Contacts of the strand formed by residues 258 - 264 (chain B) in PDB entry 1UK0
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 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B TRP* 3.9 17.8 - - + -
201B HIS 4.0 0.7 - - - -
202B GLY* 3.9 25.6 - - - +
208B PHE* 3.7 3.5 - - - -
240B VAL* 3.7 27.1 - - + +
243B SER* 4.5 0.2 - - - -
244B ALA* 4.2 16.8 - - + -
247B CYS* 4.2 4.7 - - - -
257B LEU* 1.4 75.6 - - - +
259B LEU* 1.3 78.7 + - - +
340B TYR 3.5 0.2 - - - +
341B LEU* 4.0 3.2 - - - +
342B LEU* 3.0 56.5 + - + +
344B LEU* 4.2 17.7 - - + -
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Residues in contact with LEU 259 (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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178B ILE* 3.6 23.8 - - + -
200B TRP* 3.2 12.6 - - - +
201B HIS* 3.2 39.1 + - + +
208B PHE* 3.5 24.6 - - + -
211B ILE* 3.7 23.1 - - + -
212B LEU* 4.9 2.5 - - + -
216B LEU* 4.1 14.8 - - + -
258B ILE* 1.3 78.2 - - - +
260B LEU* 1.3 63.8 + - - +
261B GLY* 5.6 0.2 - - - -
338B LEU* 3.3 35.7 - - + -
340B TYR 3.5 1.8 - - - +
341B LEU* 4.0 12.3 - - + -
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Residues in contact with LEU 260 (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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153B ILE* 4.4 16.8 - - + -
156B TYR* 3.5 28.3 - - + -
198B LEU* 3.5 33.2 - - + -
199B LEU 3.3 19.5 - - - +
200B TRP* 3.7 26.5 - - + -
259B LEU* 1.3 77.7 - - - +
261B GLY* 1.4 58.9 - - - +
338B LEU* 3.8 5.7 - - - +
339B LYS 3.1 23.1 + - - -
340B TYR* 2.9 44.9 + - + +
342B LEU* 4.4 2.2 - - + -
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Residues in contact with GLY 261 (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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197B ARG 2.9 14.6 - - - +
198B LEU* 3.1 5.4 - - - -
199B LEU 2.8 26.7 + - - -
201B HIS 5.4 0.2 - - - +
236B PHE* 4.6 10.9 - - - -
259B LEU* 5.6 0.2 - - - -
260B LEU* 1.4 74.3 - - - +
262B GLU* 1.3 65.5 + - - -
263B VAL* 3.2 9.8 + - - +
336B VAL* 5.2 3.4 - - - -
337B ASN 3.9 6.1 - - - -
338B LEU* 4.9 5.2 - - - -
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Residues in contact with GLU 262 (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 TYR* 2.9 40.1 + - - +
191B LYS* 5.4 1.6 - - - +
196B ARG* 3.1 21.9 + - + -
197B ARG 3.4 3.6 - - - -
198B LEU* 4.3 5.6 - - + +
261B GLY* 1.3 73.3 - - - -
263B VAL* 1.3 62.0 - - - +
306B VAL* 2.6 38.9 - - + +
336B VAL* 3.6 2.9 - - - +
337B ASN* 3.1 40.1 + - + +
339B LYS* 3.4 36.9 + - + +
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Residues in contact with VAL 263 (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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196B ARG* 3.0 21.7 - - - -
197B ARG 2.8 14.3 + - - -
199B LEU* 3.5 27.8 - - + -
236B PHE* 3.8 34.3 - - + -
261B GLY 3.7 7.4 - - - +
262B GLU* 1.3 77.1 - - - +
264B ALA* 1.3 62.2 + - - +
265B LEU* 2.8 23.6 + - + +
330B VAL* 3.8 25.6 - - + -
335B GLN 3.6 16.6 - - - +
336B VAL* 4.4 4.0 - - + -
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Residues in contact with ALA 264 (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 TYR* 3.7 18.4 + - + -
190B PHE* 3.8 24.5 - - + +
193B LEU* 3.8 8.1 - - + +
194B HIS 5.1 0.2 - - - +
195B ASN 4.8 0.2 - - - -
196B ARG* 3.7 15.5 - - + +
263B VAL* 1.3 73.9 - - - +
265B LEU* 1.3 61.3 + - - +
266B GLY 3.4 2.6 + - - -
330B VAL* 4.5 0.3 - - - +
335B GLN* 2.9 45.7 + - + +
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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