Contacts of the helix formed by residues 157 - 167 (chain W) in PDB entry 2Q4G
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 SER 157 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126W ASP* 2.7 26.9 + - - -
129W LEU* 2.8 35.2 - - - +
130W GLN* 5.0 1.1 - - - -
153W LEU* 3.7 10.3 - - - +
154W SER 2.9 10.4 + - - -
156W ALA* 1.3 77.9 - - - +
158W CYS* 1.3 66.9 + - - +
160W PRO* 3.1 13.0 - - - +
161W LEU* 3.1 27.2 + - - +
181W ILE* 5.5 0.9 - - - -
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Residues in contact with CYS 158 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W ALA 3.5 6.3 + - - +
157W SER* 1.3 76.5 - - - +
159W GLU* 1.3 61.2 + - - +
161W LEU* 3.7 1.7 - - - -
162W ALA* 2.7 31.2 + - - +
181W ILE* 3.5 29.6 - - - -
185W GLY* 3.4 45.5 - - - +
188W VAL* 3.6 8.6 - - + +
189W LEU* 3.4 28.2 - - + +
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Residues in contact with GLU 159 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W ALA 4.8 4.6 + - - +
156W ALA 6.4 0.2 - - - -
158W CYS* 1.3 73.5 - - - +
160W PRO* 1.4 73.9 - - + +
162W ALA* 3.1 7.0 + - - +
163W SER* 3.0 22.9 + - - -
188W VAL* 3.1 31.8 - - + +
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Residues in contact with PRO 160 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129W LEU* 5.6 0.4 - - + -
130W GLN* 3.7 32.1 - - + +
133W CYS* 3.7 27.0 - - + +
156W ALA 4.1 6.3 - - - +
157W SER* 3.1 17.7 - - - +
159W GLU* 1.4 95.9 - - + +
161W LEU* 1.3 59.3 + - - +
163W SER* 2.6 26.1 + - - +
164W VAL* 3.4 9.4 + - - +
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Residues in contact with LEU 161 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129W LEU* 4.3 12.1 - - + -
133W CYS* 3.8 20.2 - - - -
136W LEU* 5.1 0.7 - - + -
146W LEU* 4.6 13.5 - - + -
148W LEU* 3.8 31.6 - - + -
153W LEU* 5.0 0.4 - - + -
157W SER* 3.1 18.4 + - - +
158W CYS* 5.7 0.9 - - - -
160W PRO* 1.3 76.4 - - - +
162W ALA* 1.3 67.1 + - - +
164W VAL* 3.1 11.6 + - + +
165W LEU* 3.0 25.0 + - - +
174W LEU* 4.8 11.0 - - + -
176W VAL* 4.7 19.1 - - + -
189W LEU* 3.6 26.0 - - + -
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Residues in contact with ALA 162 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158W CYS 2.7 22.3 + - - +
159W GLU* 3.4 11.9 - - - +
161W LEU* 1.3 72.7 - - - +
163W SER* 1.3 63.3 + - - +
165W LEU* 3.1 10.8 + - - +
166W ARG* 3.1 28.0 + - + +
188W VAL* 3.7 23.8 - - + +
189W LEU* 4.4 2.2 - - - +
191W GLN* 5.8 0.2 - - + -
192W GLY* 4.1 15.3 - - - +
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Residues in contact with SER 163 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133W CYS* 5.2 0.3 - - - +
137W LEU* 3.5 31.9 - - - +
159W GLU 3.0 11.4 + - - -
160W PRO* 2.6 23.0 + - - +
162W ALA* 1.3 77.2 - - - +
164W VAL* 1.3 60.7 + - - +
166W ARG* 3.2 12.4 + - - +
167W ALA* 3.1 17.5 + - - +
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Residues in contact with VAL 164 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133W CYS* 4.0 23.8 - - + +
136W LEU* 4.0 37.5 - - + +
137W LEU* 3.7 11.2 - - + -
143W LEU* 6.6 0.4 - - + -
146W LEU* 5.8 1.6 - - + -
160W PRO 3.5 14.4 - - - +
161W LEU* 3.1 13.5 + - + +
163W SER* 1.3 79.0 + - - +
165W LEU* 1.3 66.7 + - + +
167W ALA* 3.0 10.9 + - - -
168W LYS* 3.2 30.7 + - + +
171W PHE* 4.9 13.2 - - + -
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Residues in contact with LEU 165 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161W LEU 3.0 19.1 + - - +
162W ALA* 3.1 11.2 + - - +
164W VAL* 1.3 77.4 - - + +
166W ARG* 1.3 62.2 + - - +
167W ALA 3.5 0.2 + - - -
168W LYS* 3.5 16.8 + - - +
171W PHE* 3.6 37.2 - - + -
174W LEU* 4.5 22.4 - - + -
189W LEU* 3.8 24.5 - - + +
193W LEU* 3.7 34.8 - - + +
196W SER* 3.1 26.0 - - - -
197W PRO* 4.8 0.3 - - - +
198W CYS* 4.2 5.5 - - - -
200W LEU* 4.8 1.1 - - + -
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Residues in contact with ARG 166 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162W ALA* 3.1 21.6 + - - +
163W SER* 3.4 11.7 - - - +
164W VAL 3.1 0.2 - - - -
165W LEU* 1.3 78.5 - - - +
167W ALA* 1.3 60.3 + - - +
168W LYS 3.5 1.0 + - - -
169W PRO* 4.8 2.4 - - - +
191W GLN* 5.1 6.3 - - - +
192W GLY* 4.6 11.9 - - - +
195W ASP* 2.6 43.0 + - + +
196W SER* 4.0 7.2 - - - +
197W PRO* 4.1 14.4 - - - +
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Residues in contact with ALA 167 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137W LEU* 3.7 27.1 - - + +
163W SER 3.1 14.2 + - - +
164W VAL 3.0 4.4 + - - +
166W ARG* 1.3 76.9 - - - +
168W LYS* 1.3 77.9 + - - +
169W PRO* 3.6 9.3 - - - +
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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