Contacts of the helix formed by residues 155 - 170 (chain F) in PDB entry 4U0Z
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 ASP 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F SER* 3.2 22.2 + - - +
151F GLU* 4.4 1.5 + - - -
153F ASP* 3.4 6.1 - - + +
154F LYS* 1.4 72.6 - - - +
156F ILE* 1.3 61.2 + - - +
157F ILE* 3.7 8.1 + - - +
158F GLN* 3.0 47.0 + - + +
159F ALA* 3.4 17.0 + - - +
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Residues in contact with ILE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F GLU* 4.3 14.8 - - + +
154F LYS 3.4 8.7 + - - +
155F ASP* 1.3 71.3 - - - +
157F ILE* 1.3 70.6 + - + +
159F ALA* 3.0 7.8 + - - +
160F ASP* 2.9 21.5 + - + -
183F THR* 3.8 24.9 - - + -
186F LEU* 3.6 32.5 - - + -
187F VAL* 3.8 29.4 - - + +
190F ILE* 3.8 20.4 - - + -
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Residues in contact with ILE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ASP* 3.4 7.3 + - - +
156F ILE* 1.3 81.7 - - + +
158F GLN* 1.4 60.9 + - - +
160F ASP* 3.4 4.2 + - - +
161F TYR* 3.2 20.7 + - + +
187F VAL* 3.8 20.1 - - + +
190F ILE* 3.8 26.5 - - + -
191F ASP* 4.5 3.4 - - - +
416F ARG* 3.5 50.5 + - - +
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Residues in contact with GLN 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F MET* 4.6 8.1 - - - +
146F PHE* 3.8 31.3 - - - -
150F SER* 4.1 14.2 - - - -
155F ASP* 3.0 35.8 + - + +
157F ILE* 1.4 72.7 - - - +
159F ALA* 1.4 65.3 + - - +
161F TYR* 3.2 14.6 + - + +
162F LEU* 3.1 40.3 + - + +
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F GLY* 3.3 26.9 - - - +
150F SER* 3.6 12.2 + - - +
151F GLU* 3.7 18.4 - - + -
155F ASP 3.4 9.1 + - - +
156F ILE* 3.0 10.0 + - + +
158F GLN* 1.4 77.2 - - - +
160F ASP* 1.4 57.8 + - - +
162F LEU* 3.1 6.8 + - - +
163F TYR* 2.9 40.3 + - + -
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Residues in contact with ASP 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F ILE* 2.9 12.2 + - + +
157F ILE 3.6 8.5 - - - +
159F ALA* 1.4 73.7 - - - +
161F TYR* 1.4 52.0 + - - +
163F TYR* 3.3 11.0 + - - +
164F THR* 2.6 41.9 + - - -
180F ARG* 3.3 17.0 + - - -
183F THR* 2.9 29.8 + - - +
184F LEU 3.5 5.9 + - - -
187F VAL* 3.3 21.2 - - + +
412F ARG* 2.8 38.5 + - - -
416F ARG* 4.9 0.5 + - - -
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Residues in contact with TYR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ILE* 3.2 13.0 + - + +
158F GLN* 3.2 17.5 - - + +
160F ASP* 1.4 74.8 + - - +
162F LEU* 1.4 67.8 + - + +
164F THR* 3.5 3.7 + - - -
165F ARG* 2.8 77.1 + - + +
401F HIS* 5.9 4.3 - + - -
405F ALA* 4.2 21.7 + - + +
408F GLU* 4.9 6.8 - - - +
410F ASP* 3.4 38.5 - - + +
412F ARG* 4.7 0.9 - - - +
413F PRO* 4.2 21.3 - - + -
416F ARG* 5.8 4.3 - - - +
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LEU* 6.0 0.7 - - + -
143F LEU* 3.4 44.2 - - + +
146F PHE* 4.1 18.4 - - + -
147F GLY* 3.8 21.1 - - - +
150F SER* 4.1 2.0 - - - +
158F GLN* 3.1 44.6 + - + +
159F ALA* 3.1 7.2 + - - +
161F TYR* 1.4 94.6 - - + +
163F TYR* 1.4 59.8 + - - +
165F ARG* 3.1 8.1 + - - +
166F ALA* 2.8 30.9 + - - +
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Residues in contact with TYR 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F THR* 3.7 38.1 - - + -
147F GLY* 3.2 12.3 - - - -
148F ILE* 3.2 24.9 + - + +
151F GLU* 2.7 29.1 + - - -
159F ALA* 2.9 33.7 + - + -
160F ASP* 3.3 3.3 + - - +
162F LEU* 1.4 71.7 - - - +
164F THR* 1.4 56.7 + - - +
166F ALA* 3.3 8.9 - - - +
167F LEU* 3.0 32.1 + - - +
176F ALA* 4.1 14.2 - - - +
179F ASN* 3.4 34.7 + - + -
180F ARG* 4.1 11.2 - - + -
183F THR* 3.7 25.1 - - + -
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Residues in contact with THR 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F ASP* 2.6 22.3 + - - -
161F TYR 3.5 5.4 - - - -
163F TYR* 1.4 72.2 - - - +
165F ARG* 1.4 65.0 + - - +
167F LEU* 3.1 13.4 + - - +
168F THR* 3.1 27.6 + - + +
180F ARG* 3.2 39.7 + - - +
410F ASP* 4.4 9.9 - - + +
412F ARG* 3.3 23.4 + - - +
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Residues in contact with ARG 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LEU* 4.4 7.7 - - - +
137F PRO* 3.5 35.7 + - - +
138F ASP* 5.5 2.0 - - - -
143F LEU* 3.4 32.0 - - + +
161F TYR* 2.8 64.1 + - + +
162F LEU* 3.1 10.1 + - - +
164F THR* 1.4 71.5 - - - +
166F ALA* 1.3 60.7 + - - +
168F THR* 2.7 27.6 + - - +
169F ILE* 3.2 18.3 - - + +
408F GLU* 5.3 14.4 - - + +
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Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 3.8 26.8 - - + +
143F LEU* 3.9 23.0 - - + +
144F THR* 4.2 5.2 - - + -
162F LEU 2.8 13.0 + - - +
163F TYR 3.3 10.5 - - - +
164F THR 3.2 0.2 - - - -
165F ARG* 1.3 75.9 - - - +
167F LEU* 1.4 57.1 + - - +
169F ILE* 3.3 7.1 + - - +
170F SER 2.9 25.4 + - - +
176F ALA* 4.1 12.6 - - + -
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Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F TYR 3.0 15.6 + - - +
164F THR* 3.1 6.4 + - - +
166F ALA* 1.4 72.6 - - - +
168F THR* 1.3 64.1 + - + +
170F SER 3.6 14.6 - - - +
171F PRO* 3.1 44.6 - - + +
173F HIS 3.9 10.1 - - - +
176F ALA* 3.7 22.7 - - + +
177F LEU* 4.0 17.5 - - + +
180F ARG* 3.6 41.5 - - + +
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Residues in contact with THR 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F THR* 3.1 22.8 + - + +
165F ARG* 2.7 25.9 + - - +
167F LEU* 1.3 75.2 - - + +
169F ILE* 1.4 71.1 + - - +
171F PRO* 4.7 2.9 - - - +
409F GLY* 6.2 2.9 - - - +
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Residues in contact with ILE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ASP* 3.4 61.0 - - + +
140F VAL* 5.0 8.3 - - + -
143F LEU* 4.9 4.7 - - + -
165F ARG* 3.2 22.4 - - + +
166F ALA* 3.5 7.2 - - - +
167F LEU 3.2 0.2 - - - -
168F THR* 1.4 89.0 - - - +
170F SER* 1.4 61.8 + - - +
171F PRO* 3.7 6.3 - - - +
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Residues in contact with SER 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.0 27.8 - - - -
166F ALA 2.9 6.1 + - - +
167F LEU* 3.3 17.8 - - - +
169F ILE* 1.4 78.2 - - - +
171F PRO* 1.4 64.6 - - - +
172F TYR 3.3 2.6 + - - -
173F HIS* 3.5 25.3 + - - +
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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