Contacts of the helix formed by residues 168 - 180 (chain O) in PDB entry 3D29
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O THR* 3.1 17.1 + - - -
167O LYS* 1.3 78.3 - - - +
169O SER* 1.3 57.6 + - - +
170O VAL* 3.4 2.9 - - - -
171O ALA* 3.6 9.2 + - - +
172O ALA* 3.0 31.5 + - - +
200O SER* 4.3 9.1 + - - -
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Residues in contact with SER 169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O LYS* 2.8 27.7 + - - -
36O THR* 4.6 0.4 + - - -
164O ALA* 3.5 26.7 - - - -
165O ILE* 3.7 11.2 - - - -
166O GLY 3.0 10.1 + - - -
167O LYS 3.4 1.2 + - - -
168O GLY* 1.3 74.6 - - - +
170O VAL* 1.3 58.4 + - - +
172O ALA* 4.2 5.2 - - - -
173O LYS* 2.7 49.6 + - - +
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Residues in contact with VAL 170 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O LYS* 4.4 10.3 - - - +
168O GLY 3.4 0.6 - - - -
169O SER* 1.3 83.0 + - - +
171O ALA* 1.3 62.8 + - - +
173O LYS* 3.7 12.6 - - - +
174O THR* 3.1 31.8 + - - +
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Residues in contact with ALA 171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O GLY* 3.6 10.4 + - - +
169O SER 3.3 0.4 - - - -
170O VAL* 1.3 80.2 - - - +
172O ALA* 1.3 62.5 + - - +
174O THR* 3.3 8.7 + - - -
175O PHE* 3.0 22.6 + - - +
199O GLU* 6.3 2.9 - - + -
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Residues in contact with ALA 172 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O THR* 4.8 4.9 - - + -
38O LEU* 5.3 0.2 - - + -
164O ALA* 3.7 23.1 - - + -
168O GLY 3.0 20.4 + - - +
169O SER 3.7 0.2 - - - +
171O ALA* 1.3 77.3 - - - +
173O LYS* 1.3 62.8 + - - +
175O PHE* 3.1 5.5 + - - +
176O LEU* 2.9 27.6 + - - +
196O THR* 3.8 21.4 - - + +
200O SER* 4.6 9.9 - - - +
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Residues in contact with LYS 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O TRP* 5.1 13.5 - - + -
163O THR* 3.4 22.4 - - - +
164O ALA 3.9 21.0 + - - +
169O SER* 2.7 43.1 + - - +
170O VAL* 3.7 10.7 - - - +
172O ALA* 1.3 71.6 - - - +
174O THR* 1.3 65.6 + - - +
176O LEU* 3.0 10.0 + - - +
177O GLU* 2.9 38.2 + - + +
56P SER* 6.0 1.6 - - - +
58P LEU* 4.4 4.8 - - + +
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Residues in contact with THR 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O VAL* 3.1 20.0 + - - +
171O ALA* 3.5 11.4 - - - -
173O LYS* 1.3 77.5 - - - +
175O PHE* 1.3 63.2 + - - +
177O GLU* 3.4 21.4 + - - +
178O LYS* 3.4 35.5 + - + +
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Residues in contact with PHE 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O ALA 3.0 13.8 + - - +
172O ALA* 3.5 8.7 - - - +
173O LYS 3.1 0.2 - - - -
174O THR* 1.3 79.6 - - - +
176O LEU* 1.3 60.8 + - - +
178O LYS* 3.4 13.1 + - + +
179O ARG* 3.1 57.5 + - + +
192O ILE* 4.4 1.8 - - + -
195O LEU* 3.9 18.4 - - + -
196O THR* 3.4 48.5 - - + -
199O GLU* 5.2 11.4 - - + -
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Residues in contact with LEU 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O LEU* 4.7 4.3 - - + -
39O GLY 4.6 1.3 - - - +
40O ILE* 3.7 26.9 - - + -
162O ALA* 4.2 7.0 - - + -
163O THR* 3.6 43.5 - - - +
164O ALA* 4.4 4.7 - - + +
172O ALA 2.9 20.1 + - - +
173O LYS* 3.6 7.2 - - - +
175O PHE* 1.3 72.8 - - - +
177O GLU* 1.3 61.4 + - - +
179O ARG* 3.2 2.6 + - - +
180O TRP* 2.8 35.7 + - + +
192O ILE* 4.1 8.1 - - + -
196O THR* 3.4 28.9 - - + +
58P LEU* 4.1 11.2 - - + -
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Residues in contact with GLU 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O LYS* 2.9 33.1 + - - +
174O THR* 3.6 15.0 + - + +
175O PHE 3.3 0.2 - - - -
176O LEU* 1.3 76.6 - - - +
178O LYS* 1.3 63.3 + - + +
180O TRP* 3.9 11.3 + - - +
56P SER* 4.5 10.4 + - - -
57P THR* 3.5 27.2 + - + +
58P LEU* 3.6 29.8 - - + +
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Residues in contact with LYS 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O THR* 3.4 30.6 + - + +
175O PHE* 3.4 17.2 + - + +
176O LEU 3.2 0.6 - - - -
177O GLU* 1.3 80.9 - - + +
179O ARG* 1.3 68.7 + - + +
180O TRP 3.6 1.6 - - - +
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Residues in contact with ARG 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O PHE* 3.1 50.4 - - + +
176O LEU 3.2 2.3 + - - +
178O LYS* 1.3 87.0 - - - +
180O TRP* 1.3 63.2 + - - +
181O ASN* 3.8 11.4 + - - -
184O LEU* 4.2 9.0 - - - +
191O HIS* 4.9 3.0 + - - -
192O ILE* 3.2 39.3 - - + +
195O LEU* 3.5 26.0 - - - +
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Residues in contact with TRP 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O ILE* 3.9 15.5 - - + -
41O LYS* 2.9 30.6 + - - -
42O ALA 6.3 0.7 - - - -
161O LYS* 3.4 57.4 + - + -
162O ALA* 4.0 13.2 - - + -
176O LEU* 2.8 19.5 + - + +
177O GLU 3.9 8.8 + - - +
178O LYS 3.6 1.6 - - - +
179O ARG* 1.3 78.4 - - - +
181O ASN* 1.3 85.1 + - - +
182O ASP* 3.6 31.0 - - + -
184O LEU* 3.5 20.7 - - + +
192O ILE* 5.6 1.3 - - + +
57P THR* 6.1 2.2 - - + -
58P LEU* 4.3 16.6 - - + +
60P GLU* 6.0 0.4 - - - -
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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