Contacts of the helix formed by residues 179 - 187 (chain C) in PDB entry 3C3P
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 ARG 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C CYS* 4.1 20.8 + - + +
136C PHE 5.5 0.4 + - - -
137C ASN* 5.1 10.9 + - - +
160C ALA* 3.7 6.3 + - - +
178C LEU* 1.3 78.3 - - - +
180C GLU* 1.3 95.9 + - - +
181C PHE* 4.5 8.4 - - + +
182C ASN* 3.0 32.0 + - - +
183C HIS* 3.4 9.7 - - - -
214C EDO 3.4 37.2 - - - +
221C EDO 4.0 26.5 + - - -
222C EDO 3.7 11.9 + - - +
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Residues in contact with GLU 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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18B PRO 3.7 5.9 - - - +
19B GLU* 3.5 28.1 - - + +
20B ALA* 3.0 38.3 + - + +
25B ALA* 5.7 1.6 - - - +
28B GLU* 5.7 0.5 - - - +
41B ARG* 3.7 8.7 + - - -
137C ASN* 5.8 2.7 - - - +
179C ARG* 1.3 104.9 + - - +
181C PHE* 1.3 63.2 + - - +
183C HIS* 2.9 25.4 + - - +
184C HIS* 3.1 11.5 + - - +
222C EDO 3.6 18.5 + - - -
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Residues in contact with PHE 181 (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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131C MSE 3.9 12.1 - - + -
133C CYS* 4.4 21.8 - - + -
137C ASN* 5.6 2.1 + - - +
138C GLY* 3.2 50.3 - - - +
139C ALA* 3.2 6.5 - - - +
142C LEU* 4.2 9.9 - - + -
155C LEU* 3.5 32.8 - - + -
157C ALA* 4.4 3.4 - - + -
179C ARG* 3.1 9.6 + - + +
180C GLU* 1.3 76.8 - - - +
182C ASN* 1.3 63.0 + - - +
184C HIS* 3.9 22.7 - + - -
185C LEU* 2.9 34.4 + - + +
203C LEU* 3.5 27.4 - - + -
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Residues in contact with ASN 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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133C CYS* 5.5 1.0 - - - -
160C ALA* 3.0 35.0 + - - +
161C LEU* 4.1 4.8 - - - +
178C LEU* 4.0 5.3 - - - +
179C ARG* 3.0 24.8 + - - +
181C PHE* 1.3 78.9 - - - +
183C HIS* 1.3 66.7 + - + +
185C LEU* 4.5 0.2 - - - +
186C SER* 3.1 30.5 + - - -
195C ILE* 3.5 33.3 - - + +
203C LEU* 3.6 21.1 - - - +
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Residues in contact with HIS 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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14B ASP 3.2 26.7 - - - -
15B GLY* 3.6 17.1 + - - -
17B LEU* 2.8 24.9 + - + +
18B PRO 4.2 0.4 + - - -
19B GLU* 4.0 14.1 - - - +
178C LEU* 5.8 0.6 - - - -
179C ARG 3.4 20.2 + - - -
180C GLU* 2.9 21.0 + - - +
182C ASN* 1.3 82.1 + - + +
184C HIS* 1.3 63.3 + - - +
186C SER* 2.9 18.8 + - - -
187C ARG* 3.6 17.4 - - - +
222C EDO 3.4 31.9 - - - -
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Residues in contact with HIS 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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19B GLU* 2.9 43.1 + - - +
139C ALA* 3.9 21.9 + - + +
142C LEU* 4.5 0.7 - - + -
180C GLU 3.1 8.4 + - - +
181C PHE* 3.6 31.9 - + + +
183C HIS* 1.3 76.9 - - - +
185C LEU* 1.3 61.9 + - - +
187C ARG* 3.0 13.7 + - - +
188C ARG* 3.1 36.2 + - - +
220C EDO 2.8 46.0 + - - -
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Residues in contact with LEU 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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142C LEU* 3.5 32.3 - - + -
155C LEU* 4.1 11.0 - - + -
181C PHE* 2.9 33.2 + - + +
182C ASN 4.5 0.4 - - - +
184C HIS* 1.3 74.4 - - - +
186C SER* 1.3 65.0 + - - +
187C ARG 3.1 1.6 - - - -
188C ARG* 3.2 22.2 + - - +
191C PHE* 4.0 22.6 - - + +
193C THR* 3.4 29.0 - - + +
203C LEU* 3.7 30.7 - - + -
205C GLY* 4.4 8.7 - - - -
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Residues in contact with SER 186 (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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187A ARG* 4.3 17.9 + - - -
182C ASN 3.1 16.8 + - - -
183C HIS* 2.9 18.2 + - - -
185C LEU* 1.3 79.1 - - - +
187C ARG* 1.3 68.6 + - - +
188C ARG 3.2 5.4 + - - +
193C THR* 3.9 15.6 + - - -
203C LEU* 6.0 0.2 - - - +
217C EDO 5.7 5.0 + - - -
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Residues in contact with ARG 187 (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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186A SER* 2.9 36.8 + - - -
187A ARG* 3.9 41.0 - - + +
189A ARG* 5.3 15.2 + - - +
15B GLY 5.4 1.2 + - - -
16B LEU* 4.0 10.1 + - - +
17B LEU 3.6 17.4 + - - -
18B PRO* 3.8 30.4 - - - +
19B GLU* 4.8 4.9 - - - +
183C HIS* 3.6 13.3 + - - +
184C HIS* 3.0 11.7 + - - +
186C SER* 1.3 86.1 + - - +
188C ARG* 1.3 57.6 + - - +
189C ARG* 3.5 5.5 + - - +
220C EDO 3.5 20.2 - - - +
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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