Contacts of the helix formed by residues 181 - 192 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B HIS* 3.4 32.8 - - + -
63B GLY 3.6 0.3 - - - +
65B GLY 2.8 32.4 + - - +
66B ILE* 3.8 6.1 - - - -
69B CYS* 3.1 24.2 - - - -
87B ARG* 3.4 20.1 - - - -
155B SER* 3.9 0.4 - - - -
179B GLU* 3.2 2.4 + - - -
180B MET* 1.3 79.9 + - - +
182B ALA* 1.3 58.5 + - - +
183B ALA 3.3 2.5 - - - -
184B GLY* 2.8 24.5 + - - -
185B ILE* 2.9 14.1 + - + +
246B FMB 2.4 38.3 + - - -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 4.6 0.6 - - - +
109B ALA* 3.6 17.0 - - + -
153B LEU* 3.8 10.3 - - + -
155B SER* 3.3 3.0 + - - +
179B GLU* 3.0 27.1 + - - +
181B GLU* 1.3 75.4 - - - +
183B ALA* 1.3 63.2 + - - +
185B ILE* 3.2 3.9 + - - +
186B TYR* 3.0 30.6 + - + -
198B THR* 3.6 28.3 - - + -
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 4.2 2.7 - - + -
109B ALA* 3.5 21.7 - - - +
110B CYS 4.1 0.2 - - - +
111B THR* 3.5 34.3 - - + -
115B VAL* 5.5 0.2 - - - -
116B ASN* 3.3 19.4 + - - +
127B ALA* 4.1 6.2 - - + +
155B SER* 2.8 22.1 + - - +
182B ALA* 1.3 73.7 - - - +
184B GLY* 1.3 62.3 + - - +
186B TYR 4.0 0.2 - - - -
187B GLY* 3.2 16.5 + - - -
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Residues in contact with GLY 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.6 32.7 - - - +
69B CYS* 4.8 0.2 - - - -
70B SER* 4.1 7.0 + - - -
115B VAL* 4.8 4.7 - - - -
119B ARG* 4.5 2.3 + - - -
181B GLU 2.8 11.4 + - - -
183B ALA* 1.3 78.0 - - - +
185B ILE* 1.3 63.8 + - - -
187B GLY* 3.2 3.2 + - - -
188B VAL* 3.1 26.3 + - - +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 5.3 4.9 - - + -
69B CYS* 3.2 33.0 - - + +
73B THR* 3.4 35.4 - - + +
85B ILE* 4.3 12.3 - - + +
87B ARG* 4.7 13.7 - - + -
181B GLU* 2.9 18.3 + - + +
182B ALA* 3.2 8.3 + - - +
184B GLY* 1.3 76.2 - - - +
186B TYR* 1.3 61.2 + - + +
188B VAL* 3.1 8.2 + - - +
189B ALA* 2.8 27.6 + - + +
196B ALA* 3.6 24.0 - - + -
197B LEU 5.4 0.7 - - - +
198B THR* 5.0 4.0 - - + -
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLY* 2.5 31.0 + - - -
108B GLY 4.1 3.1 - - - -
109B ALA* 3.9 19.7 - - + -
125B PHE* 4.5 3.2 - - - -
127B ALA* 3.3 38.4 - - + -
128B ILE 3.5 19.3 - - - +
129B ALA* 3.6 12.8 - - + +
182B ALA* 3.0 16.7 + - + +
185B ILE* 1.3 74.8 - - + +
187B GLY* 1.3 65.1 + - - +
189B ALA* 3.8 5.7 - - - +
190B ALA* 3.0 25.3 + - - +
196B ALA* 3.8 27.8 - - + -
197B LEU* 4.0 3.1 - - - -
198B THR* 3.2 41.0 + - + +
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASN* 3.5 27.1 - - - +
119B ARG* 3.8 12.1 + - - -
125B PHE* 4.4 9.6 - - - -
183B ALA 3.2 11.3 + - - -
184B GLY 3.2 3.6 + - - -
185B ILE 3.2 0.4 - - - -
186B TYR* 1.3 77.8 - - - +
188B VAL* 1.3 57.1 + - - +
190B ALA* 3.4 2.3 + - - +
191B GLU* 3.0 28.8 + - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B SER* 3.9 22.7 - - - +
73B THR* 3.5 27.1 - - - +
74B LYS* 4.0 16.4 - - + +
77B ILE* 3.9 19.7 - - + +
119B ARG* 3.7 19.0 - - - +
184B GLY 3.1 15.7 + - - +
185B ILE 3.5 7.6 - - - +
187B GLY* 1.3 73.9 - - - +
189B ALA* 1.3 64.8 + - - +
191B GLU* 3.2 3.7 + - - -
192B PHE* 3.0 34.4 + - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 4.5 2.9 - - + -
128B ILE 6.0 1.1 - - - +
185B ILE 2.8 19.0 + - - +
186B TYR* 3.8 6.5 - - + +
188B VAL* 1.3 75.6 - - - +
190B ALA* 1.3 62.1 + - - +
193B GLY* 3.1 5.0 + - - -
194B ALA* 2.8 53.3 + - + +
195B LYS 4.4 0.7 - - - -
196B ALA* 3.8 26.5 - - + +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.6 28.3 - - + -
186B TYR 3.0 17.1 + - - +
187B GLY 3.7 3.8 - - - +
189B ALA* 1.3 79.8 - - - +
191B GLU* 1.3 61.8 + - - +
192B PHE 3.5 0.3 + - - -
193B GLY* 3.5 6.8 + - - -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 2.8 39.7 + - - +
187B GLY 3.0 16.1 + - - +
188B VAL 3.2 4.0 + - - +
190B ALA* 1.3 78.2 - - - +
192B PHE* 1.3 91.9 + - + +
193B GLY 3.8 0.3 + - - -
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 3.6 40.2 - - + -
77B ILE* 3.9 26.7 - - + +
78B THR* 3.5 19.7 - - + -
119B ARG* 5.4 0.2 - - - -
188B VAL* 3.0 33.9 + - + +
191B GLU* 1.3 112.6 - - + +
193B GLY* 1.3 64.1 + - - +
194B ALA 3.6 2.4 + - - -
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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