Contacts of the helix formed by residues 181 - 192 (chain A) in PDB entry 1PR1
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 GLU 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.5 20.4 - - + +
63A GLY 3.7 4.0 - - - +
64A MET 3.6 1.2 - - - -
65A GLY* 2.7 33.6 + - - +
66A ILE* 3.9 6.1 - - - -
69A CYS* 3.2 24.4 - - + -
87A ARG* 3.2 26.0 + - - +
155A SER* 3.9 0.2 - - - -
179A GLU* 2.8 13.7 + - - -
180A MET* 1.3 74.4 + - - +
182A ALA* 1.3 62.2 + - - +
183A ALA 3.3 2.7 - - - -
184A GLY* 2.8 14.9 + - - -
185A ILE* 3.0 13.7 + - + +
245A FMB 2.4 41.4 + - - -
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Residues in contact with ALA 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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109A ALA* 3.6 17.7 - - + -
153A LEU* 3.7 12.3 - - + -
179A GLU* 2.9 30.7 + - - +
181A GLU* 1.3 71.1 - - - +
183A ALA* 1.3 58.2 + - - +
185A ILE* 3.3 2.3 + - - +
186A TYR* 2.9 36.8 + - + -
198A THR* 3.6 29.8 - - + +
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Residues in contact with ALA 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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66A ILE* 4.5 2.5 - - + -
109A ALA* 3.5 27.2 - - - +
111A THR* 3.7 29.2 - - + +
115A VAL* 5.5 0.4 - - - -
116A ASN* 3.5 15.7 - - - +
127A ALA* 4.0 10.0 - - + +
155A SER* 3.0 20.8 + - - +
182A ALA* 1.3 72.7 - - - +
184A GLY* 1.3 63.0 + - - +
186A TYR* 3.9 1.2 - - - +
187A GLY* 3.1 17.0 + - - -
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Residues in contact with GLY 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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66A ILE* 3.7 33.6 - - - +
69A CYS* 4.7 1.6 - - - -
70A SER* 4.2 7.0 + - - -
115A VAL* 4.8 5.6 - - - -
119A ARG* 4.4 1.9 + - - -
181A GLU 2.8 9.8 + - - -
183A ALA* 1.3 79.0 - - - +
185A ILE* 1.3 61.0 + - - +
187A GLY* 3.2 3.6 + - - -
188A VAL* 3.1 25.9 + - - +
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Residues in contact with ILE 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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18A MET* 5.9 0.7 - - - -
62A HIS* 4.7 6.1 - - + -
69A CYS* 3.8 22.2 - - + -
73A THR* 4.0 24.6 - - + +
85A ILE* 4.2 15.7 - - + +
87A ARG* 3.7 41.3 - - + -
181A GLU* 3.0 11.2 + - + +
182A ALA* 3.8 5.4 - - - +
184A GLY* 1.3 75.7 - - - +
186A TYR* 1.3 61.0 + - + +
188A VAL* 3.3 7.5 + - - +
189A ALA* 2.9 26.7 + - - +
196A ALA* 3.6 23.8 - - + -
197A LEU 5.9 0.4 - - - +
198A THR* 4.5 5.2 - - + -
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Residues in contact with TYR 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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106A GLY* 2.6 29.8 + - - -
108A GLY 4.2 2.9 - - - -
109A ALA* 3.9 20.6 - - + -
125A PHE* 4.6 2.7 - - - -
127A ALA* 3.4 37.2 - - + -
128A ILE 3.6 18.2 - - - +
129A ALA* 3.4 13.6 - - + +
182A ALA* 2.9 18.9 + - + +
185A ILE* 1.3 77.0 - - + +
187A GLY* 1.3 67.5 + - - +
189A ALA* 3.4 5.8 + - + +
190A ALA* 3.0 23.9 + - - +
196A ALA* 3.9 27.4 - - + -
197A LEU* 3.9 3.6 - - - -
198A THR* 3.2 41.7 + - + +
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Residues in contact with GLY 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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116A ASN* 3.6 27.1 - - - -
119A ARG* 3.9 10.8 + - - -
125A PHE* 4.3 10.1 - - - -
183A ALA 3.1 10.9 + - - -
184A GLY 3.2 3.9 + - - -
186A TYR* 1.3 77.6 - - - +
188A VAL* 1.3 55.7 + - - +
190A ALA* 3.2 4.3 + - - +
191A GLU* 2.8 29.5 + - - +
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Residues in contact with VAL 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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70A SER* 4.0 28.0 - - - +
73A THR* 3.2 30.5 - - + -
74A LYS* 3.7 15.7 - - + +
77A ILE* 4.1 4.0 - - + -
119A ARG* 3.5 20.6 - - - +
184A GLY 3.1 15.3 + - - +
185A ILE 3.7 2.2 - - - +
186A TYR 3.3 0.2 - - - -
187A GLY* 1.3 73.0 - - - +
189A ALA* 1.3 65.3 + - - +
191A GLU* 3.1 4.4 + - - -
192A PHE* 2.8 44.8 + - + +
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Residues in contact with ALA 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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73A THR* 5.8 0.2 - - + -
77A ILE* 4.4 11.4 - - + +
128A ILE 6.0 0.9 - - - +
185A ILE* 2.9 16.7 + - + +
186A TYR* 3.8 5.4 - - - +
187A GLY 3.4 0.2 - - - -
188A VAL* 1.3 76.1 - - - +
190A ALA* 1.3 56.7 + - - +
193A GLY* 3.0 12.1 + - - -
194A ALA* 2.9 49.2 + - + +
195A LYS 4.3 0.7 - - - -
196A ALA* 3.9 23.6 - - + +
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Residues in contact with ALA 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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125A PHE* 3.5 30.3 - - + -
186A TYR 3.0 13.4 + - - +
187A GLY 3.4 8.5 - - - +
189A ALA* 1.3 78.5 - - - +
191A GLU* 1.3 61.5 + - - +
192A PHE 3.5 0.2 + - - -
193A GLY* 3.6 7.2 + - - -
194A ALA 5.3 0.2 - - - -
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Residues in contact with GLU 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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119A ARG* 2.8 41.6 + - - +
187A GLY 2.8 19.1 + - - +
188A VAL 3.1 3.8 + - - +
190A ALA* 1.3 75.5 - - - +
192A PHE* 1.3 92.1 + - + +
193A GLY 3.8 0.3 + - - -
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Residues in contact with PHE 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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74A LYS* 3.4 35.2 - - + -
77A ILE* 3.8 26.8 - - + +
78A THR* 3.4 24.7 - - + -
119A ARG* 5.5 0.2 - - - -
188A VAL* 2.8 38.3 + - + +
189A ALA 3.7 0.4 - - - -
191A GLU* 1.3 110.0 - - + +
193A GLY* 1.3 65.8 + - - +
194A ALA 3.7 1.3 - - - -
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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