Contacts of the helix formed by residues 167 - 177 (chain A) in PDB entry 6YBX
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 THR 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ALA* 5.2 0.3 - - - +
156A GLU* 4.4 16.8 - - + +
157A TYR* 3.7 35.6 - - + -
165A GLY 3.6 10.8 - - - +
166A PRO* 1.3 80.8 - - - +
168A GLU* 1.3 65.6 + - - +
169A TYR* 3.4 8.6 + - - +
170A SER* 2.9 27.7 + - - +
171A ARG* 2.9 32.7 + - - +
183A TYR* 6.4 0.4 - - + -
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Residues in contact with GLU 168 (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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167A THR* 1.3 74.7 - - - +
169A TYR* 1.3 71.3 + - + +
171A ARG* 2.3 44.6 + - - +
172A PHE* 3.3 19.2 + - - +
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Residues in contact with TYR 169 (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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135A PRO* 4.5 16.8 - - + -
137A LYS* 3.7 29.3 + - + +
138A LEU* 3.6 31.0 - - + -
148A ALA* 3.7 30.5 - - + +
152A PHE* 3.6 23.6 - + - -
157A TYR* 3.4 28.9 - + - -
167A THR* 3.1 3.4 + - - +
168A GLU* 1.3 82.4 - - + +
170A SER* 1.3 66.2 + - - +
172A PHE* 3.2 15.1 + - - +
173A PHE* 3.4 19.4 - - + -
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Residues in contact with SER 170 (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 ALA* 5.7 0.2 - - - +
166A PRO* 3.4 13.2 - - - +
167A THR* 2.9 39.0 + - - -
169A TYR* 1.3 75.7 - - - +
171A ARG* 1.3 58.7 + - - +
173A PHE* 3.2 6.9 + - - -
174A LYS* 3.0 22.5 + - - +
182A SER* 3.4 37.7 + - - -
183A TYR* 3.9 16.0 - - - -
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Residues in contact with ARG 171 (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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166A PRO* 3.8 41.0 + - + +
167A THR* 2.9 16.6 + - - +
168A GLU* 2.3 44.4 + - - +
169A TYR 3.2 0.2 - - - -
170A SER* 1.3 77.9 + - - +
172A PHE* 1.3 56.7 + - - +
174A LYS* 3.9 9.1 - - + +
175A ARG* 2.9 32.1 + - - +
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Residues in contact with PHE 172 (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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130A ILE* 3.8 24.5 - - + -
133A GLN* 3.5 22.7 - - + -
134A CYS* 3.6 16.4 - - - -
135A PRO* 3.5 31.4 - - + -
145A CYS* 3.9 8.3 - - - -
168A GLU 3.3 11.7 + - - +
169A TYR 3.2 8.9 + - - +
170A SER 3.2 0.4 - - - -
171A ARG* 1.3 73.6 - - - +
173A PHE* 1.3 84.8 + + - +
175A ARG* 3.3 26.3 + - - +
176A LEU* 3.3 50.6 + - + +
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Residues in contact with PHE 173 (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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104A ASN* 3.8 31.3 - - + +
107A GLY* 4.4 3.4 - - - -
108A PHE* 4.1 14.6 - - + -
130A ILE* 3.9 31.8 - - + +
138A LEU* 3.9 15.0 - - + -
145A CYS* 3.8 17.9 - - - -
146A ASN 3.5 28.5 - - - -
147A ASP* 4.3 11.2 - - + -
148A ALA 5.2 0.9 - - - -
169A TYR 3.4 21.1 - - - -
170A SER* 3.2 9.8 + - - +
172A PHE* 1.3 83.1 - + - +
174A LYS* 1.3 56.8 + - - +
176A LEU* 3.4 1.2 + - - +
177A CYS* 2.9 33.4 + - - +
182A SER* 4.2 15.5 - - - -
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Residues in contact with LYS 174 (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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170A SER 3.0 15.3 + - - +
171A ARG* 3.9 9.9 - - + +
172A PHE 3.2 0.2 - - - -
173A PHE* 1.3 75.4 - - - +
175A ARG* 1.3 65.0 + - - +
177A CYS 4.0 1.8 - - - -
178A PRO* 2.9 56.0 + - + +
180A ALA 3.2 16.0 + - - +
181A PHE* 4.7 0.2 - - - +
182A SER* 3.8 9.3 - - - +
186A ASP* 3.0 39.6 + - - +
187A LYS* 4.4 1.8 + - - -
189A THR* 3.7 15.4 - - - +
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Residues in contact with ARG 175 (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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133A GLN* 5.7 3.4 - - - +
171A ARG 2.9 17.7 + - - +
172A PHE* 3.3 29.8 + - - +
174A LYS* 1.3 77.7 - - - +
176A LEU* 1.3 84.1 + - + +
178A PRO* 3.9 8.9 - - - +
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Residues in contact with LEU 176 (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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128A ALA* 3.4 25.6 - - + +
129A ASP 4.5 2.0 - - - +
130A ILE* 3.8 22.4 - - + +
133A GLN* 4.0 21.3 - - + -
172A PHE* 3.3 46.9 + - + +
173A PHE 4.1 1.1 - - - +
174A LYS 3.3 0.4 - - - -
175A ARG* 1.3 103.9 - - + +
177A CYS* 1.3 64.0 + - - +
178A PRO* 3.6 5.1 - - - +
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Residues in contact with CYS 177 (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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104A ASN* 3.9 7.6 - - - +
125A ARG 4.8 2.2 - - - +
126A CYS* 2.0 63.3 - - + -
127A ALA 3.9 3.1 - - - -
128A ALA* 4.2 5.4 - - - -
130A ILE* 3.9 8.1 - - + -
173A PHE 2.9 16.6 + - - +
174A LYS* 3.4 6.1 - - - +
176A LEU* 1.3 83.5 - - - +
178A PRO* 1.3 67.1 - - - +
179A ASP 3.1 3.5 + - - +
180A ALA* 3.3 16.9 + - + +
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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