Contacts of the helix formed by residues 179 - 184 (chain B) in PDB entry 1Y67
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 TYR 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ASP* 6.0 0.7 - - - -
23B THR* 5.4 1.8 - - - -
174B VAL* 3.6 13.9 - - - -
175B TRP 3.5 25.8 - - - -
176B GLU* 3.1 30.4 + - + +
178B ALA* 1.3 79.0 - - - +
180B TYR* 1.3 63.8 + + - +
181B LEU 3.4 2.6 + - - -
182B ASN* 3.4 3.5 + - - -
183B TYR* 2.8 38.5 + - + +
184B GLN 3.2 28.0 - - - -
185B ASN* 4.6 3.4 + - - -
187B ARG* 3.1 55.8 + - + +
190B TYR* 3.4 46.4 - + + -
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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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23A THR* 6.3 0.7 - - + -
26A ILE* 3.4 14.3 - - + +
27A HIS* 5.2 0.5 + - - -
31A HIS* 2.6 32.6 + + - -
177A HIS* 3.4 38.6 + - + +
180A TYR* 4.2 26.5 - - + -
181A LEU* 3.9 34.3 - - + +
176B GLU* 2.8 36.7 + - + +
177B HIS 4.4 2.0 + - - -
179B TYR* 1.3 74.6 - + - +
181B LEU* 1.3 61.5 + - - +
184B GLN* 2.9 62.9 + - + +
185B ASN* 4.1 0.4 - - - -
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Residues in contact with LEU 181 (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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22A ARG* 5.3 1.9 + - - -
180A TYR* 3.8 41.6 - - + +
181A LEU* 4.2 21.3 - - + +
184A GLN* 4.4 8.1 - - + +
20B ASP* 3.8 8.3 - - - +
22B ARG* 3.7 37.7 - - + +
23B THR* 3.4 26.1 + - - +
26B ILE* 4.2 14.8 - - + -
177B HIS 5.4 0.2 + - - -
179B TYR 3.4 0.6 - - - -
180B TYR* 1.3 77.3 - - - +
182B ASN* 1.3 57.2 + - - +
184B GLN* 3.1 13.5 + - - -
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Residues in contact with ASN 182 (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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16B GLU* 5.8 0.2 + - - -
17B PRO 3.3 25.1 + - - -
18B HIS 3.7 3.2 + - - -
20B ASP* 3.2 32.4 + - - +
179B TYR* 3.4 2.1 + - - +
180B TYR 3.3 0.4 - - - -
181B LEU* 1.3 78.5 - - - +
183B TYR* 1.3 93.1 + - + +
184B GLN* 3.7 5.8 + - - -
186B ARG* 3.4 13.0 + - - -
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Residues in contact with TYR 183 (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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17B PRO 4.0 1.4 + - - -
18B HIS* 2.7 32.9 + - - -
19B ILE* 5.3 0.7 - - - -
179B TYR* 2.8 23.4 + - + +
182B ASN* 1.3 99.7 + - + +
184B GLN* 1.3 77.0 + - - +
185B ASN 3.2 0.9 + - - -
186B ARG* 2.9 49.5 + - + +
189B ASP* 3.7 19.7 - - + -
190B TYR* 3.6 46.2 - + + -
193B ALA* 3.3 17.8 - - + +
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Residues in contact with GLN 184 (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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22A ARG* 3.4 29.3 + - - +
26A ILE* 3.8 23.4 - - + +
181A LEU* 4.3 11.3 - - + +
179B TYR* 3.2 23.8 + - - -
180B TYR* 2.9 47.8 + - + +
181B LEU 3.1 27.1 + - - -
182B ASN 3.7 6.5 + - - +
183B TYR* 1.3 75.6 - - - +
185B ASN* 1.3 71.7 + - - +
186B ARG* 3.1 27.2 + - - +
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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