Contacts of the helix formed by residues 170 - 184 (chain T) in PDB entry 1YV0
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 LYS 170 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166T LYS* 4.1 42.9 + - + +
169T GLN* 1.3 79.6 - - + +
171T ARG* 1.3 61.2 + - + +
173T LYS* 4.3 5.4 - - - -
174T LYS* 3.7 34.9 - - + +
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Residues in contact with ARG 171 (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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166T LYS 5.0 1.6 - - - +
167T ALA* 3.2 52.3 + - - +
168T ASP 4.3 0.4 - - - +
169T GLN 3.1 1.4 - - - +
170T LYS* 1.3 81.0 - - + +
172T GLY* 1.3 56.9 + - - +
173T LYS 3.2 6.7 + - - -
174T LYS* 5.1 0.2 - - - +
175T GLN* 3.5 24.8 + - - +
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Residues in contact with GLY 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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168T ASP* 3.5 20.5 + - - +
169T GLN 3.4 5.4 + - - -
171T ARG* 1.3 78.2 - - - +
173T LYS* 1.3 57.5 + - - +
175T GLN* 5.1 2.0 - - - -
176T THR* 2.4 27.3 + - - -
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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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168T ASP 5.5 0.2 - - - +
169T GLN* 3.2 38.6 + - + +
170T LYS* 4.8 3.8 - - - -
171T ARG 3.2 0.8 - - - -
172T GLY* 1.3 80.6 - - - +
174T LYS* 1.3 63.4 + - + +
175T GLN 3.3 1.3 - - - -
176T THR* 3.3 9.5 + - + +
177T ALA* 2.9 24.4 + - - +
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Residues in contact with LYS 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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87I LYS* 5.4 7.9 - - - +
170T LYS* 3.7 31.4 + - + +
171T ARG 5.1 0.4 - - - +
173T LYS* 1.3 76.5 - - + +
175T GLN* 1.3 61.5 + - - +
177T ALA* 2.9 23.6 + - + +
178T ARG* 2.9 13.0 + - - +
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Residues in contact with GLN 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 ARG 3.5 19.8 + - - +
172T GLY* 5.1 1.6 - - - -
173T LYS 3.3 0.2 - - - -
174T LYS* 1.3 74.4 - - - +
176T THR* 1.3 62.8 + - - +
177T ALA 2.9 5.2 - - - -
178T ARG* 3.1 41.7 + - - +
179T GLU* 3.5 22.5 - - + +
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Residues in contact with THR 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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172T GLY* 2.4 27.7 + - - +
173T LYS* 3.3 14.5 + - + +
174T LYS 3.1 0.2 - - - -
175T GLN* 1.3 78.6 - - - +
177T ALA* 1.3 57.6 + - - +
179T GLU* 4.7 5.1 - - - +
180T THR* 3.4 21.3 + - - +
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Residues in contact with ALA 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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79I TYR* 4.5 4.3 + - - +
173T LYS 2.9 11.6 + - - +
174T LYS* 2.9 20.3 + - + +
176T THR* 1.3 80.1 - - - +
178T ARG* 1.3 52.0 + - - +
180T THR* 3.4 9.7 - - + +
181T LYS* 2.7 38.0 + - + +
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Residues in contact with ARG 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 LYS 2.9 11.0 + - - +
175T GLN* 3.1 37.1 + - + +
177T ALA* 1.3 74.1 - - - +
179T GLU* 1.3 58.3 + - + +
181T LYS* 2.7 15.9 + - + +
182T LYS* 2.5 71.6 + - - +
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Residues in contact with GLU 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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175T GLN* 3.5 26.1 - - + +
176T THR* 5.0 4.9 - - - +
178T ARG* 1.3 72.5 - - + +
180T THR* 1.3 54.1 + - - +
181T LYS 2.7 8.8 + - - -
182T LYS* 4.3 6.3 - - - +
183T LYS* 2.7 38.9 + - + +
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Residues in contact with THR 180 (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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79I TYR* 4.2 12.9 + - - +
176T THR* 3.4 21.1 + - - +
177T ALA* 3.4 9.8 + - + +
178T ARG 3.2 0.6 - - - -
179T GLU* 1.3 77.4 - - - +
181T LYS* 1.3 59.7 + - - +
183T LYS* 4.3 14.2 + - - +
184T VAL* 3.9 19.5 - - + +
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Residues in contact with LYS 181 (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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76I GLU* 5.6 6.9 - - - +
79I TYR* 3.2 46.7 - - + -
80I ASP* 3.5 21.5 + - - -
177T ALA* 2.7 15.7 + - + +
178T ARG* 2.7 22.3 + - + +
180T THR* 1.3 79.0 - - - +
182T LYS* 1.3 63.9 + - + +
183T LYS 3.0 2.3 + - - -
184T VAL* 3.5 9.0 + - - +
185T LEU* 3.1 23.7 - - + +
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Residues in contact with LYS 182 (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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178T ARG* 2.5 60.0 + - - +
179T GLU* 4.0 5.4 - - - +
181T LYS* 1.3 75.1 - - + +
183T LYS* 1.3 57.7 + - - +
185T LEU* 3.0 30.6 + - + +
186T ALA* 3.6 7.4 + - - +
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Residues in contact with LYS 183 (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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179T GLU* 2.7 24.0 + - + +
180T THR* 4.5 12.1 + - - +
181T LYS 3.0 1.0 + - - -
182T LYS* 1.3 68.3 - - - +
184T VAL* 1.3 65.0 + - + +
185T LEU 2.3 18.1 + - - -
186T ALA* 3.1 15.3 + - - +
187T GLU* 3.7 14.2 + - - +
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Residues in contact with VAL 184 (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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78I ARG* 6.2 2.5 - - - +
79I TYR* 5.8 8.5 - - + -
180T THR* 3.9 17.2 + - + +
181T LYS 3.5 4.8 + - - +
183T LYS* 1.3 86.5 - - + +
185T LEU* 1.3 63.5 + - - +
187T GLU* 2.8 28.5 - - - +
188T ARG* 5.2 6.6 + - - +
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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