Contacts of the strand formed by residues 223 - 233 (chain B) in PDB entry 1WG8
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 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B ARG* 4.3 4.7 + - - +
90B VAL* 3.7 13.7 - - - +
92B GLY* 4.0 12.1 - - - +
93B ILE* 4.0 13.9 - - + -
219B ALA 3.1 21.2 + - - +
220B ALA* 4.0 8.5 - - - +
221B GLU 3.3 3.3 - - - +
222B VAL* 1.3 77.4 - - - +
224B ALA* 1.3 58.5 + - - +
225B PRO* 4.6 0.3 - - - +
227B GLY* 3.5 30.7 - - - +
228B ARG 3.8 15.3 - - - +
229B LEU* 4.0 26.2 - - + +
251B LEU* 4.7 4.9 - - + -
282B LYS* 2.8 46.9 - - + +
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Residues in contact with ALA 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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21B ARG* 5.8 1.3 - - - +
89B ARG* 4.2 16.8 - - + -
90B VAL 2.9 24.6 + - - +
91B ASP* 4.5 12.6 - - - +
222B VAL 3.5 1.0 + - - -
223B LEU* 1.3 76.7 - - - +
225B PRO* 1.3 81.9 - - + +
226B GLY 3.2 0.3 + - - -
227B GLY* 2.9 16.2 + - - -
282B LYS* 3.7 4.7 - - - +
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Residues in contact with PRO 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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21B ARG* 4.8 7.6 + - - -
89B ARG* 5.7 1.6 - - + -
223B LEU 4.0 0.9 - - - +
224B ALA* 1.3 91.2 - - + +
226B GLY* 1.3 61.6 + - - +
227B GLY 3.4 0.2 + - - -
282B LYS* 4.2 8.7 - - + +
283B GLU 4.5 5.8 - - - +
284B ALA* 3.7 31.2 - - + +
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Residues in contact with GLY 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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21B ARG* 5.0 11.0 + - - -
225B PRO* 1.3 71.6 - - - +
227B GLY* 1.3 60.9 + - - +
228B ARG* 3.9 6.2 + - - +
281B GLU* 3.9 20.8 - - - +
282B LYS 2.7 21.8 + - - -
283B GLU* 4.8 0.8 - - - +
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Residues in contact with GLY 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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21B ARG* 5.3 1.6 - - - -
91B ASP* 3.3 20.9 - - - -
223B LEU* 3.5 16.2 - - - +
224B ALA* 2.9 18.2 + - - -
225B PRO 3.2 0.6 + - - -
226B GLY* 1.3 80.0 - - - +
228B ARG* 1.3 61.2 + - - -
281B GLU* 3.3 1.7 - - - -
282B LYS 2.8 25.5 + - - -
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Residues in contact with ARG 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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16B ASP 4.4 1.0 + - - -
17B LEU* 2.8 66.0 + - - +
18B LEU* 4.2 16.9 - - - +
19B ALA* 4.1 15.4 - - + +
91B ASP 3.7 5.7 + - - -
92B GLY* 3.4 3.3 - - - -
93B ILE 3.0 26.0 + - - +
223B LEU* 3.8 3.7 - - - +
226B GLY 4.3 4.6 + - - +
227B GLY* 1.3 75.2 - - - -
229B LEU* 1.3 59.8 + - - +
230B VAL* 3.9 4.5 - - + -
254B LEU* 3.1 37.1 - - - +
279B ALA* 5.7 0.4 - - + -
280B ALA 3.3 2.7 - - - +
281B GLU* 2.9 37.9 + - - -
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Residues in contact with LEU 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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93B ILE* 3.6 19.7 - - + +
215B PHE* 4.9 2.7 - - + -
216B LEU* 4.1 22.2 - - + +
219B ALA* 4.2 20.6 - - + -
220B ALA 5.0 0.9 - - - +
223B LEU* 4.0 14.5 - - + +
228B ARG* 1.3 72.3 - - - +
230B VAL* 1.3 66.2 + - - +
231B VAL* 3.4 23.9 + - + +
245B PHE* 4.3 10.5 - - + -
246B LEU* 4.6 12.1 - - + +
251B LEU* 4.0 23.1 - - + -
279B ALA* 3.1 6.9 - - - +
280B ALA 2.8 35.7 + - - +
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Residues in contact with VAL 230 (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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14B ALA* 4.1 21.3 - - + +
17B LEU* 3.9 28.3 - - + +
18B LEU* 3.3 31.6 - - + +
93B ILE 2.9 9.7 + - - +
94B LEU* 3.2 21.7 - - + +
95B ALA 2.9 24.6 + - - -
228B ARG* 4.4 1.8 - - + -
229B LEU* 1.3 77.8 - - - +
231B VAL* 1.3 66.2 + - - +
277B LEU* 4.2 18.6 - - + -
278B ARG 3.6 3.6 - - - +
279B ALA* 4.1 3.8 - - + -
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Residues in contact with VAL 231 (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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95B ALA* 3.3 19.3 - - + +
97B LEU* 4.0 17.7 - - + -
212B LEU* 5.0 2.7 - - + -
215B PHE* 4.7 0.7 - - + -
216B LEU* 4.1 16.6 - - + -
229B LEU* 3.4 30.5 - - + +
230B VAL* 1.3 74.5 - - - +
232B ILE* 1.3 67.3 + - - +
233B ALA 4.0 0.7 - - - +
242B VAL* 3.7 38.4 - - + +
246B LEU* 5.6 1.3 - - + -
276B LYS 3.7 1.6 - - - +
277B LEU* 3.5 2.4 - - - +
278B ARG* 2.9 35.3 + - - +
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Residues in contact with ILE 232 (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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9B VAL* 3.7 28.5 - - + +
10B LEU* 4.5 2.0 - - + -
14B ALA* 4.7 4.9 - - + -
36B HIS* 4.3 7.4 - - - +
94B LEU* 4.9 7.2 - - + -
95B ALA 2.8 13.5 + - - +
96B ASP* 4.0 22.9 - - + +
97B LEU* 3.1 26.0 + - - +
231B VAL* 1.3 77.5 - - - +
233B ALA* 1.3 58.9 + - - +
234B PHE* 3.4 28.4 - - + -
275B ALA* 3.8 17.0 - - + -
276B LYS 3.6 10.1 - - - +
277B LEU* 3.8 26.7 - - + +
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Residues in contact with ALA 233 (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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97B LEU* 4.0 9.4 - - + -
231B VAL 4.0 1.2 - - - -
232B ILE* 1.3 71.2 - - - +
234B PHE* 1.3 65.5 + - - +
238B GLU* 3.6 11.9 - - + +
239B ASP* 3.6 44.6 - - + +
242B VAL* 4.6 7.2 - - + -
275B ALA* 3.5 3.5 - - - -
276B LYS* 2.8 36.5 + - - +
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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