Contacts of the helix formed by residues 160 - 167 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B TYR* 2.6 38.6 + - - +
133B LYS* 2.7 41.1 + - - -
155C LEU* 5.0 2.1 - - - +
158C GLY 3.9 5.4 + - - +
159C VAL* 1.3 81.8 - - - +
161C GLN* 1.3 65.6 + - - +
162C PHE* 3.3 12.3 - - + -
163C ILE* 3.3 12.0 + - - +
164C SER* 3.4 9.1 + - - -
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Residues in contact with GLN 161 (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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137B GLU* 6.0 0.7 - - - +
159C VAL 4.2 0.2 + - - -
160C GLU* 1.3 72.7 - - - +
162C PHE* 1.3 59.1 + - - +
164C SER* 2.4 51.9 + - - -
165C ASP* 4.7 0.2 - - - +
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Residues in contact with PHE 162 (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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129B TYR* 3.5 48.2 - + - -
132B LEU* 3.6 32.2 - - + +
133B LYS* 3.3 60.1 - - + +
137B GLU* 3.4 46.6 - - + +
140C ARG* 4.4 5.7 + - - -
160C GLU* 3.9 12.1 - - + -
161C GLN* 1.3 78.5 - - - +
163C ILE* 1.3 65.0 + - + +
164C SER 3.5 0.2 - - - -
165C ASP* 3.4 13.6 - - - +
166C ILE* 5.5 0.3 - - - +
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Residues in contact with ILE 163 (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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125B TYR* 3.7 14.6 - - - +
129B TYR* 3.2 40.8 - - + -
132B LEU* 4.6 0.7 - - + -
143C LEU* 3.9 14.1 - - + -
147C HIS* 3.8 17.0 - - + -
153C CYS* 4.1 7.9 - - - -
154C GLY* 4.7 2.7 - - - -
159C VAL* 3.4 26.7 - - + -
160C GLU 3.3 10.4 + - - +
161C GLN 3.1 0.4 - - - -
162C PHE* 1.3 89.1 - - + +
164C SER* 1.3 65.4 + - - +
165C ASP* 3.0 5.6 + - - -
166C ILE* 3.1 30.0 + - + +
167C CYS* 3.6 5.5 - - - -
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Residues in contact with SER 164 (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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159C VAL* 4.1 12.8 - - - -
160C GLU 3.4 7.3 + - - -
161C GLN* 2.4 43.9 + - - -
163C ILE* 1.3 77.6 - - - +
165C ASP* 1.3 62.9 + - - +
166C ILE 3.4 1.2 + - - -
167C CYS* 3.7 15.5 + - - +
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Residues in contact with ASP 165 (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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140B ARG* 4.8 11.8 + - - -
165B ASP* 5.4 1.6 - - - +
140C ARG* 4.5 12.4 + - - -
144C LYS* 5.7 1.2 - - - -
148C TYR* 5.7 0.3 + - - -
161C GLN 4.7 0.2 - - - +
162C PHE 3.4 21.3 - - - +
163C ILE* 3.9 1.0 - - - -
164C SER* 1.3 77.8 + - - +
166C ILE* 1.3 73.8 + - - +
167C CYS 3.6 3.1 - - - +
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Residues in contact with ILE 166 (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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132B LEU* 4.6 4.9 - - + -
140C ARG* 3.7 45.5 - - + +
143C LEU* 3.9 9.2 - - + -
144C LYS* 4.1 25.9 - - + +
147C HIS* 2.9 37.1 + - + +
148C TYR* 3.9 12.6 - - - -
162C PHE 5.8 0.4 - - - +
163C ILE* 3.1 32.5 + - + +
165C ASP* 1.3 93.3 - - - +
167C CYS* 1.3 61.8 + - - +
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Residues in contact with CYS 167 (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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148C TYR* 3.7 8.7 + - - -
153C CYS* 2.0 49.4 - - + -
159C VAL* 3.7 18.6 - - - -
163C ILE 3.6 10.8 - - - -
164C SER* 3.7 13.0 + - - +
165C ASP 3.6 4.0 - - - +
166C ILE* 1.3 79.7 - - - +
168C PRO* 1.3 73.9 - - + +
169C LYS* 3.7 4.3 + - - +
178C VAL* 5.4 2.9 - - + -
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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