Contacts of the helix formed by residues 171 - 179 (chain A) in PDB entry 1YTB
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 ARG 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ILE* 1.3 70.9 - - - +
172A LEU* 1.3 64.6 + - - +
173A GLU* 3.3 2.5 - - + -
174A GLY* 3.2 9.2 + - - +
175A LEU* 3.1 21.1 + - - +
236A GLU 3.1 22.6 + - - -
237A PHE* 2.7 46.3 + - + +
238A ARG* 2.8 39.0 + - - +
239A LYS* 3.5 24.9 - - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ILE* 3.3 13.3 + - + +
171A ARG* 1.3 72.3 - - - +
173A GLU* 1.3 57.5 + - - +
175A LEU* 3.4 2.8 + - + -
176A ALA* 2.9 26.9 + - - +
185A TYR* 3.6 28.5 - - + +
191A PRO 3.6 24.0 - - - +
193A LEU* 3.3 24.4 - - + +
206A ILE* 3.6 44.2 - - + +
207A PHE 4.3 3.6 - - - -
208A VAL* 3.7 31.1 - - + +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG 3.3 0.4 - - - -
172A LEU* 1.3 76.2 - - - +
174A GLY* 1.3 64.5 + - - +
176A ALA* 3.5 5.6 + - - +
177A PHE* 3.1 26.5 + - - +
185A TYR* 3.7 26.7 - - + +
187A PRO* 5.8 0.3 - - - +
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG* 3.2 13.9 + - - +
173A GLU* 1.3 75.2 - - - +
175A LEU* 1.3 60.0 + - - +
177A PHE* 3.2 9.6 + - - +
178A SER* 2.9 30.8 + - - -
237A PHE* 3.5 17.6 - - - -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ILE* 4.1 22.4 - - + -
171A ARG 3.1 14.6 + - - +
172A LEU* 3.7 4.9 - - + +
174A GLY* 1.3 74.8 - - - +
176A ALA* 1.3 53.4 + - - +
178A SER 3.2 0.3 + - - -
179A HIS* 2.7 51.2 + - + +
183A SER* 4.4 0.9 - - - +
193A LEU* 4.0 15.0 - - + -
195A TYR* 4.1 12.8 - - + -
206A ILE* 4.5 12.8 - - + -
233A VAL* 3.8 28.7 - - + +
234A LEU* 4.2 18.6 - - + -
237A PHE* 3.7 21.1 - - + -
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU 2.9 18.5 + - - +
173A GLU* 3.8 11.9 - - - +
175A LEU* 1.3 76.2 - - - +
177A PHE* 1.3 56.7 + - - +
180A GLY* 3.0 29.5 - - - -
183A SER* 3.9 16.4 - - - -
185A TYR* 4.0 19.5 - - + +
193A LEU* 3.8 11.2 - - + +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 3.1 24.6 + - - +
174A GLY* 3.2 8.0 + - - +
176A ALA* 1.3 78.2 - - - +
178A SER* 1.3 65.4 + - - +
180A GLY* 3.7 5.7 + - - -
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLY 2.9 16.2 + - - -
175A LEU 3.7 1.1 - - - -
177A PHE* 1.3 83.9 - - - +
179A HIS* 1.3 76.0 + - - +
180A GLY 3.3 1.6 + - - -
236A GLU* 4.8 3.3 + - - -
237A PHE* 3.5 23.6 - - - -
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 2.7 27.3 + - + +
176A ALA 3.7 3.4 - - - -
178A SER* 1.3 103.3 + - - +
180A GLY* 1.3 63.8 - - - +
181A THR* 3.3 3.1 - - - -
182A PHE* 3.1 16.3 + + + -
183A SER* 3.0 22.1 + - - +
195A TYR* 2.9 39.2 + - + -
233A VAL* 3.6 32.1 - - + +
236A GLU* 4.6 6.7 + - - -
237A PHE* 4.6 1.3 - + - -
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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