Contacts of the helix formed by residues 4 - 11 (chain F) in PDB entry 1Y3A
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 THR 4 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ARG* 5.3 3.4 - - - +
203B GLY* 3.8 25.6 - - - +
204B GLN 3.5 9.9 - - - +
205B ARG* 4.1 15.3 - - + +
211B TRP* 3.5 1.3 + - - -
3F VAL* 1.3 93.7 - - - +
5F TRP* 1.3 66.8 + - - +
6F TYR* 3.8 9.6 + - - +
7F ASP* 2.7 37.1 + - - +
8F PHE* 3.1 4.2 + - - +
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Residues in contact with TRP 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.9 26.8 - - + +
40B GLY* 4.9 4.3 + - - +
201B VAL* 3.7 17.7 + - + -
202B GLY 3.3 26.7 + - - -
203B GLY* 5.3 2.6 - - - -
204B GLN 4.3 0.2 + - - -
211B TRP* 3.3 39.3 - + + +
215B PHE* 3.7 16.6 - + + -
223B PHE* 4.8 4.0 - + - -
249B LEU* 4.0 34.3 - - + -
252B SER* 3.6 15.7 - - - -
253B ILE* 3.4 34.8 - - + -
4F THR* 1.3 74.7 - - - +
6F TYR* 1.3 89.1 + - + +
8F PHE* 3.3 4.8 + - - +
9F LEU* 3.0 33.5 + - + +
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Residues in contact with TYR 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LYS* 3.3 54.2 + - + +
249B LEU* 3.9 25.8 - - + -
252B SER* 3.5 25.1 - - - -
4F THR* 3.1 9.1 + - - +
5F TRP* 1.3 98.0 - + + +
7F ASP* 1.3 77.4 + - - +
9F LEU* 3.2 3.3 + - - +
10F MET* 3.1 65.1 + - + +
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Residues in contact with ASP 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ARG* 5.7 0.2 - - - -
3F VAL* 3.4 23.3 - - + +
4F THR* 2.7 24.2 + - - +
6F TYR* 1.3 93.4 - - - +
8F PHE* 1.3 58.0 + - - +
10F MET* 3.9 4.7 - - - +
11F GLU* 2.8 33.4 + - - +
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Residues in contact with PHE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ARG* 4.1 37.0 - - + -
211B TRP* 3.6 31.2 - - + -
212B ILE* 3.3 35.2 - - + -
215B PHE* 4.1 23.1 - + + -
3F VAL* 3.5 6.0 - - + +
4F THR 3.1 14.0 + - - +
5F TRP 3.4 7.2 - - - +
6F TYR 3.2 0.4 - - - -
7F ASP* 1.3 80.3 - - - +
9F LEU* 1.3 68.3 + - + +
11F GLU* 3.6 25.8 + - - +
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Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 4.1 23.3 - - + -
252B SER* 3.7 20.6 - - - +
253B ILE* 3.5 31.9 - - + -
256B ASN* 3.3 35.9 + - - +
259B PHE* 4.1 14.6 - - + -
5F TRP* 3.0 32.5 + - + +
6F TYR 3.2 4.5 + - - +
8F PHE* 1.3 82.9 - - + +
10F MET* 1.3 63.8 + - - +
11F GLU 3.8 4.9 - - - +
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Residues in contact with MET 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ASP* 6.6 0.7 - - + -
252B SER* 3.4 29.8 - - - -
6F TYR* 3.1 52.1 + - + +
7F ASP* 3.9 5.8 - - - +
9F LEU* 1.3 74.5 - - - +
11F GLU* 1.3 69.3 + - - +
12F ASP* 3.5 15.2 + - - +
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ARG* 2.9 44.1 + - - -
7F ASP 2.8 16.9 + - - +
8F PHE* 3.6 20.3 - - - +
9F LEU 3.4 7.0 - - - +
10F MET* 1.3 79.7 - - - +
12F ASP* 1.3 71.5 + - - +
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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