Contacts of the strand formed by residues 256 - 261 (chain A) in PDB entry 1WK8
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 GLU 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ARG* 2.6 50.6 + - - -
220A GLU 4.3 0.9 - - - -
221A LYS* 3.4 28.2 + - - +
223A SER* 4.7 2.4 + - - -
251A PHE 3.6 0.2 - - - +
252A GLN* 3.3 8.6 + - - +
253A VAL* 3.0 42.2 + - + +
254A GLY 3.3 0.6 - - - -
255A ASP* 1.3 85.8 - - - +
257A ALA* 1.3 60.7 + - - +
258A LEU* 3.6 28.6 + - + +
377A PHE* 4.2 4.2 - - - -
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Residues in contact with ALA 257 (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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219A LEU* 3.9 27.6 - - + -
220A GLU 3.6 15.5 + - - +
221A LYS 3.1 7.0 + - - +
222A ALA* 3.2 5.2 - - + +
223A SER 2.9 25.6 + - - -
250A ALA* 4.8 3.4 - - + -
251A PHE 3.2 6.5 - - - +
252A GLN* 4.7 0.9 - - - +
256A GLU* 1.3 73.7 - - - +
258A LEU* 1.3 63.1 + - - +
259A ILE* 5.3 0.9 - - + -
276A LEU* 3.9 17.9 - - + -
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Residues in contact with LEU 258 (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 ARG* 4.4 7.2 - - + +
223A SER* 3.4 20.0 - - - +
225A LEU* 4.1 21.1 - - + -
249A ALA 3.5 2.1 - - - +
251A PHE* 2.8 38.0 + - - +
253A VAL* 4.0 19.3 - - + -
256A GLU* 3.6 30.5 - - + +
257A ALA* 1.3 80.1 - - - +
259A ILE* 1.3 62.1 + - - +
260A LEU* 4.0 12.1 - - + -
269A LEU* 4.7 3.4 - - + -
377A PHE* 3.5 37.5 - - + -
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Residues in contact with ILE 259 (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 LEU* 4.0 24.2 - - + -
217A LEU* 4.2 8.3 - - + -
219A LEU* 3.9 22.4 - - + -
222A ALA* 4.9 0.7 - - + -
223A SER 2.9 12.3 + - - +
224A LEU* 4.2 23.1 - - + -
225A LEU 3.0 24.4 + - - -
248A TYR* 4.5 3.1 - - + -
249A ALA 3.2 7.6 - - - +
250A ALA* 4.0 17.7 - - + -
257A ALA 5.1 2.0 - - - +
258A LEU* 1.3 75.5 - - - +
260A LEU* 1.3 67.6 + - - +
279A PHE* 4.0 20.4 - - + -
284A LEU* 4.5 10.8 - - + -
287A LEU* 5.0 1.3 - - + -
317A ILE* 3.4 10.4 - - + +
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Residues in contact with LEU 260 (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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225A LEU* 4.1 7.6 - - + -
248A TYR* 3.4 10.9 - - - -
249A ALA* 2.9 26.9 + - - +
251A PHE* 3.8 23.3 - - + -
258A LEU* 3.8 13.5 - - + +
259A ILE* 1.3 80.8 - - - +
261A GLU* 1.3 67.6 + - - +
262A GLU* 4.2 0.3 - - - -
264A LEU* 4.2 2.2 - - + -
265A GLY* 3.6 29.6 - - - +
268A LEU* 3.9 22.4 - - + -
269A LEU* 4.2 11.4 - - + -
314A GLY 5.1 0.7 - - - +
315A THR* 3.3 37.2 - - + +
317A ILE* 4.1 2.9 - - - -
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Residues in contact with GLU 261 (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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246A TYR* 3.9 27.1 - - + +
247A THR* 3.6 14.2 + - - +
248A TYR* 3.3 17.6 - - + -
251A PHE* 4.5 0.2 - - - -
260A LEU* 1.3 73.3 - - - +
262A GLU* 1.3 64.8 + - - +
263A GLY* 3.1 13.6 + - - -
264A LEU* 2.9 37.3 + - + +
265A GLY* 2.8 32.2 + - - -
311A GLN* 3.5 26.3 + - + +
315A THR 2.8 18.8 + - - +
316A GLY* 4.1 7.4 - - - -
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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