Contacts of the strand formed by residues 225 - 234 (chain B) in PDB entry 5K7W
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 ALA 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LYS* 3.6 12.2 - - - +
186B PHE 4.0 3.8 - - - -
189B ILE* 4.3 6.7 - - + -
221B ILE 3.2 11.7 + - - +
222B ASP 3.8 8.7 + - - +
223B GLU 3.8 0.8 - - - -
224B ILE* 1.3 80.3 - - - +
226B ALA* 1.3 63.5 + - - +
227B PRO* 3.8 1.2 - - - +
229B SER* 3.6 11.0 - - - +
253B TYR* 3.3 25.6 - - - +
293B LYS* 3.8 19.3 - - + +
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Residues in contact with ALA 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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185B LYS* 3.8 9.6 - - + -
186B PHE 2.9 25.4 + - - +
187B ASP* 4.2 1.8 - - - +
224B ILE 3.7 1.8 + - - -
225B ALA* 1.3 74.0 - - - +
227B PRO* 1.3 75.8 - - + +
228B ARG 3.1 14.6 - - - +
229B SER* 2.8 18.0 + - - -
293B LYS* 3.5 6.1 - - - +
342B ARG* 3.8 24.9 - - - +
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Residues in contact with PRO 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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185B LYS* 4.7 10.1 - - + -
225B ALA 3.8 2.7 - - - +
226B ALA* 1.3 86.1 - - + +
228B ARG* 1.3 56.8 + - + +
229B SER 4.0 0.2 - - - -
293B LYS* 3.5 10.8 - - + +
294B GLY* 3.3 24.3 + - - -
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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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187B ASP* 4.5 1.0 - - - +
226B ALA* 3.6 10.6 - - - +
227B PRO* 1.3 78.7 - - + +
229B SER* 1.3 63.8 + - - +
293B LYS 3.3 5.4 - - - -
294B GLY* 4.5 1.1 - - - -
295B THR 3.7 18.4 - - - +
296B VAL* 3.4 17.9 - - + -
301B ASP* 3.8 27.3 + - - +
303B ASP* 4.5 12.9 + - - -
304B PHE* 3.3 62.2 - - + +
384B TYR* 3.4 24.5 + - - -
385B LEU* 4.8 3.4 - - - +
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE 3.4 18.8 - - - -
187B ASP 3.2 16.6 - - - -
189B ILE* 6.4 0.7 - - - -
225B ALA* 3.6 15.3 - - - +
226B ALA 2.8 18.7 + - - -
228B ARG* 1.3 76.5 - - - +
230B PHE* 1.3 76.0 + - - +
253B TYR* 4.2 2.6 + - - -
292B ILE* 3.7 1.6 - - - +
293B LYS* 2.8 38.8 + - - +
296B VAL* 5.3 0.2 - - - +
304B PHE* 4.3 1.7 - - - -
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A TRP* 4.6 5.2 - + - -
187B ASP 3.0 6.5 + - - +
188B VAL* 3.3 5.7 - - + -
189B ILE* 3.1 23.8 + - - +
229B SER* 1.3 82.5 - - - +
231B ILE* 1.3 61.0 + - - +
232B PHE* 3.8 19.7 - - + -
253B TYR* 4.0 5.5 + - - -
256B CYS* 4.7 1.1 - - - -
290B MET* 3.7 16.8 - - + -
291B GLY 3.2 16.6 - - - +
292B ILE* 3.6 38.1 - - + -
296B VAL* 4.1 8.7 - - + -
304B PHE* 3.7 26.9 - + - -
305B ILE* 3.7 10.8 - - + -
337B PHE* 3.6 35.0 - + + -
338B CYS* 4.4 10.8 - - + -
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Residues in contact with ILE 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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189B ILE* 3.3 18.2 - - + +
191B LEU* 4.4 10.3 - - + -
221B ILE* 3.9 14.8 - - + -
230B PHE* 1.3 74.5 - - - +
232B PHE* 1.3 77.6 + - - +
233B LEU* 4.7 2.9 - - + +
248B LEU* 3.5 25.8 - - + -
251B TRP* 3.8 33.2 - - + -
253B TYR* 3.6 35.9 - - + +
289B LEU 5.1 0.4 - - - +
290B MET* 3.2 6.2 - - - +
291B GLY 2.9 35.8 + - - +
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Residues in contact with PHE 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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476A LEU* 6.4 0.4 - - + -
188B VAL* 4.2 6.7 - - + -
189B ILE 2.8 17.1 + - - +
190B LEU* 3.4 17.6 - - + +
191B LEU* 2.8 27.4 + - - +
230B PHE* 3.8 22.9 - - + -
231B ILE* 1.3 77.5 - - - +
233B LEU* 1.3 59.8 + - - +
259B ILE* 4.0 22.9 - - + -
288B CYS* 3.8 13.7 - - - -
289B LEU 3.4 4.9 - - - -
290B MET* 3.6 42.8 - - + -
330B ILE* 4.9 0.7 - - + -
333B ILE* 5.4 3.4 - - + -
334B ILE* 3.7 50.7 - - + -
337B PHE* 4.6 8.5 - + + -
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Residues in contact with LEU 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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191B LEU* 3.7 37.0 - - + +
193B PRO* 4.2 11.7 - - + -
213B TRP* 4.2 11.2 - - + -
216B ILE* 4.9 0.7 - - + -
231B ILE* 4.9 4.7 - - + -
232B PHE* 1.3 71.9 - - - +
234B TRP* 1.3 68.7 + - - +
235B CYS* 3.3 25.6 + - - -
244B GLY* 3.8 25.6 - - - +
247B CYS* 4.5 0.2 - - + -
248B LEU* 4.5 13.5 - - + -
251B TRP* 4.2 17.7 - - + -
288B CYS* 3.7 3.9 - - - -
289B LEU* 2.8 40.2 + - + +
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Residues in contact with TRP 234 (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 LEU* 3.8 24.9 - - + +
191B LEU 3.0 17.2 + - - +
192B GLU* 3.8 26.7 + - + -
193B PRO* 4.3 7.8 - - - +
195B LEU* 4.4 2.9 - - - +
198B TYR* 3.8 19.2 + - - +
213B TRP* 4.2 5.0 - - - -
233B LEU* 1.3 80.7 - - - +
235B CYS* 1.3 58.8 + - - +
236B GLY 3.7 0.9 - - - -
259B ILE* 4.8 1.8 - - + -
261B TRP* 4.0 32.8 - + + -
286B GLU* 4.3 17.0 - - + -
287B HIS 3.8 7.4 - - - -
288B CYS* 3.7 31.0 - - + -
314B ILE* 4.8 3.4 - - + -
326B LYS* 3.6 35.2 - - + +
327B PRO* 4.1 12.6 - - + -
330B ILE* 3.9 30.7 - - + +
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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