Contacts of the helix formed by residues 177 - 185 (chain A) in PDB entry 4U2M
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LEU 3.0 13.1 + - - +
174A MET 3.8 5.2 + - - +
175A ALA 3.8 1.4 - - - -
176A CYS* 1.3 79.5 - - - +
178A GLY* 1.3 57.9 + - - +
179A LEU* 3.2 2.8 + - - +
180A PHE* 3.1 32.3 + - - -
181A TYR* 3.0 26.7 + - - +
213A MET* 4.1 1.8 - - - -
235A LEU* 2.8 23.3 + - - +
236A GLN 4.8 0.4 - - - -
237A MET* 4.1 14.8 - - - -
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 1.3 69.7 - - - +
179A LEU* 1.3 65.7 + - - +
181A TYR* 3.3 10.3 + - - +
182A SER* 3.1 25.6 + - - -
235A LEU 3.5 4.4 + - - -
236A GLN* 3.4 27.5 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 3.2 8.1 + - - +
178A GLY* 1.3 77.1 - - - +
180A PHE* 1.3 61.2 + - + +
182A SER* 3.1 9.2 + - - -
183A ILE* 2.9 49.0 + - + +
197A LEU* 4.7 4.3 - - + -
234A TYR* 3.6 61.7 - - + +
235A LEU* 3.4 16.2 + - + +
236A GLN* 3.6 18.6 - - - +
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.8 32.3 - - + -
173A LEU* 3.7 42.0 - - + +
174A MET* 4.5 0.4 - - - -
177A SER* 3.1 24.8 + - - +
179A LEU* 1.3 76.8 - - + +
181A TYR* 1.3 67.4 + - - +
183A ILE* 4.1 20.6 - - + -
184A PHE* 2.9 55.1 + + + -
195A ILE* 4.6 2.5 - - + -
197A LEU* 4.4 10.3 - - + -
206A PHE* 4.1 23.3 - + - -
213A MET* 4.5 4.5 - - + -
235A LEU* 3.9 22.0 - - + -
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Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.2 19.1 - - + +
174A MET* 3.9 35.3 - - + +
177A SER 3.0 14.0 + - - +
178A GLY* 3.5 13.2 - - - +
179A LEU 3.2 0.2 - - - -
180A PHE* 1.3 77.9 - - - +
182A SER* 1.3 69.0 + - - +
184A PHE 3.4 0.5 + - - -
185A THR* 2.8 59.3 + - + +
32C GLY 5.2 2.1 + - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLY 3.1 12.4 + - - -
179A LEU* 3.1 14.3 + - - -
181A TYR* 1.3 82.9 - - - +
183A ILE* 1.3 66.3 + - - +
185A THR* 3.4 7.9 + - - -
186A ASP* 3.3 23.0 + - - +
236A GLN* 5.2 3.9 + - - -
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 2.9 45.0 + - + +
180A PHE* 3.8 19.7 - - + +
182A SER* 1.3 78.3 - - - +
184A PHE* 1.3 71.8 + - + +
186A ASP* 3.3 20.1 + - - +
189A LYS* 3.6 34.4 - - + +
190A CYS 4.0 1.2 + - - -
195A ILE* 4.0 39.3 - - + -
197A LEU* 4.7 4.7 - - + -
234A TYR* 5.9 0.2 - - - +
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.3 13.2 - - + +
157A VAL* 4.5 6.5 - - + -
170A LYS* 3.7 66.2 - - + -
173A LEU* 4.0 13.5 - - + -
174A MET* 3.7 21.2 - - + +
180A PHE* 2.9 55.7 + + + +
183A ILE* 1.3 82.8 - - + +
185A THR* 1.3 60.9 + - - +
186A ASP 3.5 0.2 - - - -
189A LYS 5.0 2.9 - - - -
190A CYS* 3.2 26.9 - - - +
195A ILE* 4.1 22.9 - - + -
33C VAL* 4.1 5.0 - - - +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.0 9.9 - - + -
174A MET* 3.9 10.3 - - + -
181A TYR* 2.8 51.4 + - + +
182A SER* 3.4 9.7 + - - -
184A PHE* 1.3 80.0 - - - +
186A ASP* 1.3 61.4 + - - +
187A GLN 3.7 1.7 + - - -
32C GLY 3.9 20.2 - - - +
33C VAL* 3.8 20.0 - - + +
34C HIS* 4.6 3.5 + - - +
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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