Contacts of the helix formed by residues 168 - 180 (chain B) in PDB entry 3SDI
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 ASN 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B SER* 4.6 1.0 + - - -
36B THR* 4.4 3.8 + - - +
166B GLY 3.7 0.8 + - - -
167B ALA* 1.3 80.1 - - - +
169B THR* 1.3 65.0 + - - +
170B SER* 3.2 3.8 - - - +
171B ALA* 3.3 11.9 + - + +
172B ALA* 3.0 23.6 + - - +
200B THR* 3.0 40.0 + - - -
202B THR* 5.1 0.4 - - - +
203B ASP* 3.3 26.0 + - - +
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Residues in contact with THR 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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164B SER* 3.6 21.3 + - - +
165B VAL* 3.6 28.3 - - - -
166B GLY 3.1 26.3 + - - +
167B ALA 4.1 0.9 - - - +
168B ASN* 1.3 75.9 - - - +
170B SER* 1.3 59.9 + - - +
172B ALA* 4.6 0.4 - - - -
173B GLN* 2.7 40.2 + - - +
56C LEU* 6.4 0.2 - - - -
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Residues in contact with SER 170 (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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168B ASN* 5.0 1.1 - - - -
169B THR* 1.3 82.1 + - - +
171B ALA* 1.3 60.4 + - - +
173B GLN* 3.8 5.6 - - - +
174B THR* 2.9 31.7 + - - -
56C LEU* 5.9 4.5 - - - -
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Residues in contact with ALA 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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168B ASN* 3.3 16.4 + - + +
170B SER* 1.3 79.6 - - - +
172B ALA* 1.3 62.8 + - - +
174B THR* 3.5 4.9 + - - -
175B LEU* 3.3 30.0 + - + +
200B THR* 3.8 16.6 - - + -
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Residues in contact with ALA 172 (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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36B THR* 4.9 4.5 - - + -
38B ILE* 4.7 7.0 - - + -
164B SER* 3.9 19.3 - - - +
168B ASN 3.0 16.4 + - - +
169B THR 3.9 2.5 - - - +
171B ALA* 1.3 75.1 - - - +
173B GLN* 1.3 65.4 + - - +
175B LEU 3.4 0.3 + - - -
176B LEU* 3.0 31.8 + - + +
196B THR* 3.8 23.4 - - + +
200B THR* 3.9 12.5 - - + +
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Residues in contact with GLN 173 (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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160B TRP* 4.5 3.2 - - - -
162B ALA 3.5 21.4 + - - -
163B ILE* 3.8 17.0 - - - +
164B SER* 3.3 28.2 + - - -
169B THR* 2.7 23.3 + - - +
170B SER* 3.8 6.3 - - - +
171B ALA 3.3 0.2 - - - -
172B ALA* 1.3 75.0 - - - +
174B THR* 1.3 57.8 + - - +
176B LEU* 3.5 5.7 + - - +
177B GLN* 3.0 38.2 + - - +
56C LEU* 3.9 30.3 - - + -
57C LYS 4.0 9.7 + - - -
58C LEU* 3.9 18.2 - - - +
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Residues in contact with THR 174 (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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170B SER* 2.9 19.1 + - - -
171B ALA* 3.8 4.7 - - - -
173B GLN* 1.3 77.7 - - - +
175B LEU* 1.3 58.1 + - - +
177B GLN* 3.4 10.5 + - + +
178B MET* 3.0 38.2 + - + +
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Residues in contact with LEU 175 (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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171B ALA* 3.3 19.5 + - + +
172B ALA 3.8 5.4 - - - +
173B GLN 3.4 0.4 - - - -
174B THR* 1.3 75.0 - - - +
176B LEU* 1.3 63.4 + - - +
178B MET* 3.4 18.5 - - + +
179B ASP* 3.2 25.5 + - - +
192B LEU* 4.6 2.7 - - - +
196B THR* 3.8 20.4 - - + +
199B LYS* 4.0 41.7 - - + +
200B THR* 3.7 25.1 - - + -
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Residues in contact with LEU 176 (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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38B ILE* 4.5 7.4 - - + -
40B ILE* 3.9 31.4 - - + -
162B ALA* 4.3 6.3 - - + -
163B ILE 4.1 28.0 - - - +
164B SER* 4.6 5.2 - - - -
172B ALA* 3.0 26.7 + - + +
173B GLN* 3.8 20.2 - - - +
175B LEU* 1.3 73.8 - - - +
177B GLN* 1.3 66.0 + - - +
180B TYR* 3.0 31.4 + - - +
192B LEU* 4.0 10.3 - - + -
196B THR* 3.8 24.0 - - + +
58C LEU* 4.0 11.4 - - + -
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Residues in contact with GLN 177 (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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173B GLN* 3.0 27.6 + - - +
174B THR* 3.6 9.9 - - + +
176B LEU* 1.3 78.2 - - - +
178B MET* 1.3 64.7 + - - +
180B TYR* 4.1 7.6 + - - +
56C LEU* 5.9 0.8 - - - +
57C LYS* 3.9 53.1 + - - +
58C LEU* 3.9 14.7 - - + +
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Residues in contact with MET 178 (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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174B THR* 3.0 24.2 + - + +
175B LEU* 3.4 21.5 - - + +
177B GLN* 1.3 81.2 - - - +
179B ASP* 1.3 76.7 + - - +
180B TYR 3.7 2.9 + - - +
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Residues in contact with ASP 179 (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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175B LEU 3.2 12.8 + - - +
178B MET* 1.3 95.1 - - - +
180B TYR* 1.3 63.2 + - - +
181B LYS* 3.6 7.4 + - - +
184B MET* 4.8 3.6 - - - +
192B LEU* 4.2 25.3 - - + +
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Residues in contact with TYR 180 (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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40B ILE* 3.9 18.2 - - + -
41B MET* 2.7 31.8 + - - -
42B ALA* 4.9 0.5 - - - -
161B LYS* 3.5 35.9 - - + +
162B ALA* 4.4 7.2 - - + -
176B LEU* 3.0 21.0 + - - +
177B GLN 4.1 4.2 + - - +
178B MET 3.6 5.5 - - - +
179B ASP* 1.3 77.8 - - - +
181B LYS* 1.3 67.3 + - - +
182B ASP* 3.7 32.9 + - - -
184B MET* 3.4 26.0 - - + -
192B LEU* 4.1 10.0 - - + +
58C LEU* 4.0 23.8 - - + -
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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