Contacts of the helix formed by residues 179 - 186 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A CYS* 5.6 7.6 - - + -
160A ALA 3.5 3.8 + - - +
163A ARG* 3.2 30.6 - - - +
178A LEU* 1.3 76.4 - - - +
180A GLU* 1.3 66.6 + - - +
181A PHE 3.3 2.7 - - - +
182A ASN* 3.0 37.3 + - - +
183A HIS* 3.4 9.2 - - - -
217A EDO 3.5 30.2 - - - +
221A PEG 4.1 12.1 - - - -
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Residues in contact with GLU 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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137A ASN* 3.7 25.9 + - - +
139A ALA* 4.9 7.3 - - - +
179A ARG* 1.3 82.4 - - + +
181A PHE* 1.3 65.8 + - - +
183A HIS* 3.0 19.3 + - + +
184A HIS* 3.1 14.4 + - + +
221A PEG 3.3 26.1 + - - +
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Residues in contact with PHE 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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131A MSE 3.9 15.0 - - + -
133A CYS* 4.4 15.5 - - + -
137A ASN* 6.1 0.2 - - - -
138A GLY* 3.3 48.7 - - - +
139A ALA 3.4 4.7 - - - +
142A LEU* 4.3 7.6 - - + -
155A LEU* 3.5 34.3 - - + -
157A ALA* 4.3 9.6 - - + -
179A ARG* 3.2 3.2 + - + +
180A GLU* 1.3 79.4 + - - +
182A ASN* 1.3 57.6 + - - +
184A HIS* 3.9 23.1 - + + -
185A LEU* 2.8 43.7 + - + +
203A LEU* 3.5 24.2 - - + -
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Residues in contact with ASN 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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133A CYS* 5.4 0.9 - - - -
160A ALA* 3.0 34.2 + - - +
161A LEU* 4.1 0.8 - - - +
178A LEU* 3.7 3.2 - - - +
179A ARG 3.0 16.8 + - - +
181A PHE* 1.3 77.6 - - - +
183A HIS* 1.3 59.0 + - - +
185A LEU* 4.5 0.3 - - - +
186A SER* 3.1 31.4 + - - -
195A ILE* 3.6 28.5 - - + +
203A LEU* 3.4 27.1 - - - +
12B TYR* 3.3 25.1 + - - +
16B LEU* 4.0 7.9 - - + +
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Residues in contact with HIS 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 ARG 3.4 19.7 - - - -
180A GLU* 3.0 11.1 + - + +
182A ASN* 1.3 75.1 - - - +
184A HIS* 1.3 63.8 + - - +
186A SER* 3.1 10.8 + - - -
187A ARG* 3.0 36.9 + - - +
221A PEG 3.3 28.8 + - - -
12B TYR* 2.8 32.3 + + - -
16B LEU* 3.7 18.0 - - + +
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Residues in contact with HIS 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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139A ALA* 3.7 29.2 - - + +
142A LEU* 4.7 0.9 - - + -
180A GLU* 3.1 14.6 + - + +
181A PHE* 3.5 31.2 - + + +
183A HIS* 1.3 76.5 - - - +
185A LEU* 1.3 62.8 + - + +
187A ARG* 2.9 24.4 + - - +
188A ARG* 3.0 53.8 + - + +
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Residues in contact with LEU 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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142A LEU* 3.6 30.3 - - + -
155A LEU* 3.7 24.2 - - + -
181A PHE* 2.8 28.5 + - + +
182A ASN 4.5 0.7 - - - +
184A HIS* 1.3 77.0 - - - +
186A SER* 1.3 62.6 + - - +
187A ARG 3.0 0.2 - - - -
188A ARG* 3.1 22.6 + - + +
191A PHE* 4.0 22.0 - - + +
193A THR* 3.3 26.9 + - + +
203A LEU* 3.9 26.5 - - + -
205A GLY* 4.2 9.9 - - - -
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Residues in contact with SER 186 (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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182A ASN 3.1 21.6 + - - -
183A HIS* 3.1 13.5 + - - -
185A LEU* 1.3 77.2 - - - +
187A ARG* 1.3 67.5 + - - +
188A ARG 3.4 1.7 + - - +
191A PHE 6.1 0.2 - - - -
193A THR* 4.6 14.3 - - - +
218A EDO 5.4 9.5 - - - -
16B LEU* 4.1 26.8 + - - +
18B PRO* 5.4 1.4 - - - +
187C ARG* 2.9 19.5 + - - -
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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