Contacts of the helix formed by residues 160 - 167 (chain B) in PDB entry 6RLR
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 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.5 0.4 - - - -
155B LEU* 5.3 1.4 - - - +
158B GLY 3.6 7.1 + - - +
159B VAL* 1.3 81.5 - - - +
161B GLN* 1.3 67.9 + - - +
162B PHE* 3.3 13.5 - - + -
163B ILE* 3.3 13.4 + - + +
164B SER* 3.4 8.5 + - - -
129C TYR* 2.5 35.4 + - - +
133C LYS* 2.6 41.6 + - - -
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Residues in contact with GLN 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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173A LEU* 3.6 23.5 + - - +
159B VAL 4.1 0.6 + - - -
160B GLU* 1.3 72.7 - - - +
162B PHE* 1.3 59.2 + - - +
164B SER* 2.4 52.5 + - - -
165B ASP* 4.4 0.7 - - - +
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Residues in contact with PHE 162 (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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140B ARG* 4.4 6.1 + - - -
160B GLU* 3.8 13.9 - - + -
161B GLN* 1.3 78.1 - - - +
163B ILE* 1.3 65.8 + - + +
164B SER 3.5 0.2 - - - -
165B ASP* 3.3 13.9 - - - +
166B ILE* 5.3 0.9 - - - +
129C TYR* 3.5 48.2 - + - -
132C LEU* 3.7 26.4 - - + +
133C LYS* 3.7 46.0 - - + -
137C GLU* 3.7 45.1 - - + +
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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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143B LEU* 4.0 14.8 - - + -
147B HIS* 3.7 25.1 - - + -
153B CYS* 4.1 10.8 - - - -
154B GLY* 4.6 4.7 - - - -
159B VAL* 4.0 13.9 - - + -
160B GLU 3.3 15.1 + - - +
161B GLN 3.1 0.6 - - - -
162B PHE* 1.3 92.5 - - + +
164B SER* 1.3 66.9 + - - +
165B ASP* 3.0 5.3 + - - -
166B ILE* 3.1 29.2 + - + +
167B CYS* 3.6 6.4 - - - -
125C TYR* 3.9 3.1 - - - +
129C TYR* 3.1 43.7 - - + +
132C LEU* 4.6 0.9 - - + -
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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
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171A ASP* 6.0 1.2 - - - +
172A VAL* 3.4 25.5 + - - +
173A LEU* 3.6 34.3 - - - -
159B VAL* 4.1 3.6 - - - -
160B GLU 3.4 4.8 + - - -
161B GLN* 2.4 36.2 + - - -
163B ILE* 1.3 77.8 - - - +
165B ASP* 1.3 63.2 + - - +
166B ILE 3.5 0.7 + - - -
167B CYS* 3.6 9.0 + - - +
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Residues in contact with ASP 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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140B ARG* 3.1 24.6 + - - -
144B LYS* 5.5 2.6 - - - -
148B TYR* 5.7 1.0 + - - -
161B GLN 4.4 0.3 - - - +
162B PHE 3.3 22.9 - - - +
163B ILE 3.9 0.2 - - - -
164B SER* 1.3 78.5 + - - +
166B ILE* 1.3 63.1 + - - +
167B CYS 3.6 3.3 + - - +
165C ASP* 5.4 1.9 - - - +
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Residues in contact with ILE 166 (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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140B ARG* 3.7 59.9 - - + +
143B LEU* 3.9 9.9 - - + -
144B LYS* 4.0 28.4 - - + +
147B HIS* 2.9 33.3 + - + +
148B TYR* 3.8 11.7 - - - -
162B PHE 5.3 0.4 - - - +
163B ILE* 3.1 31.4 + - + +
165B ASP* 1.3 83.7 - - - +
167B CYS* 1.3 58.6 + - - +
132C LEU* 4.4 7.4 - - + -
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Residues in contact with CYS 167 (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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172A VAL* 4.3 6.5 - - + +
147B HIS* 3.4 22.9 - - - -
148B TYR* 3.7 11.1 + - - -
153B CYS* 2.0 57.0 - - + -
163B ILE* 3.6 12.1 - - - -
164B SER 3.6 11.1 + - - +
165B ASP 3.6 3.1 - - - +
166B ILE* 1.3 80.1 + - - +
168B PRO* 1.4 73.5 - - + +
169B LYS* 3.7 4.2 + - - +
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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