - + -
211B GLU* 1.3 74.9 - - - +
213B ALA* 1.3 72.7 + - - +
214B THR* 4.2 3.6 - - + -
228B ILE* 3.8 3.0 - - - +
229B PHE* 2.9 67.6 + + + +
234B ILE* 4.0 18.1 - - + +
237B ILE* 5.2 5.6 - - + -
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Residues in contact with ALA 213 (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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44B VAL* 3.7 1.9 - - - +
45B LEU* 2.7 51.8 + - + +
65B LEU* 3.5 17.9 - - + -
73B ALA* 6.0 2.2 - - + -
212B PHE* 1.3 78.4 - - - +
214B THR* 1.3 66.4 + - - +
215B ILE* 6.3 1.3 - - + -
227B LYS 3.2 13.0 - - - +
228B ILE* 3.8 18.6 - - + -
229B PHE* 4.0 2.0 - - - -
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Residues in contact with THR 214 (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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43B ILE 3.4 9.9 - - - +
44B VAL* 4.4 4.9 - - + -
185B VAL* 4.6 3.6 - - + -
189B ILE* 4.1 23.8 - - + -
212B PHE* 4.2 7.0 - - + -
213B ALA* 1.3 79.1 - - - +
215B ILE* 1.3 65.6 + - - +
216B ARG* 4.0 20.0 + - - +
225B TYR 3.7 1.3 - - - +
226B GLN* 3.6 2.8 - - - +
227B LYS* 3.0 48.9 + - - +
229B PHE* 3.6 21.7 - - + -
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLY* 3.1 5.5 - - - -
43B ILE* 2.9 44.6 + - + +
45B LEU* 5.5 2.2 - - + -
71B LYS 4.1 14.1 - - - +
73B ALA* 4.3 7.2 - - + +
137B ALA* 3.2 44.6 - - + +
138B GLY 4.1 1.3 - - - +
139B TYR* 4.8 3.6 - - + -
145B TYR* 3.7 15.0 - - + -
213B ALA* 6.3 0.9 - - + -
214B THR* 1.3 77.0 - - - +
216B ARG* 1.3 59.4 + - - +
224B VAL* 3.6 28.5 - - + -
225B TYR 3.5 3.4 - - - +
226B GLN* 4.0 23.3 - - + +
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Residues in contact with ARG 216 (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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41B ASP* 4.1 19.1 + - - +
145B TYR* 3.3 5.6 - - - -
185B VAL* 3.5 33.5 - - + +
186B ASP* 2.8 34.3 + - - -
189B ILE* 3.9 11.5 - - - +
214B THR* 4.0 15.3 + - - +
215B ILE* 1.3 75.7 - - - +
217B LYS* 1.3 58.4 + - - +
218B GLY* 3.1 26.0 + - - +
224B VAL* 3.4 5.1 - - - +
225B TYR* 2.8 40.3 + - + +
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Residues in contact with LYS 217 (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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41B ASP* 3.9 8.3 + - + +
139B TYR* 2.9 44.6 + - - -
145B TYR* 2.6 27.5 + - + +
216B ARG* 1.3 69.1 - - - +
218B GLY* 1.3 50.3 - - - +
219B ALA 2.5 30.0 + - - +
221B ASP 4.0 14.1 - - - +
222B GLY* 5.2 5.2 - - - -
223B GLU* 3.3 22.0 - - - +
224B VAL* 4.5 6.3 - - - -
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Residues in contact with GLY 218 (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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41B ASP 5.0 2.0 + - - -
216B ARG* 3.1 26.6 - - - +
217B LYS* 1.3 72.5 - - - +
219B ALA* 1.3 57.1 + - - +
220B ASN 4.3 0.2 - - - -
225B TYR* 4.5 11.1 - - - +
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Residues in contact with ALA 219 (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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217B LYS 2.5 17.4 + - - +
218B GLY* 1.3 75.0 - - - -
220B ASN* 1.3 55.6 + - - +
221B ASP 2.6 25.3 + - - +
223B GLU* 3.4 32.9 - - + +
224B VAL* 3.9 0.9 - - - -
225B TYR* 3.6 29.6 - - + +
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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