Contacts of the helix formed by residues 160 - 165 (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 PHE 160 (chain B).
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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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Residues in contact with LYS 161 (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* 4.8 0.4 - - - +
67A THR* 2.9 27.0 + - - +
68A LYS* 2.9 29.2 + - - +
69A SER* 4.4 5.9 - - - +
84B LYS* 5.3 1.2 - - - +
156B SER 3.8 0.2 + - - -
157B LYS 3.6 19.0 + - - +
158B ILE 4.3 10.3 - - - +
159B TYR 3.7 1.6 + - - -
160B PHE* 1.3 75.9 - - - +
162B ASN* 1.3 64.2 + - - +
164B SER* 3.7 7.2 - - - -
165B CYS* 3.2 28.4 + - - +
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Residues in contact with ASN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 4.5 14.4 + - + +
99B GLU* 5.9 0.4 - - - +
132B ARG* 3.0 27.8 + - - +
160B PHE 3.2 1.2 + - - -
161B LYS* 1.3 78.8 - - - +
163B ILE* 1.3 62.4 + - + +
165B CYS* 3.8 8.2 - - - -
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Residues in contact with ILE 163 (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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94B LEU* 3.7 22.4 - - + -
96B GLU* 4.7 9.0 - - + -
99B GLU* 3.9 28.0 - - + +
103B HIS* 4.7 3.6 - - + -
127B ASP* 3.6 24.0 - - + +
128B GLY 3.2 21.8 - - - +
129B GLY* 3.6 20.6 - - - +
132B ARG* 3.6 15.7 - - - +
160B PHE* 2.9 41.8 + - + +
162B ASN* 1.3 84.8 - - + +
164B SER* 1.3 63.7 + - - +
165B CYS* 3.4 2.0 + - - -
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP 3.6 7.4 - - - -
128B GLY* 4.6 1.1 - - - -
156B SER* 2.9 41.8 + - - -
157B LYS* 3.2 16.4 + - - +
160B PHE 2.8 11.6 + - - -
161B LYS* 3.5 5.6 + - - -
163B ILE* 1.3 75.7 - - - +
165B CYS* 1.3 61.2 + - - +
166B GLY 3.2 4.6 + - - -
167B TYR* 3.3 32.9 + - - +
168B GLU* 6.0 0.2 - - - +
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Residues in contact with CYS 165 (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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132B ARG* 3.8 27.4 - - - -
161B LYS 3.2 15.2 + - - +
162B ASN* 3.8 17.5 - - - -
163B ILE 3.4 0.4 - - - -
164B SER* 1.3 75.7 - - - +
166B GLY* 1.3 64.2 + - - +
167B TYR 3.2 0.2 - - - -
168B GLU* 3.3 25.6 + - - +
169B ASP 4.5 0.3 + - - -
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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