Contacts of the helix formed by residues 182 - 192 (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 GLY 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ARG 3.8 0.2 + - - -
181B GLU* 1.4 76.9 + - - +
183B GLU* 1.3 56.2 + - - +
184B CYS 3.9 0.2 - - - -
185B GLN* 3.0 16.7 + - - +
186B ARG* 2.9 27.1 + - - +
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Residues in contact with GLU 183 (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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179B GLU* 6.2 0.4 - - + -
180B ARG* 2.9 58.9 + - + +
181B GLU 2.7 10.3 + - - -
182B GLY* 1.3 64.7 - - - -
184B CYS* 1.4 72.3 + - - +
185B GLN 2.8 1.2 + - - -
186B ARG* 2.8 35.8 + - - +
187B TYR* 2.7 25.2 + - - +
215B GLY* 6.1 0.2 - - - -
336B VAL* 3.1 16.7 - - - +
337B ASN* 3.9 4.9 - - - +
338B LEU* 2.8 39.7 + - - +
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Residues in contact with CYS 184 (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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179B GLU* 6.1 3.0 - - - +
180B ARG 4.4 1.4 + - - -
182B GLY 3.9 0.2 - - - -
183B GLU* 1.4 76.2 - - - +
185B GLN* 1.4 57.2 + - - +
187B TYR* 3.4 3.6 - - - -
188B LYS* 2.8 58.9 + - - +
191B LYS* 3.9 24.9 - - - -
337B ASN* 3.4 29.1 + - - +
339B LYS* 5.6 1.3 - - - -
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Residues in contact with GLN 185 (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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182B GLY* 3.0 17.2 + - - +
183B GLU 2.8 5.9 - - - -
184B CYS* 1.4 74.4 - - - +
186B ARG* 1.3 62.9 + - - +
188B LYS* 3.3 47.8 + - - +
189B PRO* 3.9 6.2 - - - +
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Residues in contact with ARG 186 (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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180B ARG* 3.0 25.6 - - - +
182B GLY 2.9 13.9 + - - +
183B GLU* 2.8 36.4 + - - +
185B GLN* 1.3 76.4 - - - +
187B TYR* 1.4 54.9 - - - +
188B LYS 3.3 2.6 + - - -
189B PRO* 3.5 11.4 - - - +
190B PHE* 4.4 1.6 - - - -
214B GLN 4.8 4.6 + - - -
215B GLY* 5.9 1.8 - - - -
216B LEU 5.3 4.2 + - - -
333B ILE* 2.9 44.4 + - - +
334B ALA* 3.3 38.2 - - + +
336B VAL* 3.8 8.5 + - - +
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Residues in contact with TYR 187 (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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183B GLU 2.7 16.5 + - - +
184B CYS* 3.4 3.4 - - - +
186B ARG* 1.4 69.3 - - - +
188B LYS* 1.3 65.2 + - - +
189B PRO* 3.7 0.4 - - - -
190B PHE* 4.1 5.8 - - + -
191B LYS* 3.1 38.6 + - + +
196B ARG* 3.5 18.7 + - - +
262B GLU* 2.9 46.7 - - + +
264B ALA* 3.7 28.9 + - + -
334B ALA 3.6 15.7 + - - -
335B GLN* 4.0 6.1 - - - -
336B VAL* 3.3 26.7 + - - +
337B ASN* 2.9 30.3 - - + +
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Residues in contact with LYS 188 (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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184B CYS* 2.8 49.8 + - - +
185B GLN* 3.3 41.5 + - - +
187B TYR* 1.3 75.4 - - - +
189B PRO* 1.4 74.0 - - + +
190B PHE 2.7 4.1 + - - -
191B LYS* 3.1 34.6 + - + +
192B GLN* 3.8 8.7 + - - +
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Residues in contact with PRO 189 (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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185B GLN 3.9 7.6 - - - +
186B ARG 3.5 15.9 - - - +
188B LYS* 1.4 89.4 - - + +
190B PHE* 1.4 72.6 + - + +
192B GLN* 3.4 16.1 + - + +
193B LEU* 4.5 2.1 + - - +
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Residues in contact with PHE 190 (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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186B ARG 4.4 5.4 - - - -
187B TYR* 3.6 5.3 + - + -
188B LYS 2.7 3.6 + - - -
189B PRO* 1.4 87.6 - - + +
191B LYS* 1.3 67.9 + - - +
192B GLN 3.3 0.2 + - - -
193B LEU* 3.3 29.3 + - + +
264B ALA* 3.8 20.5 - - + +
285B HIS* 6.6 0.2 - + - -
332B ASP* 3.3 20.0 - - + -
334B ALA* 3.5 42.8 - - + +
335B GLN* 3.7 32.3 - - + -
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Residues in contact with LYS 191 (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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184B CYS* 3.9 20.0 - - - -
187B TYR* 3.1 49.3 + - + +
188B LYS* 3.1 26.1 + - + +
190B PHE* 1.3 76.7 - - - +
192B GLN* 1.3 72.9 + - + +
193B LEU 3.0 7.3 + - - +
196B ARG* 3.2 47.2 + - - +
262B GLU* 5.5 1.1 - - - -
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Residues in contact with GLN 192 (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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188B LYS 3.8 5.2 + - - +
189B PRO* 3.4 11.7 + - + +
190B PHE 3.1 2.4 - - - -
191B LYS* 1.3 83.8 + - + +
193B LEU* 1.3 59.6 + - - +
194B HIS 3.9 0.3 + - - -
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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