Contacts of the helix formed by residues 177 - 185 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C LEU 3.0 11.8 + - - +
174C MET 3.8 5.4 - - - +
175C ALA 3.7 1.0 - - - -
176C CYS* 1.3 80.8 - - - +
178C GLY* 1.3 58.4 + - - +
179C LEU* 3.2 2.8 + - - +
180C PHE* 3.1 32.5 + - - -
181C TYR* 2.9 26.7 + - - +
213C MET* 4.1 11.2 - - - -
235C LEU* 2.8 23.3 + - - +
236C GLN 4.8 0.2 - - - -
237C MET* 4.4 4.3 - - - -
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Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C SER* 1.3 72.4 + - - +
179C LEU* 1.3 61.8 + - - +
181C TYR* 3.3 10.9 + - - +
182C SER* 3.1 25.5 + - - -
235C LEU 3.5 4.8 + - - -
236C GLN* 3.5 28.0 + - - +
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C SER* 3.2 8.5 + - - +
178C GLY* 1.3 75.2 - - - +
180C PHE* 1.3 61.0 + - + +
182C SER* 3.1 9.8 + - - -
183C ILE* 2.9 47.8 + - + +
197C LEU* 4.7 3.4 - - + -
234C TYR* 3.6 62.1 - - + +
235C LEU* 3.4 16.4 + - + +
236C GLN* 3.6 20.0 - - - +
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Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ILE* 3.8 31.9 - - + -
173C LEU* 3.7 45.5 - - + +
174C MET* 4.4 0.7 - - - -
177C SER* 3.1 25.4 + - - +
179C LEU* 1.3 76.5 - - + +
181C TYR* 1.3 66.9 + - - +
183C ILE* 4.1 20.4 - - + -
184C PHE* 2.9 51.4 + + + -
195C ILE* 4.6 2.5 - - + -
197C LEU* 4.4 9.6 - - + -
206C PHE* 4.0 25.4 - + - -
213C MET* 4.5 4.3 - - + -
235C LEU* 3.9 21.8 - - + -
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.2 9.6 - - + +
174C MET* 3.8 35.3 - - + +
177C SER 2.9 14.5 + - - +
178C GLY* 3.5 12.3 - - - +
179C LEU 3.2 0.2 - - - -
180C PHE* 1.3 76.8 - - - +
182C SER* 1.3 69.8 + - - +
184C PHE* 3.8 0.7 - - - -
185C THR* 2.8 59.7 + - + +
226D MET* 3.6 45.8 - - + +
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Residues in contact with SER 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLY 3.1 12.8 + - - -
179C LEU* 3.1 15.0 + - - -
181C TYR* 1.3 82.3 - - - +
183C ILE* 1.3 65.6 + - - +
185C THR* 3.4 7.5 + - - -
186C ASP* 3.2 23.6 + - - +
236C GLN* 5.1 4.3 + - - -
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Residues in contact with ILE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C LEU* 2.9 45.0 + - + +
180C PHE* 3.9 21.1 - - + +
182C SER* 1.3 76.7 - - - +
184C PHE* 1.3 67.9 + - + +
186C ASP* 3.3 24.5 + - - +
189C LYS* 3.7 34.9 - - + +
190C CYS 3.9 1.4 + - - -
195C ILE* 4.0 40.4 - - + -
197C LEU* 4.7 4.5 - - + -
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Residues in contact with PHE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 4.4 13.7 - - + +
157C VAL* 4.5 3.6 - - + -
159C ILE* 4.8 0.2 - - + -
170C LYS* 3.7 65.3 - - + -
173C LEU* 3.9 13.9 - - + -
174C MET* 3.7 18.9 - - + +
180C PHE* 2.9 55.1 + + + +
181C TYR 3.8 0.2 - - - -
183C ILE* 1.3 83.3 - - + +
185C THR* 1.3 60.2 + - - +
186C ASP 3.5 0.4 - - - -
189C LYS 5.1 1.1 - - - -
190C CYS* 3.2 26.4 - - - +
192C LEU 5.4 0.4 - - - -
195C ILE* 4.1 26.2 - - + -
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Residues in contact with THR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 4.1 17.5 - - + -
174C MET* 3.9 10.5 - - + -
181C TYR* 2.8 55.3 + - + +
182C SER* 3.4 10.3 + - - -
183C ILE 3.3 0.2 - - - -
184C PHE* 1.3 78.0 - - - +
186C ASP* 1.3 60.6 + - - +
187C GLN* 3.6 2.3 + - - -
190C CYS* 4.9 1.6 - - - -
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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