Contacts of the strand formed by residues 196 - 204 (chain A) in PDB entry 1WK9
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 LYS 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLY* 1.3 79.7 - - - +
197A LEU* 1.3 61.9 + - - +
198A TYR* 3.7 37.3 + - + +
215A VAL* 3.5 23.4 - - - +
334A GLU* 4.2 27.5 + - + +
335A GLU 3.2 10.5 - - - +
336A ASP* 2.8 31.5 + - - +
337A TYR* 3.9 7.5 - - - -
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Residues in contact with LEU 197 (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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196A LYS* 1.3 72.1 - - - +
198A TYR* 1.3 62.0 + - - +
199A THR* 5.1 1.9 + - - +
213A ALA* 4.0 18.8 - - + -
214A THR* 3.7 24.7 - - - +
215A VAL* 3.6 20.2 - - + -
265A GLY* 5.4 7.4 - - - -
333A LYS 4.0 0.2 - - - +
334A GLU* 3.3 3.3 - - - -
335A GLU* 2.7 68.0 + - + +
337A TYR* 4.0 21.0 - - + +
999A TSB 5.5 0.4 - - - +
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Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS* 3.7 37.4 + - + +
197A LEU* 1.3 74.5 - - - +
199A THR* 1.3 62.3 + - - +
200A LEU* 4.1 10.3 + - + -
212A ILE 3.7 0.9 - - - +
213A ALA* 3.1 3.3 - - - +
214A THR* 2.9 47.6 + - + +
215A VAL 5.0 1.3 - - - -
217A PRO* 3.8 26.7 - - + -
318A ARG* 5.3 6.6 - - + +
319A ARG* 6.0 0.2 - - - -
322A VAL* 3.5 40.0 - - + +
331A LEU* 4.0 19.5 - - + -
333A LYS 3.5 2.0 - - - -
334A GLU* 3.7 31.2 - - + -
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Residues in contact with THR 199 (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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197A LEU* 5.1 2.1 + - - +
198A TYR* 1.3 74.6 + - - +
200A LEU* 1.3 63.2 + - - +
211A GLU* 3.9 30.7 - - + +
212A ILE 3.3 9.6 - - - +
213A ALA* 4.2 9.0 - - - +
266A THR* 4.0 11.4 - - + +
331A LEU* 3.7 4.9 - - - +
332A VAL* 2.8 34.7 + - + -
333A LYS* 2.9 46.1 + - - +
335A GLU* 4.3 4.9 + - - -
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Residues in contact with LEU 200 (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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198A TYR* 4.7 9.4 - - + +
199A THR* 1.3 75.6 - - - +
201A ARG* 1.3 62.3 + - - +
202A TYR* 4.0 21.2 - - + -
210A ILE 3.8 0.2 - - - +
211A GLU* 3.1 5.4 - - - +
212A ILE* 2.8 35.9 + - + +
214A THR* 4.4 13.7 - - + -
217A PRO* 5.2 2.2 - - + -
220A VAL* 3.7 30.7 - - + -
246A PRO* 5.3 1.1 - - + -
270A LYS* 6.0 0.2 - - + -
325A PHE* 3.8 37.5 - - + -
330A HIS* 3.1 18.2 - - + +
331A LEU* 3.9 21.3 - - + -
332A VAL* 4.1 3.4 - - - -
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Residues in contact with ARG 201 (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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200A LEU* 1.3 73.9 - - - +
202A TYR* 1.3 64.4 + - - +
209A PHE* 3.7 46.4 - - + -
210A ILE 3.6 4.3 - - - -
211A GLU* 4.3 8.4 + - + +
246A PRO* 3.9 0.9 - - - +
329A GLY* 2.6 36.6 + - - -
330A HIS* 2.9 47.8 + - - +
331A LEU 4.0 13.5 + - - -
332A VAL* 3.4 36.1 - - + +
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Residues in contact with TYR 202 (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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200A LEU* 4.0 24.0 - - + +
201A ARG* 1.3 78.1 - - - +
203A GLU* 1.3 64.0 + - - +
204A VAL 3.4 0.2 + - - -
209A PHE* 3.2 4.3 - - - -
210A ILE* 2.9 43.3 + - + +
212A ILE* 4.3 18.2 - - + -
220A VAL* 3.5 17.4 - - + +
223A ASP* 2.5 30.9 + - - -
226A ILE* 3.9 24.5 - - + -
243A ALA* 4.4 10.3 - - + -
244A ARG 3.7 13.7 - - - +
245A ILE* 4.3 5.8 - - - -
246A PRO* 3.6 33.2 - - + -
252A ILE* 4.6 5.2 - - + -
270A LYS* 3.7 9.2 - - - +
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Residues in contact with GLU 203 (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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201A ARG 4.1 0.4 + - - -
202A TYR* 1.3 71.0 - - - +
204A VAL* 1.3 61.4 + - - +
208A GLY 3.6 8.3 - - - +
209A PHE* 3.3 35.9 - - + -
243A ALA* 3.3 3.8 - - - -
244A ARG* 2.6 79.7 + - + +
251A TRP* 3.9 5.8 - - + -
330A HIS* 3.5 13.5 - - - -
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Residues in contact with VAL 204 (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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203A GLU* 1.3 75.8 - - - +
205A GLU* 1.3 78.4 + - - +
206A GLY 3.2 0.3 + - - -
207A GLY* 3.0 27.5 + - - +
208A GLY 2.9 13.1 + - - +
209A PHE 3.6 6.3 - - - +
210A ILE* 3.6 44.2 - - + +
238A LEU* 4.1 28.9 - - + -
241A LYS* 4.5 6.7 - - + +
242A ARG 3.7 8.1 - - - +
243A ALA* 5.0 0.4 - - + -
251A TRP* 4.1 4.9 - - - -
254A ILE* 4.5 7.6 - - + -
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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