Contacts of the helix formed by residues 183 - 192 (chain A) in PDB entry 1P1C
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 ASP 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A MET* 4.4 3.1 - - - -
181A TYR* 3.5 4.9 - - - +
182A THR* 1.3 84.0 - - - +
184A ILE* 1.3 62.2 + - - +
185A THR* 2.6 32.1 + - - +
186A ALA* 2.8 43.4 + - + +
187A MET 3.0 9.5 + - - -
226A GLN* 5.8 0.7 - - - +
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Residues in contact with ILE 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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173A TRP* 5.7 0.2 - - + -
177A MET* 3.8 14.6 - - + -
182A THR 4.1 1.2 - - - -
183A ASP* 1.3 71.9 + - - +
185A THR* 1.3 64.3 + - + +
187A MET* 3.6 14.8 - - + +
188A PHE* 3.3 20.1 + - - +
210A VAL* 3.7 35.0 - - + -
222A TYR* 3.8 9.4 - - - +
224A PHE* 3.9 15.7 - - + -
226A GLN* 3.4 31.5 - - + +
227A MET 3.5 2.0 - - - -
228A ILE* 3.3 45.9 - - + +
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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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183A ASP* 2.6 20.8 + - - +
184A ILE* 1.3 77.0 - - + +
186A ALA* 1.3 60.6 + - - +
187A MET 3.3 0.2 - - - -
188A PHE* 3.8 3.2 - - - +
189A GLU* 3.0 30.3 + - - +
208A THR* 4.0 11.4 - - - +
210A VAL* 3.6 30.3 - - + -
228A ILE* 3.7 12.3 - - + -
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Residues in contact with ALA 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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181A TYR* 3.9 12.1 - - + -
183A ASP* 2.8 35.7 + - + +
185A THR* 1.3 80.0 - - - +
187A MET* 1.3 54.9 + - - +
189A GLU* 3.6 5.9 + - - +
190A GLU* 3.0 30.8 + - - +
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Residues in contact with MET 187 (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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173A TRP* 4.0 46.4 - - + -
176A LEU* 4.1 10.3 - - + -
177A MET* 3.0 39.9 - - + -
181A TYR* 3.4 27.3 - - + -
183A ASP 3.0 4.4 + - - +
184A ILE* 3.6 33.0 - - + +
186A ALA* 1.3 75.3 - - - +
188A PHE* 1.3 64.3 + - + +
191A THR* 2.8 49.8 + - - +
192A GLN* 4.5 1.3 - - - -
228A ILE* 4.6 5.2 - - + -
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Residues in contact with PHE 188 (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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167A TYR* 3.4 25.1 - + - -
173A TRP* 4.3 8.7 - + - -
184A ILE 3.3 14.7 + - - +
185A THR* 3.8 5.4 - - - +
187A MET* 1.3 83.0 - - + +
189A GLU* 1.3 56.8 + - - +
192A GLN* 2.6 47.5 + - + +
193A VAL* 3.0 22.1 + - + -
196A LEU* 3.9 10.5 - - + -
206A ILE* 3.2 28.5 - - + -
208A THR* 4.2 8.1 - - + -
228A ILE* 4.2 24.0 - - + -
230A PRO* 3.4 40.8 - - + -
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Residues in contact with GLU 189 (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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185A THR 3.0 20.0 + - - +
186A ALA* 3.7 6.5 - - - +
188A PHE* 1.3 79.6 - - - +
190A GLU* 1.3 57.3 + - - +
193A VAL* 3.2 24.3 - - - +
194A PRO* 3.2 23.6 - - - +
203A ARG* 2.4 40.8 + - - -
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Residues in contact with GLU 190 (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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180A LYS* 3.2 14.2 + - - -
181A TYR* 2.7 34.3 + - + +
186A ALA 3.0 18.4 + - - +
189A GLU* 1.3 76.7 - - - +
191A THR* 1.3 62.1 + - - +
194A PRO* 3.4 15.7 - - - +
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Residues in contact with THR 191 (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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148A PHE* 3.8 16.6 - - - -
176A LEU* 4.1 12.5 - - + +
181A TYR* 3.0 36.3 - - + +
187A MET* 2.8 31.5 + - + +
190A GLU* 1.3 75.9 - - - +
192A GLN* 1.3 80.4 + - - +
194A PRO* 3.9 4.7 - - - +
195A ALA* 4.9 2.6 - - - +
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Residues in contact with GLN 192 (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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144A HIS 4.8 3.6 + - - -
147A GLN* 2.8 26.0 + - - +
148A PHE* 3.1 11.3 - - - -
167A TYR* 2.6 34.0 + - - +
172A SER* 5.1 0.6 + - - -
173A TRP* 3.3 28.0 - - - +
176A LEU* 4.7 3.8 - - - +
187A MET* 4.5 0.9 - - - -
188A PHE* 2.6 49.5 + - + +
191A THR* 1.3 99.2 + - - +
193A VAL* 1.3 62.3 + - - +
194A PRO* 3.2 2.9 - - - -
195A ALA* 3.3 8.5 + - - +
196A LEU* 3.2 22.3 + - - +
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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