Contacts of the helix formed by residues 167 - 177 (chain A) in PDB entry 1R6W
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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165A ALA 4.1 0.4 + - - +
166A TRP* 1.3 78.0 - - - +
168A PRO* 1.3 76.9 - - + +
169A LEU* 3.5 8.1 + - - +
170A LYS* 3.2 36.7 + - + +
171A GLY* 3.0 18.7 + - - -
193A CYS* 4.2 3.3 - - - -
194A LYS* 4.6 18.8 - - + -
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Residues in contact with PRO 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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166A TRP 4.7 0.2 - - - +
167A THR* 1.3 86.9 - - + +
169A LEU* 1.3 62.7 + - - +
171A GLY* 3.3 2.7 + - - +
172A GLN* 3.0 38.6 + - - +
193A CYS* 4.7 6.7 - - - -
198A ASP* 3.5 42.2 - - + +
202A PHE* 5.7 1.9 - - + -
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Residues in contact with LEU 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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167A THR* 3.2 8.5 + - - +
168A PRO* 1.3 79.2 - - - +
170A LYS* 1.3 64.4 + - + +
172A GLN* 3.1 20.6 + - + +
173A GLN* 2.7 68.9 + - + +
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Residues in contact with LYS 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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139A ALA* 3.2 16.1 - - + +
165A ALA 4.7 6.8 + - - +
166A TRP* 3.6 33.2 - - + -
167A THR* 3.2 29.6 + - - +
169A LEU* 1.3 78.1 - - + +
171A GLY* 1.3 57.2 + - - +
173A GLN* 3.2 18.9 + - - +
174A PHE* 2.9 26.7 + - - +
194A LYS* 6.3 0.6 - - - +
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Residues in contact with GLY 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 TRP* 3.8 23.0 - - - +
167A THR 3.0 13.3 + - - -
168A PRO* 3.7 4.0 - - - -
169A LEU 3.2 0.2 - - - -
170A LYS* 1.3 75.7 - - - +
172A GLN* 1.3 56.2 + - - +
174A PHE* 3.4 2.3 + - - +
175A ALA* 3.0 23.2 + - - +
193A CYS* 5.3 1.6 - - - -
202A PHE* 3.4 29.9 - - - -
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Residues in contact with GLN 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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168A PRO* 3.0 28.6 + - - +
169A LEU* 3.1 27.0 + - + +
171A GLY* 1.3 74.8 - - - +
173A GLN* 1.3 64.3 + - - +
175A ALA* 3.9 5.4 - - - +
176A LYS* 2.9 27.4 + - - +
202A PHE* 6.0 0.4 - - + -
205A GLU* 4.1 18.5 + - + +
206A THR* 5.2 9.9 - - + -
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Residues in contact with GLN 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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139A ALA* 3.9 14.9 + - + +
140A VAL* 4.5 16.0 - - + +
169A LEU* 2.7 50.7 + - + +
170A LYS* 3.2 22.6 + - - +
172A GLN* 1.3 75.0 - - + +
174A PHE* 1.3 62.8 + - - +
176A LYS* 3.7 10.3 + - - +
177A TYR* 3.2 28.6 - - + -
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Residues in contact with PHE 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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134A VAL* 4.5 3.8 - - + -
139A ALA* 3.6 12.2 - - + +
142A ASP* 3.7 17.0 - - + -
143A GLY* 3.4 43.8 - - - -
146A VAL* 3.9 9.9 - - + -
160A LEU* 3.8 23.6 - - + -
166A TRP* 3.4 33.7 - + + -
170A LYS 2.9 13.6 + - - +
171A GLY 3.5 9.2 - - - +
173A GLN* 1.3 79.2 - - - +
175A ALA* 1.3 67.1 + - - +
177A TYR 3.2 10.7 + - - -
178A VAL* 3.8 18.4 - - + +
186A ILE* 4.5 2.2 - - + -
189A LEU* 3.9 17.9 - - + -
202A PHE* 4.3 4.7 - + - -
208A ILE* 4.1 16.4 - - + -
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Residues in contact with ALA 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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171A GLY 3.0 16.6 + - - +
172A GLN* 3.2 3.8 + - - +
174A PHE* 1.3 82.5 - - - +
176A LYS* 1.3 63.3 + - - +
178A VAL* 2.9 14.3 + - - +
183A ARG* 2.8 24.7 + - - +
202A PHE* 4.5 0.9 - - + -
206A THR* 3.6 28.9 - - + -
208A ILE* 3.8 19.3 - - + -
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Residues in contact with LYS 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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172A GLN 2.9 17.7 + - - +
173A GLN* 3.9 10.9 - - - +
174A PHE 3.2 0.4 - - - -
175A ALA* 1.3 77.9 - - - +
177A TYR* 1.3 93.1 + - + +
178A VAL 3.6 3.6 + - - +
180A PRO* 6.0 0.7 - - - +
183A ARG* 4.2 7.5 + - - +
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Residues in contact with TYR 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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140A VAL* 3.9 35.9 - - + +
143A GLY* 3.7 21.5 - - - -
144A MET* 3.7 25.4 - - + +
147A ASN* 3.3 25.1 + - - +
173A GLN* 3.2 23.3 - - - -
174A PHE 3.2 3.9 + - - +
175A ALA 3.1 1.0 - - - -
176A LYS* 1.3 109.2 + - + +
178A VAL* 1.3 61.5 + - - +
179A ASN 3.7 0.6 + - - -
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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