Contacts of the helix formed by residues 149 - 160 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B SER* 2.7 29.9 + - - -
70B LYS 5.3 0.2 + - - -
71B TYR* 3.8 15.3 - - + +
72B GLN* 2.9 31.9 + - - +
74B VAL* 4.7 0.7 - - - +
147B GLU* 2.7 27.2 + - - +
148B ILE* 1.3 74.1 - - + +
150B GLU* 1.3 58.1 + - - +
151B THR* 3.0 21.5 + - - -
152B VAL* 2.9 35.3 + - + +
153B ILE 3.8 0.7 + - - -
401B MTA 3.7 0.9 - - - +
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Residues in contact with GLU 150 (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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148B ILE 4.0 3.6 + - - -
149B ASP* 1.3 73.4 + - - +
151B THR* 1.3 61.9 + - - +
153B ILE* 3.1 18.9 + - + +
154B GLU* 3.2 31.1 + - + +
176B ILE* 3.9 46.1 - - + +
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Residues in contact with THR 151 (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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65B TYR* 3.7 22.9 - - - +
67B THR* 4.6 6.5 - - + -
69B SER* 4.1 20.4 - - - -
74B VAL* 4.7 8.1 - - + -
149B ASP* 3.0 13.1 + - - -
150B GLU* 1.3 79.0 - - - +
152B VAL* 1.3 62.6 + - - +
154B GLU* 3.8 11.4 + - + +
155B VAL* 3.0 29.3 + - + +
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Residues in contact with VAL 152 (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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72B GLN* 3.6 22.4 - - - +
74B VAL* 4.7 7.2 - - + -
86B LEU* 4.4 14.1 - - + +
88B LEU* 4.1 15.9 - - + -
126B GLY 3.9 17.5 - - - -
127B ASP* 4.0 4.5 - - - +
147B GLU* 4.5 1.8 - - - -
149B ASP* 2.9 19.1 + - + +
151B THR* 1.3 78.5 - - - +
153B ILE* 1.3 62.4 + - - +
155B VAL* 3.9 6.3 - - - +
156B SER* 3.0 22.5 + - - -
401B MTA 3.4 36.3 - - + +
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Residues in contact with ILE 153 (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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126B GLY* 3.5 17.5 - - - +
145B ILE* 5.7 0.7 - - + -
147B GLU* 3.9 16.8 - - + -
150B GLU* 3.1 11.6 + - + +
152B VAL* 1.3 77.2 - - - +
154B GLU* 1.3 59.7 + - + +
156B SER* 3.2 2.6 + - - -
157B LYS* 2.9 52.7 + - + +
167B TYR* 3.5 37.0 - - + +
174B VAL* 3.9 17.0 - - + -
176B ILE* 3.7 30.1 - - + -
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Residues in contact with GLU 154 (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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154A GLU* 3.8 38.5 - - + +
157A LYS* 3.8 34.2 + - - +
158A ILE* 5.6 3.4 - - + -
150B GLU* 3.2 36.3 + - + +
151B THR* 3.8 12.3 + - + +
152B VAL 3.3 0.2 - - - -
153B ILE* 1.3 79.4 - - + +
155B VAL* 1.3 63.0 + - + +
157B LYS* 3.3 4.6 + - + +
158B ILE* 3.1 28.9 + - - +
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Residues in contact with VAL 155 (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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158A ILE* 5.1 3.4 - - + -
65B TYR* 3.4 41.3 - - + +
74B VAL* 4.3 8.7 - - + -
76B VAL* 3.4 31.6 - - + -
86B LEU* 4.4 7.4 - - + -
151B THR* 3.0 21.2 + - + +
152B VAL* 3.9 6.1 - - - +
154B GLU* 1.3 75.9 - - + +
156B SER* 1.3 59.2 + - - +
158B ILE* 3.3 2.4 + - - -
159B TYR* 2.8 40.5 + - + +
160B PHE* 4.9 3.1 - - + -
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Residues in contact with SER 156 (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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86B LEU* 5.8 2.7 - - - -
126B GLY 4.1 1.6 - - - -
127B ASP* 2.7 44.3 + - - +
152B VAL* 3.0 19.1 + - - -
153B ILE 3.2 3.8 + - - -
155B VAL* 1.3 79.3 - - - +
157B LYS* 1.3 56.9 + - - +
160B PHE* 2.9 43.8 + - - +
164B SER* 2.9 17.2 + - - -
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Residues in contact with LYS 157 (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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65A TYR* 4.7 0.9 + - - -
150A GLU* 2.6 36.7 + - + +
151A THR* 5.6 2.0 + - - +
154A GLU* 3.5 21.4 + - - +
153B ILE* 2.9 40.9 + - + +
154B GLU* 3.7 4.9 - - + +
156B SER* 1.3 75.0 - - - +
158B ILE* 1.3 62.0 + - - +
161B LYS* 3.6 19.1 + - - +
164B SER* 3.2 20.6 + - - +
167B TYR* 3.8 28.5 - - + +
168B GLU* 6.2 0.2 - - - -
174B VAL* 6.0 1.6 - - - +
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Residues in contact with ILE 158 (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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65A TYR* 2.7 51.4 + - + +
151A THR* 4.1 11.4 - - + +
154A GLU* 3.7 35.2 - - + +
155A VAL* 3.9 22.2 - - + +
158A ILE* 4.0 14.8 - - + -
159A TYR* 5.1 2.5 - - + -
154B GLU 3.1 20.5 + - - +
155B VAL 3.8 2.9 - - - +
156B SER 3.2 0.2 - - - -
157B LYS* 1.3 81.4 - - - +
159B TYR* 1.3 86.0 + - + +
160B PHE 3.7 0.7 - - - -
161B LYS* 4.3 7.8 - - - +
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Residues in contact with TYR 159 (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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65A TYR* 4.1 11.0 - + - -
158A ILE* 3.6 17.7 - - + +
159A TYR* 2.6 36.0 + - - -
64B LEU* 3.8 33.7 + - + -
65B TYR* 3.7 28.8 - + + -
76B VAL* 4.0 16.6 - - + -
84B LYS* 2.5 41.3 + - + +
155B VAL* 2.8 37.8 + - + +
158B ILE* 1.3 95.7 - - + +
160B PHE* 1.3 70.0 + - + +
161B LYS* 3.7 2.2 - - - -
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Residues in contact with PHE 160 (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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76B VAL* 3.8 27.1 - - + -
84B LYS* 3.5 32.8 - - + +
85B VAL 3.7 28.3 - - - -
86B LEU* 3.9 19.3 - - + -
94B LEU* 3.6 11.9 - - + -
96B GLU* 4.2 11.0 - - + -
127B ASP* 6.2 0.2 - - + -
155B VAL* 4.2 1.6 - - + -
156B SER* 2.9 33.2 + - - +
159B TYR* 1.3 85.5 - - + +
161B LYS* 1.3 59.7 + - - +
162B ASN 3.3 3.1 - - - -
163B ILE* 2.9 33.5 + - + -
164B SER* 2.8 25.6 + - - -
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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