Contacts of the helix formed by residues 168 - 180 (chain T) 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 GLY 168 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36T THR* 3.6 19.3 - - - +
166T GLY 3.3 1.0 + - - -
167T LYS* 1.3 76.2 - - - +
169T ARG* 1.3 62.1 + - - +
170T GLN* 3.5 4.9 + - - -
171T SER* 3.7 2.0 + - - -
172T ALA* 3.1 23.7 + - - +
201T ALA* 3.5 27.4 - - - +
204T ASP* 3.9 12.1 - - - -
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Residues in contact with ARG 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T GLU* 3.4 55.8 + - - +
36T THR* 5.0 0.2 - - - -
164T ALA* 3.9 4.7 - - - +
165T THR* 3.9 22.0 - - - +
166T GLY 2.9 26.8 + - - +
167T LYS* 3.2 4.9 + - - +
168T GLY* 1.3 77.4 - - - +
170T GLN* 1.3 73.3 + - + +
172T ALA* 3.3 6.3 + - - +
173T LYS* 2.7 60.7 + - + +
301T MG 3.5 23.4 - - - -
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Residues in contact with GLN 170 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167T LYS 2.7 27.1 + - - -
168T GLY 3.6 1.9 - - - -
169T ARG* 1.3 93.8 - - + +
171T SER* 1.3 77.4 + - - +
173T LYS* 3.6 9.2 - - - +
174T ALA* 2.8 26.0 + - - +
204T ASP* 2.9 20.8 + - - +
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Residues in contact with SER 171 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168T GLY* 3.8 5.8 + - - -
170T GLN* 1.3 78.8 + - - +
172T ALA* 1.3 58.6 + - - +
174T ALA* 3.2 6.7 + - - +
175T GLU* 2.9 34.0 + - - +
199T LEU* 4.7 7.2 - - - -
201T ALA* 4.3 15.8 - - - -
203T GLU* 5.9 0.2 - - - +
204T ASP* 2.8 31.7 + - - -
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Residues in contact with ALA 172 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T THR* 4.8 2.0 - - - +
38T ILE* 4.1 6.1 - - + -
164T ALA* 3.6 18.2 - - + -
168T GLY 3.1 17.2 + - - +
169T ARG* 3.5 4.3 - - - +
171T SER* 1.3 78.7 - - - +
173T LYS* 1.3 57.2 + - - +
175T GLU* 3.2 3.6 + - - +
176T LEU* 2.9 35.9 + - - +
196T ILE* 3.8 26.6 - - + +
201T ALA* 4.3 7.8 - - + +
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Residues in contact with LYS 173 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150T MET* 5.4 7.0 - - - +
164T ALA* 3.8 23.1 - - + +
169T ARG* 2.7 44.0 + - + +
170T GLN* 3.3 9.6 + - + +
172T ALA* 1.3 72.6 - - - +
174T ALA* 1.3 62.1 + - - +
176T LEU* 3.6 3.8 + - - +
177T GLU* 3.1 34.4 + - - +
301T MG 2.7 29.7 - - - -
56U ASP* 5.4 8.7 + - - +
58U LEU* 3.7 22.2 - - + +
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Residues in contact with ALA 174 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170T GLN 2.8 13.6 + - - +
171T SER* 3.4 10.1 - - - +
173T LYS* 1.3 76.3 - - - +
175T GLU* 1.3 63.6 + - - +
177T GLU* 3.1 12.7 + - - +
178T LYS* 3.1 40.7 + - - +
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Residues in contact with GLU 175 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T SER* 2.9 18.5 + - - +
172T ALA* 3.5 8.5 - - - +
174T ALA* 1.3 75.5 - - - +
176T LEU* 1.3 62.9 + - - +
178T LYS* 3.2 39.0 + - - +
179T LEU* 3.2 23.2 + - - +
195T LYS* 3.1 21.7 + - - +
196T ILE* 3.7 25.4 - - + -
199T LEU* 3.5 32.6 - - + +
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Residues in contact with LEU 176 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ILE* 4.2 9.9 - - + -
39T GLY 4.5 2.2 - - - +
40T ILE* 3.9 25.4 - - + -
162T GLY* 4.2 7.2 - - - -
163T ALA 3.9 33.2 - - - +
164T ALA* 4.2 8.1 - - + -
172T ALA* 2.9 32.3 + - + +
173T LYS* 3.7 5.2 - - - +
175T GLU* 1.3 75.5 - - - +
177T GLU* 1.3 57.6 + - - +
179T LEU* 3.1 13.1 + - + +
180T VAL* 3.0 30.2 + - + +
196T ILE* 3.6 22.2 - - + -
58U LEU* 3.5 16.8 - - + -
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Residues in contact with GLU 177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T LYS* 3.1 27.4 + - - +
174T ALA* 3.1 13.0 + - - +
176T LEU* 1.3 72.7 - - - +
178T LYS* 1.3 65.3 + - + +
180T VAL* 3.1 35.8 + - - +
56U ASP* 4.4 9.3 - - - +
57U LYS* 3.1 40.9 + - + +
58U LEU* 3.9 22.0 - - + +
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Residues in contact with LYS 178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174T ALA* 3.1 28.3 + - - +
175T GLU* 3.2 39.4 + - - +
177T GLU* 1.3 79.0 - - + +
179T LEU* 1.3 57.9 + - + +
180T HIS* 3.0 47.3 - - + +
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Residues in contact with LEU 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T ILE* 4.9 6.3 - - + -
175T GLU 3.2 10.2 + - - +
176T LEU* 3.1 16.7 + - + +
178T LYS* 1.3 76.5 - - + +
180T VAL* 1.3 117.5 + - + +
184T LEU* 4.9 14.1 - - + -
192T GLN* 3.5 44.9 - - + +
195T LYS* 5.2 5.8 - - - +
196T ILE* 3.7 23.8 - - + -
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Residues in contact with VAL 180 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161T LYS* 4.0 44.2 - - + +
162T GLY* 5.6 0.4 - - - -
176T LEU* 3.0 20.7 + - + +
177T GLU* 3.8 6.5 - - - +
179T LEU* 1.3 76.4 - - + +
180T ASP* 1.3 89.9 + - - +
57U LYS* 4.2 16.4 - - + +
58U LEU* 3.9 20.6 - - + -
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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