Contacts of the helix formed by residues 161 - 171 (chain B) in PDB entry 3C98
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 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLN* 4.1 0.9 - - - -
159B THR* 5.6 6.3 - - + -
160B THR* 1.3 80.0 - - - +
162B SER* 1.3 65.9 + - - +
163B GLU* 3.9 4.3 + - - +
164B GLU* 3.2 31.7 + - - +
165B LEU* 3.0 19.1 + - - +
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Residues in contact with SER 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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143B GLU* 5.5 1.6 + - - -
146B LYS* 3.6 23.1 + - - +
150B GLN* 4.0 15.5 - - - +
161B THR* 1.3 73.5 - - - +
163B GLU* 1.3 62.7 + - - +
165B LEU* 3.3 6.7 + - - +
166B GLU* 3.2 19.8 + - - +
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Residues in contact with GLU 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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161B THR* 3.3 4.9 + - - +
162B SER* 1.3 76.1 - - - +
164B GLU* 1.3 65.7 + - - +
166B GLU* 3.0 23.8 + - - +
167B ASP* 3.2 29.9 + - - +
170B GLU* 4.8 4.9 - - - +
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Residues in contact with GLU 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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158B ARG* 4.0 16.7 + - - +
159B THR 4.7 2.5 - - - +
160B THR* 4.3 13.6 - - + -
161B THR* 3.2 34.6 + - - +
163B GLU* 1.3 79.6 - - - +
165B LEU* 1.3 60.0 + - - +
167B ASP* 3.6 17.0 + - + +
168B MET* 3.6 20.8 - - - +
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Residues in contact with LEU 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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146B LYS* 3.6 37.7 - - + +
149B ILE* 4.5 10.3 - - + -
150B GLN* 3.4 49.4 - - - +
153B LEU* 4.3 13.0 - - + -
160B THR* 3.7 9.4 - - + +
161B THR 3.0 11.6 + - - +
162B SER* 3.5 9.6 - - - +
163B GLU 3.1 0.2 - - - -
164B GLU* 1.3 77.1 - - - +
166B GLU* 1.3 61.5 + - - +
167B ASP 3.2 0.7 - - - -
168B MET* 3.3 18.2 + - - +
169B LEU* 3.6 24.4 + - + +
177B PHE* 5.4 2.6 - - + -
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Residues in contact with GLU 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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315A ARG* 3.1 36.9 + - + +
142B ARG* 3.0 31.3 + - - -
146B LYS* 3.5 18.7 + - - +
162B SER 3.2 11.9 + - - +
163B GLU* 3.0 21.4 + - - +
165B LEU* 1.3 75.9 - - - +
167B ASP* 1.3 62.0 + - - +
168B MET 3.3 0.2 - - - -
169B LEU* 3.5 9.7 - - - +
170B GLU* 2.8 49.2 + - + +
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Residues in contact with ASP 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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163B GLU* 3.2 30.0 + - - +
164B GLU* 3.7 14.0 - - + +
165B LEU 3.2 0.4 - - - -
166B GLU* 1.3 80.8 - - - +
168B MET* 1.3 60.7 + - + +
169B LEU 3.4 0.3 + - - -
170B GLU* 4.2 10.9 - - - +
171B SER* 2.8 31.2 + - - +
176B ILE* 4.7 0.9 - - - +
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Residues in contact with MET 168 (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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153B LEU* 5.0 10.5 - - + -
158B ARG* 5.2 11.9 - - - +
160B THR* 4.9 8.7 - - - -
164B GLU* 3.6 20.9 - - - +
165B LEU* 3.7 13.9 - - - +
166B GLU 3.3 0.8 - - - -
167B ASP* 1.3 78.5 - - + +
169B LEU* 1.3 60.5 + - - +
171B SER 3.6 6.8 - - - +
172B GLY* 4.3 2.8 - - - -
176B ILE* 3.4 59.6 - - + +
177B PHE* 3.4 39.4 - - + +
199B HIS* 5.1 1.9 + - - -
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Residues in contact with LEU 169 (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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142B ARG* 3.8 20.2 - - - +
146B LYS* 4.6 6.7 - - + -
149B ILE* 4.6 6.1 - - + -
165B LEU* 3.6 26.5 - - + +
166B GLU* 3.4 23.0 + - - +
168B MET* 1.3 77.2 - - - +
170B GLU* 1.3 66.8 + - - +
171B SER 2.8 3.1 + - - -
172B GLY* 3.4 12.8 + - - -
177B PHE* 3.6 20.2 - - + -
199B HIS* 3.5 35.1 + - + +
202B ILE* 4.6 17.0 - - + -
206B GLU* 5.8 1.3 - - - +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 5.4 1.3 - - - +
163B GLU* 4.8 4.7 - - - +
166B GLU* 2.8 37.0 + - + +
167B ASP* 4.2 12.8 - - - +
169B LEU* 1.3 72.3 - - - +
171B SER* 1.3 58.8 + - - +
172B GLY 4.1 0.7 + - - -
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Residues in contact with SER 171 (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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167B ASP* 2.8 18.5 + - - +
168B MET 3.6 9.7 - - - +
169B LEU 3.0 2.4 - - - -
170B GLU* 1.3 79.3 - - - +
172B GLY* 1.3 62.3 + - - +
173B ASN* 3.6 2.8 + - - -
176B ILE* 3.7 10.7 - - - +
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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