Contacts of the helix formed by residues 149 - 160 (chain C) in PDB entry 3RIE
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 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C SER* 2.4 29.6 + - - -
70C LYS* 5.0 0.5 + - - +
71C TYR* 3.8 14.7 - - + +
72C GLN* 3.1 31.1 + - - +
74C VAL* 4.8 0.9 - - - +
147C GLU* 2.7 27.8 + - - +
148C ILE* 1.3 75.2 - - + +
150C GLU* 1.3 64.9 + - - +
151C THR* 3.1 22.7 + - - -
152C VAL* 3.0 28.0 + - + +
153C ILE 3.8 0.7 + - - -
401C MTA 3.7 1.6 - - - +
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Residues in contact with GLU 150 (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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70C LYS* 5.7 5.8 + - - +
148C ILE 3.8 4.2 + - - -
149C ASP* 1.3 75.3 + - - +
151C THR* 1.3 61.9 + - - +
153C ILE* 3.1 17.3 + - + +
154C GLU* 3.2 30.5 + - + +
176C ILE* 3.8 42.1 - - + +
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Residues in contact with THR 151 (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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65C TYR* 4.9 2.9 - - - +
67C THR* 3.8 28.3 - - + -
69C SER* 3.5 18.5 - - - -
70C LYS* 5.2 0.9 + - - +
74C VAL* 4.1 7.6 - - + -
149C ASP* 3.1 14.4 + - - -
150C GLU* 1.3 73.7 - - - +
152C VAL* 1.3 65.4 + - - +
154C GLU* 3.6 18.0 + - - +
155C VAL* 2.8 40.9 + - + +
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLN* 4.0 1.8 - - - +
74C VAL* 4.9 5.6 - - + -
86C LEU* 4.5 13.5 - - + +
88C LEU* 4.0 26.5 - - + -
126C GLY 3.9 18.8 - - - -
127C ASP* 4.0 4.0 - - - +
147C GLU* 4.4 1.6 - - - +
149C ASP* 3.0 29.7 + - + +
151C THR* 1.3 77.8 - - - +
153C ILE* 1.3 63.1 + - - +
155C VAL* 3.5 5.1 + - - +
156C SER* 3.1 21.8 + - - -
401C MTA 3.5 36.1 - - + +
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Residues in contact with ILE 153 (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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126C GLY* 3.5 17.7 - - - +
145C ILE* 5.5 1.1 - - + -
147C GLU* 4.0 17.0 - - + -
150C GLU* 3.1 11.5 + - + +
152C VAL* 1.3 74.9 - - - +
154C GLU* 1.3 66.8 + - + +
156C SER* 3.3 1.6 + - - -
157C LYS* 3.0 50.2 + - - +
167C TYR* 3.5 34.9 - - + +
174C VAL* 3.7 31.4 - - + -
176C ILE* 3.8 16.4 - - + -
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Residues in contact with GLU 154 (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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150C GLU* 3.2 33.1 + - + +
151C THR* 3.2 22.7 + - - +
153C ILE* 1.3 80.1 - - + +
155C VAL* 1.3 65.3 + - + +
157C LYS* 3.1 19.2 + - - +
158C ILE* 3.2 24.4 + - + +
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Residues in contact with VAL 155 (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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65C TYR* 3.5 33.0 - - + -
74C VAL* 4.3 12.6 - - + -
76C VAL* 3.3 34.3 - - + -
86C LEU* 4.4 7.2 - - + -
151C THR* 2.8 33.9 + - + +
152C VAL* 4.0 4.7 - - - +
154C GLU* 1.3 73.0 - - + +
156C SER* 1.3 58.2 + - - +
158C ILE* 3.3 6.6 + - + -
159C TYR* 2.9 40.7 + - + +
160C PHE* 5.1 0.9 - - + -
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Residues in contact with SER 156 (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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86C LEU* 5.7 2.5 - - - -
126C GLY 4.1 1.1 - - - -
127C ASP* 2.6 45.0 + - - +
152C VAL* 3.1 18.4 + - - -
153C ILE 3.3 4.0 + - - -
154C GLU 3.2 0.2 - - - -
155C VAL* 1.3 78.3 - - - +
157C LYS* 1.4 55.2 + - - +
160C PHE* 3.0 42.0 + - - +
164C SER* 2.7 24.5 + - - -
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Residues in contact with LYS 157 (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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153C ILE* 3.0 40.3 + - + +
154C GLU* 3.1 10.3 + - - +
156C SER* 1.4 80.1 - - - +
158C ILE* 1.3 57.4 + - + +
161C LYS* 3.1 29.3 + - - +
164C SER* 3.4 17.5 - - - +
167C TYR* 3.9 26.9 - - + +
168C GLU* 6.0 0.2 + - - -
174C VAL* 6.2 1.0 - - - +
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Residues in contact with ILE 158 (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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65C TYR* 5.9 5.4 - - + -
84C LYS* 5.5 0.3 + - - -
154C GLU* 3.2 21.5 + - + +
155C VAL* 3.8 11.4 - - + +
157C LYS* 1.3 80.3 - - + +
159C TYR* 1.3 94.8 + - + +
161C LYS* 2.8 22.6 + - - +
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Residues in contact with TYR 159 (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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64C LEU* 3.3 48.0 + - + -
65C TYR* 3.7 35.1 - + + +
76C VAL* 4.0 11.0 - - + -
84C LYS* 2.7 36.4 + - + +
155C VAL* 2.9 31.8 + - + +
158C ILE* 1.3 103.9 - - + +
160C PHE* 1.3 81.9 + - + +
161C LYS 3.7 1.3 - - - -
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Residues in contact with PHE 160 (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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76C VAL* 3.8 23.6 - - + -
84C LYS* 3.5 35.7 - - + +
85C VAL 3.7 28.3 - - - -
86C LEU* 3.7 22.7 - - + -
94C LEU* 3.7 12.6 - - + -
96C GLU* 4.1 10.3 - - + -
127C ASP* 6.1 0.2 - - + -
155C VAL 4.2 0.4 - - - -
156C SER* 3.0 33.0 + - - +
159C TYR* 1.3 88.5 - - + +
161C LYS* 1.3 53.5 + - - +
162C ASN* 3.2 3.6 - - - -
163C ILE* 2.7 49.8 + - + -
164C SER* 2.8 12.5 + - - -
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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