Contacts of the helix formed by residues 149 - 160 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A SER* 2.6 27.9 + - - -
70A LYS* 5.0 0.7 + - - +
71A TYR* 3.9 14.7 - - + +
72A GLN* 2.7 30.8 + - - +
74A VAL* 4.7 1.2 - - - +
147A GLU* 2.7 26.3 + - - +
148A ILE* 1.3 82.8 - - + +
150A GLU* 1.4 63.1 + - - +
151A THR* 3.2 23.1 + - - -
152A VAL* 3.0 20.7 + - + +
153A ILE 3.8 0.5 + - - -
401A MTA 3.7 2.2 - - - +
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Residues in contact with GLU 150 (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 ILE 3.9 4.0 + - - -
149A ASP* 1.4 73.0 + - - +
151A THR* 1.3 68.7 + - - +
153A ILE* 3.2 7.0 + - + +
154A GLU* 3.0 45.6 + - + +
176A ILE* 3.6 43.4 - - + +
157B LYS* 2.6 38.1 + - + -
168B GLU* 4.0 16.3 - - - +
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Residues in contact with THR 151 (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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67A THR* 3.8 29.4 - - + -
69A SER* 3.7 16.3 - - - -
70A LYS 5.3 0.3 + - - -
74A VAL* 4.3 6.7 - - + -
149A ASP* 3.1 15.3 + - - -
150A GLU* 1.3 83.6 - - - +
152A VAL* 1.3 51.2 + - - +
154A GLU* 3.8 11.3 + - - +
155A VAL* 2.7 53.3 + - + +
157B LYS* 5.6 2.2 + - - +
158B ILE* 4.1 9.3 - - + +
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Residues in contact with VAL 152 (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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72A GLN* 3.8 23.1 - - - +
74A VAL* 5.0 4.7 - - + -
86A LEU* 4.4 14.5 - - + +
88A LEU* 4.0 17.0 - - + -
126A GLY* 3.8 19.3 - - - -
127A ASP* 3.8 4.3 - - - +
147A GLU* 4.4 1.3 - - - +
149A ASP* 3.0 18.3 + - + +
151A THR* 1.3 77.3 - - - +
153A ILE* 1.3 58.1 + - - +
155A VAL* 3.3 6.0 + - - +
156A SER* 2.8 28.6 + - - -
401A MTA 3.3 35.9 - - + +
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Residues in contact with ILE 153 (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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126A GLY* 3.6 17.5 - - - +
145A ILE* 5.3 1.6 - - + -
147A GLU* 4.0 15.5 - - + -
149A ASP 4.5 0.4 - - - +
150A GLU* 3.2 8.3 + - - +
152A VAL* 1.3 77.2 - - - +
154A GLU* 1.4 60.7 + - + +
156A SER* 3.1 3.3 + - - -
157A LYS* 2.8 57.2 + - + +
167A TYR* 3.5 33.4 - - + +
174A VAL* 3.6 31.9 - - + -
176A ILE* 3.7 17.9 - - + -
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Residues in contact with GLU 154 (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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150A GLU* 3.0 45.4 + - + +
151A THR* 3.8 11.4 + - - -
153A ILE* 1.4 79.7 - - + +
155A VAL* 1.3 64.3 + - - +
157A LYS* 3.3 4.9 + - - +
158A ILE* 3.2 30.1 + - + +
154B GLU* 3.8 39.1 - - + +
157B LYS* 3.5 23.2 + - - +
158B ILE* 3.7 25.8 - - + +
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Residues in contact with VAL 155 (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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65A TYR* 3.8 29.2 - - + -
74A VAL* 4.4 6.1 - - + -
76A VAL* 3.4 33.0 - - + -
86A LEU* 4.6 11.4 - - + -
151A THR* 2.7 32.8 + - + +
152A VAL* 3.8 6.1 - - - +
154A GLU* 1.3 73.4 - - - +
156A SER* 1.4 57.1 + - - +
158A ILE* 3.2 2.3 + - - -
159A TYR* 2.9 41.6 + - + +
160A PHE* 4.7 3.4 - - + -
158B ILE* 3.9 12.6 - - + -
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Residues in contact with SER 156 (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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86A LEU* 6.0 2.0 - - - -
126A GLY 4.1 1.3 - - - -
127A ASP* 2.7 44.7 + - - +
152A VAL* 2.8 18.0 + - - -
153A ILE 3.6 4.0 - - - -
155A VAL* 1.4 78.9 - - - +
157A LYS* 1.3 56.7 + - - +
160A PHE* 2.8 48.2 + - - +
163A ILE* 4.5 0.2 - - - +
164A SER* 2.9 17.9 + - - -
167A TYR* 5.3 0.2 - - - -
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Residues in contact with LYS 157 (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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153A ILE* 2.8 44.2 + - + +
154A GLU* 3.3 5.8 + - - +
156A SER* 1.3 72.5 - - - +
158A ILE* 1.3 63.6 + - + +
161A LYS* 3.5 21.9 - - - +
164A SER* 3.3 10.7 + - - +
167A TYR* 3.8 38.9 - - + +
174A VAL* 5.7 3.2 - - - +
154B GLU* 3.8 29.7 + - - +
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Residues in contact with ILE 158 (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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154A GLU* 3.2 19.9 + - + +
155A VAL 3.7 2.5 - - - +
156A SER 3.2 0.8 - - - -
157A LYS* 1.3 82.9 - - + +
159A TYR* 1.3 89.7 + - + +
160A PHE 3.6 0.7 - - - -
161A LYS* 3.6 23.6 + - - +
64B LEU 5.8 0.2 - - - +
65B TYR* 4.0 33.0 - - + +
154B GLU* 5.4 2.5 - - + +
155B VAL* 5.1 6.7 - - + +
158B ILE* 4.0 28.3 - - + -
159B TYR* 3.6 22.7 - - + +
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Residues in contact with TYR 159 (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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64A LEU* 3.8 40.6 + - + -
65A TYR* 3.8 26.5 - + + +
76A VAL* 4.1 8.5 - - + -
84A LYS* 2.5 38.4 + - + +
155A VAL* 2.9 39.2 + - + +
158A ILE* 1.3 93.9 - - + +
160A PHE* 1.3 74.3 + - + +
161A LYS* 3.7 1.8 - - - -
64B LEU* 4.3 8.2 + - - +
158B ILE* 5.1 2.2 - - + -
159B TYR* 2.6 34.9 + + - -
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Residues in contact with PHE 160 (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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76A VAL* 3.8 28.9 - - + -
84A LYS* 3.3 36.6 - - + +
85A VAL 3.7 26.7 - - - -
86A LEU* 3.8 20.9 - - + -
94A LEU* 3.8 11.0 - - + -
96A GLU* 4.3 7.9 - - + -
127A ASP* 6.2 0.7 - - + -
155A VAL* 4.3 1.6 - - + -
156A SER* 2.8 33.9 + - - +
159A TYR* 1.3 87.1 - - + +
161A LYS* 1.4 58.2 + - - +
162A ASN 3.3 2.7 - - - -
163A ILE* 2.9 34.1 + - + -
164A SER* 2.9 25.8 + - - -
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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