Contacts of the helix formed by residues 182 - 192 (chain B) in PDB entry 1USK
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 PHE 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B ILE* 3.8 36.3 - - + -
179B GLU* 3.4 33.9 - - + -
180B LYS 4.0 5.4 - - - -
181B ASP* 1.3 71.7 - - - +
183B SER* 1.3 63.6 + - - +
184B ALA 3.2 3.1 - - - -
185B LEU* 3.1 20.4 + - + +
186B ILE* 3.0 30.7 + - + +
205B GLU* 3.8 21.3 - - + -
208B GLN* 3.7 28.0 - - + -
209B MET* 3.7 37.5 - - + -
212B GLN* 2.9 19.2 + - - +
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Residues in contact with SER 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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181B ASP* 3.0 27.7 + - - -
182B PHE* 1.3 76.3 - - - +
184B ALA* 1.3 58.8 + - - +
186B ILE* 3.5 8.6 + - - +
187B ALA* 3.0 28.2 + - - +
212B GLN* 3.9 3.4 + - - -
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Residues in contact with ALA 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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181B ASP 5.1 1.2 + - - +
182B PHE 3.2 0.8 - - - -
183B SER* 1.3 79.6 + - - +
185B LEU* 1.3 64.2 + - - +
187B ALA* 3.6 6.6 + - - +
188B ARG* 3.3 21.7 + - - +
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Residues in contact with LEU 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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144B ILE* 3.7 31.2 - - + -
171B PHE* 4.5 10.8 - - + -
173B ASP* 6.2 0.2 - - + -
175B ILE* 4.5 14.1 - - + -
182B PHE* 3.1 24.8 + - + +
184B ALA* 1.3 78.8 - - - +
186B ILE* 1.3 63.9 + - + +
188B ARG* 3.2 7.7 + - + +
189B LEU* 3.1 43.0 + - + +
209B MET* 3.5 41.5 - - + -
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Residues in contact with ILE 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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182B PHE* 3.0 28.7 + - + +
183B SER* 3.7 8.7 - - - +
185B LEU* 1.3 76.9 - - + +
187B ALA* 1.3 61.4 + - - +
189B LEU* 3.4 16.5 + - + +
190B LYS* 3.2 23.1 + - + +
209B MET* 4.0 18.2 - - + +
212B GLN* 4.5 7.6 - - + +
213B ALA* 3.6 34.3 - - + +
216B VAL* 3.5 33.9 - - + -
218B LEU* 3.7 14.3 - - + +
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Residues in contact with ALA 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 SER 3.0 17.8 + - - +
184B ALA* 3.8 7.6 - - - +
185B LEU 3.2 0.2 - - - -
186B ILE* 1.3 78.3 - - - +
188B ARG* 1.3 57.6 + - - +
190B LYS* 3.4 10.9 + - - +
191B LYS* 3.1 28.2 + - - +
298D GLU* 4.0 27.9 - - - +
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Residues in contact with ARG 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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171B PHE* 3.5 60.7 - - + +
172B PHE 5.4 0.4 + - - -
173B ASP* 3.6 23.0 + - - +
184B ALA 3.3 10.6 + - - +
185B LEU* 3.2 12.2 + - - +
187B ALA* 1.3 78.0 - - - +
189B LEU* 1.3 63.4 + - - +
191B LYS* 4.2 24.3 - - - +
192B GLU* 3.1 32.9 + - + +
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Residues in contact with LEU 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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142B ALA* 4.0 1.3 - - + -
144B ILE* 5.8 0.2 - - + -
171B PHE* 4.0 17.0 - - + -
185B LEU* 3.1 33.8 + - + +
186B ILE* 3.7 18.4 - - + +
187B ALA 3.3 0.2 - - - -
188B ARG* 1.3 76.2 - - - +
190B LYS* 1.3 62.4 + - - +
193B ASN* 3.2 4.0 + - - -
194B ILE* 3.0 50.5 + - + +
197B VAL* 3.5 34.3 - - + -
218B LEU* 4.0 29.1 - - + +
220B THR* 4.9 2.9 - - + +
222B PHE* 4.3 11.2 - - + -
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Residues in contact with LYS 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 ILE* 3.2 13.7 + - + +
187B ALA* 3.6 12.3 - - - +
189B LEU* 1.3 80.0 - - - +
191B LYS* 1.3 61.3 + - - +
193B ASN* 3.3 20.1 + - - +
216B VAL* 2.6 50.0 + - + +
217B GLY 4.1 11.5 + - - -
218B LEU* 3.8 17.8 - - + +
92D GLU 5.2 5.4 - - - +
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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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187B ALA 3.1 13.3 + - - +
188B ARG* 4.0 27.7 - - - +
189B LEU 3.4 0.2 - - - -
190B LYS* 1.3 79.8 - - - +
192B GLU* 1.3 79.8 + - + +
193B ASN* 3.3 11.4 + - - -
69D GLY* 5.3 1.6 - - - +
71D LYS* 3.7 39.3 - - + +
297D ASP* 3.2 34.0 + - - +
298D GLU* 5.9 6.3 - - + +
299D PRO* 5.8 7.4 - - + -
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Residues in contact with GLU 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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140B ARG* 2.9 41.8 + - - +
170B VAL* 3.4 16.7 - - + +
171B PHE* 4.6 5.8 - - + -
188B ARG* 3.1 30.0 + - + +
191B LYS* 1.3 99.4 + - + +
193B ASN* 1.3 68.3 + - - +
194B ILE* 3.2 20.8 + - + +
71D LYS* 5.1 5.3 + - - -
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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