Contacts of the helix formed by residues 173 - 179 (chain C) in PDB entry 3O65
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 CYS 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C LEU 4.6 0.4 - - - +
25C GLN* 3.5 47.8 - - + +
125C ARG* 3.7 6.1 - - - -
171C PRO 4.4 1.6 - - - +
172C ASP* 1.3 77.8 - - - +
174C GLU* 1.3 67.0 + - - +
175C ALA* 4.1 4.7 - - - -
176C ASP* 3.4 40.5 + - - +
177C GLN* 3.1 27.2 + - - +
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Residues in contact with GLU 174 (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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2A MSE 4.5 10.7 - - + +
132A PHE* 4.4 5.4 - - - -
141A PRO 3.9 6.8 - - - +
142A GLU* 3.8 16.8 - - - +
143A LEU* 3.1 47.0 + - + +
4C PHE* 4.1 25.5 + - + +
173C CYS* 1.3 74.4 - - - +
175C ALA* 1.3 57.9 + - - +
177C GLN* 3.1 14.9 + - - +
178C LEU* 2.8 31.1 + - - +
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Residues in contact with ALA 175 (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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4C PHE* 3.6 27.8 + - - +
5C ILE* 4.2 1.6 - - + -
25C GLN* 4.6 0.6 + - - +
127C PHE* 3.4 33.0 - - + -
173C CYS* 3.4 4.1 - - - -
174C GLU* 1.3 77.4 - - - +
176C ASP* 1.3 63.4 + - - +
178C LEU* 3.1 13.6 + - - +
179C LEU* 3.1 19.3 + - - +
181E ILE* 3.9 16.2 - - + -
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Residues in contact with ASP 176 (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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125C ARG* 2.7 41.6 + - - -
126C LYS 4.2 3.8 - - - +
127C PHE* 3.8 9.5 - - - -
128C GLY 5.0 3.7 + - - +
170C LEU* 5.1 2.3 - - - +
171C PRO 4.2 6.6 - - - +
172C ASP* 5.1 2.4 - - - -
173C CYS* 3.4 22.4 + - - +
174C GLU 3.4 0.2 - - - -
175C ALA* 1.3 78.6 - - - +
177C GLN* 1.3 56.0 + - - +
179C LEU* 3.4 4.4 + - - +
180C GLN* 3.1 29.3 + - - +
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Residues in contact with GLN 177 (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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143A LEU* 3.6 33.4 + - + +
144A ILE* 4.3 0.3 - - - -
145A SER* 3.8 22.7 + - - -
172C ASP* 5.1 10.6 - - + +
173C CYS 3.1 19.9 + - - +
174C GLU* 3.1 19.5 + - - +
176C ASP* 1.3 75.1 - - - +
178C LEU* 1.3 65.5 + - - +
180C GLN* 3.4 36.9 + - - +
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Residues in contact with LEU 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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130A HIS* 3.1 44.8 - - + +
143A LEU* 4.0 10.7 - - + +
4C PHE* 3.4 39.3 - - + -
174C GLU 2.8 13.0 + - - +
175C ALA* 3.4 9.9 - - - +
177C GLN* 1.3 78.1 - - - +
179C LEU* 1.3 74.0 + - + +
180C GLN 3.6 4.2 + - - +
181E ILE* 4.0 11.9 - - + -
182E ILE* 3.7 19.7 - - + -
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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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127C PHE* 3.6 9.0 - - + +
128C GLY* 3.4 41.6 - - - +
130C HIS* 5.0 2.5 - - + -
175C ALA 3.1 13.3 + - - +
176C ASP 3.7 3.1 - - - +
178C LEU* 1.3 92.3 - - + +
180C GLN* 1.3 63.7 + - - +
181C ILE* 3.6 16.1 + - - +
181E ILE* 3.3 35.9 - - + -
182E ILE* 6.1 1.3 - - + -
185E GLU* 3.8 35.2 - - + +
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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