Contacts of the strand formed by residues 196 - 202 (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 ARG 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B TYR* 3.5 19.9 + - - +
191B LYS* 3.2 58.4 + - - +
193B LEU 4.1 15.5 - - - +
195B ASN* 1.3 75.3 - - - +
197B ARG* 1.4 62.4 + - - +
262B GLU* 3.1 24.0 + - + -
263B VAL 3.0 8.7 - - - +
264B ALA* 3.7 15.3 - - + -
304B ASP 5.1 3.8 + - - -
305B GLY* 3.7 23.7 + - - +
306B VAL* 3.1 28.0 - - + +
307B ASP* 3.1 15.4 + - - +
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Residues in contact with ARG 197 (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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195B ASN* 2.8 30.3 + - - -
196B ARG* 1.4 74.6 - - - +
198B LEU* 1.3 64.5 + - - +
199B LEU* 3.7 27.6 + - + +
238B ASP* 5.3 0.4 + - - -
261B GLY 2.9 1.4 - - - +
262B GLU* 3.4 1.4 - - - -
263B VAL* 2.8 33.3 + - - -
265B LEU* 3.8 22.0 - - + +
268B MET* 3.3 26.7 - - - +
288B LYS* 5.2 3.6 - - - +
306B VAL* 3.9 2.9 - - - -
307B ASP* 3.4 31.9 + - + +
309B PRO* 3.9 19.4 - - + +
328B TYR* 3.7 18.3 + - - -
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Residues in contact with LEU 198 (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* 6.4 0.9 - - + -
156B TYR* 2.7 24.5 + - + -
197B ARG* 1.3 73.9 - - - +
199B LEU* 1.3 60.5 + - - +
260B LEU* 3.5 46.7 - - + -
261B GLY 3.1 11.0 - - - +
262B GLU* 4.3 1.6 - - + +
306B VAL* 3.8 10.0 - - + +
307B ASP 2.6 17.7 + - - +
308B VAL* 3.7 30.7 - - + -
309B PRO* 3.3 10.4 - - - +
339B LYS* 3.8 29.2 - - + -
340B TYR* 4.2 9.6 - - + -
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Residues in contact with LEU 199 (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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156B TYR* 3.9 3.6 - - - +
197B ARG* 3.9 27.1 - - + +
198B LEU* 1.3 83.6 - - - +
200B TRP* 1.4 64.7 - - - +
201B HIS 4.0 0.2 + - - -
236B PHE* 4.0 19.9 - - + -
237B ALA 3.1 14.1 - - - +
238B ASP* 3.9 9.6 - - + -
260B LEU* 3.3 8.7 - - - -
261B GLY* 2.8 31.8 + - - +
263B VAL* 3.5 29.8 - - + -
265B LEU* 4.8 5.8 - - + -
309B PRO* 4.5 0.7 - - + -
328B TYR* 3.4 40.2 - - + -
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Residues in contact with TRP 200 (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* 4.6 2.9 - - + -
156B TYR* 3.3 54.8 - + + -
157B VAL* 3.1 31.0 - - + -
199B LEU* 1.4 75.1 - - - +
201B HIS* 1.3 59.2 - - - +
236B PHE* 3.6 4.2 - - - -
237B ALA 2.6 47.2 + - - +
239B MET 3.4 20.5 + - - +
240B VAL* 3.5 30.4 - - + +
243B SER* 2.9 10.4 + - - +
258B ILE* 3.9 23.6 - - + -
259B LEU 3.2 14.1 - - - +
260B LEU* 3.7 27.1 - - + -
342B LEU* 3.6 27.1 - - + -
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Residues in contact with HIS 201 (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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199B LEU 4.0 0.6 + - - -
200B TRP* 1.3 74.0 - - - +
202B GLY* 1.4 56.8 + - - +
203B SER* 3.9 21.7 + - - -
216B LEU* 3.1 44.9 - - + +
234B ILE* 4.1 12.3 - - + +
235B TYR* 2.7 25.0 + - + -
236B PHE* 3.5 17.7 - - + -
258B ILE* 4.0 4.4 - - - -
259B LEU* 3.2 35.1 + - + +
261B GLY 5.9 0.2 - - - +
502B FRM 3.4 40.9 + - + +
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Residues in contact with GLY 202 (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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201B HIS* 1.4 67.2 + - - +
203B SER* 1.3 65.6 + - - -
243B SER* 2.7 32.3 + - - -
246B TYR* 3.4 10.7 - - - +
247B CYS* 4.2 3.6 - - - -
258B ILE* 3.9 13.5 - - - +
502B FRM 2.8 31.9 + - - +
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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