Contacts of the helix formed by residues 166 - 178 (chain B) in PDB entry 4JU5
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 SER 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B PHE* 4.7 2.9 - - - -
163B ASP* 2.7 39.7 + - - +
164B VAL 3.3 0.2 - - - -
165B GLU* 1.3 81.4 - - - +
167B ASP* 1.3 65.5 + - - +
168B SER* 3.7 9.8 + - - -
169B ALA* 3.1 14.7 + - - +
170B LYS* 3.0 21.1 + - - +
201B ASP* 4.7 4.2 + - - -
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B GLU 5.0 0.7 - - - +
166B SER* 1.3 74.0 - - - +
168B SER* 1.3 62.6 + - - +
170B LYS* 3.2 23.1 + - - +
171B GLN* 3.0 31.4 + - + +
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Residues in contact with SER 168 (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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161B PHE* 3.9 13.1 - - - -
166B SER* 3.7 11.6 + - - -
167B ASP* 1.3 76.1 - - - +
169B ALA* 1.3 58.0 + - - +
171B GLN* 3.2 5.3 + - - +
172B PHE* 2.9 24.1 + - - +
201B ASP* 4.6 4.5 + - - +
220B VAL* 3.4 41.6 - - - +
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Residues in contact with ALA 169 (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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161B PHE* 3.8 27.5 - - + -
163B ASP 3.5 7.0 - - - +
164B VAL* 3.4 21.5 - - - +
166B SER* 3.1 21.6 + - - +
168B SER* 1.3 78.1 + - - +
170B LYS* 1.3 58.6 + - - +
172B PHE* 3.1 5.2 + - - +
173B LEU* 2.8 33.7 + - - +
186B ILE* 4.8 3.8 - - + -
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Residues in contact with LYS 170 (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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164B VAL 4.6 3.3 + - - +
165B GLU* 3.8 32.1 - - - +
166B SER 3.0 14.0 + - - +
167B ASP* 3.2 21.6 + - - +
169B ALA* 1.3 71.9 - - - +
171B GLN* 1.3 56.5 + - + +
173B LEU* 3.1 13.1 + - + +
174B GLN* 2.8 40.0 + - + +
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Residues in contact with GLN 171 (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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167B ASP* 3.0 23.1 + - + +
168B SER 3.3 7.9 - - - +
170B LYS* 1.3 76.4 - - + +
172B PHE* 1.3 57.5 + - - +
174B GLN* 3.4 8.1 + - - +
175B ALA* 3.0 25.6 + - - +
220B VAL* 3.6 22.2 - - + +
221B THR* 3.7 15.7 - - - +
222B LYS* 3.1 34.5 + - - +
225B LEU* 4.3 2.2 - - - -
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Residues in contact with PHE 172 (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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137B ALA* 4.1 16.8 - - + -
157B VAL* 3.8 20.6 - - + -
158B ILE 4.1 0.9 - - - -
159B GLY* 3.3 30.1 - - - -
161B PHE* 3.5 34.3 - + + -
168B SER 2.9 7.0 + - - +
169B ALA 3.4 9.4 - - - +
171B GLN* 1.3 73.5 - - - +
173B LEU* 1.3 63.0 + - + +
175B ALA* 2.9 5.9 + - + +
176B ALA* 2.9 24.5 + - + +
184B PHE* 3.8 24.0 - + + -
185B GLY 3.3 16.4 - - - -
186B ILE* 4.3 13.9 - - + -
203B VAL* 4.2 8.7 - - + -
225B LEU* 3.5 22.4 - - + +
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Residues in contact with LEU 173 (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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136B ALA* 3.7 21.1 - - + +
137B ALA* 3.9 30.1 - - + +
164B VAL* 4.4 20.6 - - + +
169B ALA 2.8 21.9 + - - +
170B LYS* 3.1 13.0 + - + +
172B PHE* 1.3 73.6 - - + +
174B GLN* 1.3 60.5 + - - +
176B ALA* 3.3 5.8 + - - +
177B GLU* 3.2 20.4 + - - +
186B ILE* 4.2 22.7 - - + -
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Residues in contact with GLN 174 (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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170B LYS* 2.8 18.3 + - + +
171B GLN* 3.6 9.6 - - - +
172B PHE 3.2 0.2 - - - -
173B LEU* 1.3 74.7 - - - +
175B ALA* 1.3 63.4 + - - +
177B GLU* 3.5 15.8 + - - +
178B ALA* 3.3 21.7 + - - +
222B LYS* 3.1 43.4 + - + -
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Residues in contact with ALA 175 (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 GLN 3.0 12.2 + - - +
172B PHE* 2.9 11.2 + - + +
174B GLN* 1.3 76.0 - - - +
176B ALA* 1.3 61.7 + - - +
178B ALA* 3.3 12.0 + - - +
179B ILE* 3.6 7.6 + - - +
184B PHE* 4.1 10.1 - - + -
222B LYS* 4.0 11.4 - - + +
225B LEU* 3.9 29.8 - - + -
226B LEU* 3.8 19.7 - - + +
229B ILE* 5.2 5.4 - - + -
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Residues in contact with ALA 176 (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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136B ALA 3.9 21.2 - - - +
137B ALA* 4.3 4.0 - - + -
172B PHE* 2.9 11.8 + - + +
173B LEU* 3.4 13.0 - - - +
174B GLN 3.3 0.2 - - - -
175B ALA* 1.3 77.0 - - - +
177B GLU* 1.3 55.8 + - - +
179B ILE 2.8 24.9 - - - +
180B ASP* 4.3 1.0 - - - +
184B PHE* 3.5 44.2 - - + -
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Residues in contact with GLU 177 (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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136B ALA* 3.2 31.5 + - - +
173B LEU 3.2 11.3 + - - +
174B GLN* 3.9 17.7 - - - +
175B ALA 3.3 0.4 - - - -
176B ALA* 1.3 72.3 - - - +
178B ALA* 1.3 60.5 + - - +
179B ILE 3.2 6.0 + - - -
180B ASP* 3.8 12.7 - - - +
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Residues in contact with ALA 178 (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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174B GLN 3.3 13.9 + - - +
175B ALA 3.3 7.5 + - - +
177B GLU* 1.3 78.3 - - - +
179B ILE* 1.3 63.6 + - - +
222B LYS* 4.9 6.7 - - + -
226B LEU* 4.1 25.1 - - + -
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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