Contacts of the strand formed by residues 206 - 215 (chain A) in PDB entry 1WKB
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 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.0 59.2 + - + +
183A VAL 4.9 4.9 - - - -
184A ARG* 3.7 21.5 - - - +
205A PRO* 1.3 73.6 - - - +
207A LEU* 1.3 64.4 + - - +
208A ASP* 4.2 2.4 + - - +
441A TYR* 3.8 14.8 - - + -
442A GLU 3.7 4.0 - - - -
443A PHE* 3.9 13.5 - - + +
458A ILE* 3.6 31.9 - - + -
906A SO4 3.3 26.5 + - - +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PRO* 4.4 17.0 - - + -
206A ILE* 1.3 79.0 - - - +
208A ASP* 1.3 62.9 + - - +
209A TYR* 3.4 33.8 + - + +
230A LEU* 4.3 18.8 - - + -
441A TYR* 3.3 7.8 - - - +
442A GLU 2.7 39.2 + - - +
443A PHE 4.9 0.4 - - - +
444A ALA* 3.9 29.2 - - + -
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.7 10.7 + - - -
206A ILE 4.4 2.6 - - - +
207A LEU* 1.3 72.0 - - - +
209A TYR* 1.3 66.7 + - - +
210A ILE* 3.6 8.9 + - + +
229A THR 4.9 0.2 - - - +
230A LEU* 4.1 10.4 - - - +
439A ILE* 4.0 21.5 - - + +
440A MET 4.2 2.2 - - - -
441A TYR* 3.6 29.6 + - - -
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Residues in contact with TYR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 3.9 28.1 - - + +
208A ASP* 1.3 73.7 - - - +
210A ILE* 1.3 59.0 + - - +
228A ALA* 3.6 31.6 - - + -
229A THR* 3.9 14.1 - - - -
230A LEU* 3.7 35.0 - - + +
317A ASN* 3.4 28.3 + - - -
318A ALA* 4.1 5.8 - - + -
439A ILE* 3.2 6.6 - - - +
440A MET* 2.9 44.7 + - + +
442A GLU* 3.7 33.2 - - + -
443A PHE 5.5 0.4 + - - -
907A SO4 5.3 1.8 - - - -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ASP* 4.5 6.3 - - + +
209A TYR* 1.3 73.0 - - - +
211A ILE* 1.3 59.9 + - - +
212A ILE* 3.7 13.2 + - + -
227A ALA 3.4 2.4 - - - +
228A ALA* 3.3 1.0 - - - -
229A THR* 2.9 43.2 + - + +
230A LEU* 6.0 0.4 - - - -
232A PRO* 4.2 20.6 - - + -
424A LYS* 5.6 2.2 - - - +
428A ALA* 4.1 16.8 - - + -
431A MET* 4.1 12.3 - - + -
432A LEU* 4.3 14.8 - - + -
437A ALA* 3.7 24.7 - - + -
438A GLU 3.4 1.8 - - - +
439A ILE* 4.1 22.0 - - + -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A TYR 4.4 0.9 - - - +
210A ILE* 1.3 75.8 - - - +
212A ILE* 1.3 62.3 + - - +
213A LYS* 3.4 5.1 + - + +
226A PRO* 4.0 14.4 - - + -
227A ALA 3.4 4.0 - - - +
228A ALA* 3.8 11.9 - - + -
263A TRP* 3.9 28.5 - - + -
273A LEU* 4.9 2.2 - - + -
278A ARG* 4.1 9.4 - - - +
319A THR* 3.6 24.5 - - + -
437A ALA* 3.2 2.5 - - - -
438A GLU* 2.5 63.9 + - + +
439A ILE 4.5 0.2 - - - -
440A MET* 3.6 26.9 - - + +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.9 16.4 - - + -
211A ILE* 1.3 69.4 - - - +
213A LYS* 1.3 60.4 + - - +
214A PHE* 3.0 34.9 + - + -
225A LEU 3.4 0.2 - - - +
226A PRO* 3.9 0.7 - - - -
227A ALA 2.9 37.5 + - - +
229A THR* 3.9 14.6 - - + -
232A PRO 4.4 2.7 - - - +
235A VAL* 3.9 20.2 - - + -
299A PRO* 3.9 16.4 - - + -
300A VAL* 5.1 0.2 - - + -
323A MET* 3.9 23.1 - - + -
431A MET* 3.9 29.4 - - + -
436A ILE* 4.0 6.1 - - + +
437A ALA* 4.1 1.6 - - + -
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 4.2 8.3 - - + +
212A ILE* 1.3 66.7 - - - +
214A PHE* 1.3 66.0 + - - +
215A GLU* 3.6 3.1 + - - +
224A TYR* 3.7 34.3 - - + -
226A PRO* 4.1 15.3 - - + -
261A GLU* 2.7 39.9 + - - +
263A TRP* 3.9 7.2 - - + -
299A PRO* 3.3 19.3 - - - +
435A GLY* 3.5 21.4 + - - +
436A ILE* 3.0 20.4 + - - +
438A GLU* 2.8 37.6 + - + -
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Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ILE* 3.0 44.0 + - + -
213A LYS* 1.3 74.5 - - - +
215A GLU* 1.3 56.5 + - - +
224A TYR* 3.4 5.9 - - - +
225A LEU* 2.9 38.9 + - + +
227A ALA* 4.4 6.5 - - + -
235A VAL* 4.9 1.3 - - + -
238A VAL* 3.7 22.7 - - + -
241A MET* 3.5 34.8 - - + -
296A VAL* 3.2 24.9 - - + -
297A ARG 3.4 17.0 - - - -
298A ASN* 3.6 28.7 - - + -
299A PRO* 3.6 3.8 - - + -
305A VAL* 4.6 2.0 - - + -
323A MET* 4.2 17.9 - - + -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS 4.0 6.5 - - - +
214A PHE* 1.3 71.2 - - - +
216A LEU* 1.3 61.0 + - - +
217A ARG* 3.8 11.2 + - + +
223A ILE 4.2 3.6 - - - -
224A TYR* 4.3 16.8 - - + -
295A TYR 4.4 0.2 - - - +
296A VAL* 2.8 6.6 - - - +
297A ARG* 2.6 85.0 + - + +
299A PRO* 3.2 20.4 - - - +
436A ILE* 5.2 2.3 - - - +
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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