Contacts of the helix formed by residues 64 - 70 (chain N) in PDB entry 1YI2
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 SER 64 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269 C 5.6 2.5 - - - -
1219 C 5.8 3.6 - - - -
42N HIS* 3.6 22.7 - - - -
62N HIS* 2.9 26.0 + - - +
63N SER* 1.3 75.4 + - - +
65N ASP* 1.3 62.0 + - - +
66N LEU 2.9 10.0 + - - -
67N ALA* 3.6 16.3 + - - +
68N GLU 4.7 0.2 + - - -
75N THR* 4.8 2.0 - - - +
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Residues in contact with ASP 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209 A 6.0 0.7 - - - -
1219 C 5.4 11.2 - - - +
62N HIS* 2.4 44.0 + - - +
64N SER* 1.3 77.2 + - - +
66N LEU* 1.3 61.5 + - - +
67N ALA 3.5 0.7 - - - -
68N GLU* 3.5 33.0 - - - +
69N TYR* 3.5 11.4 - - - -
87N LEU* 3.7 5.4 - - - +
91N ARG* 3.0 37.6 + - - -
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Residues in contact with LEU 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N HIS 3.7 2.2 + - - +
63N SER* 2.9 19.7 - - - +
64N SER 2.9 0.6 - - - -
65N ASP* 1.3 76.4 - - - +
67N ALA* 1.3 54.8 + - - +
68N GLU 3.0 1.8 - - - -
69N TYR* 2.8 36.9 + - + +
70N GLY 3.8 0.2 + - - -
71N TRP* 3.7 28.3 + - + +
80N SER* 4.0 26.0 - - - +
83N LEU* 3.9 37.5 - - + +
84N THR* 4.2 6.3 - - - +
87N LEU* 4.2 20.2 - - + -
175N LEU* 3.9 16.2 - - + +
179N LEU* 5.1 5.8 - - + -
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Residues in contact with ALA 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N SER 4.4 0.6 + - - -
64N SER 3.6 11.5 + - - +
66N LEU* 1.3 73.5 - - - +
68N GLU* 1.3 53.0 + - - +
69N TYR 2.6 17.8 + - - -
70N GLY* 2.6 15.6 + - - -
71N TRP* 3.2 32.9 + - + +
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Residues in contact with GLU 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219 C 5.6 1.0 + - - -
64N SER 4.7 0.8 + - - -
65N ASP* 3.5 35.8 + - - +
66N LEU 3.0 0.2 - - - -
67N ALA* 1.3 76.2 - - - +
69N TYR* 1.3 78.5 + - + +
91N ARG* 4.9 3.6 + - - -
185N GLU 5.6 0.7 - - - +
186N LEU 5.8 0.2 - - - +
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Residues in contact with TYR 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N ASP 3.5 21.5 - - - -
66N LEU* 2.8 11.1 + - + +
67N ALA 2.6 6.1 + - - -
68N GLU* 1.3 95.9 + - + +
70N GLY* 1.3 55.8 + - - +
71N TRP 3.7 0.9 - - - -
87N LEU* 4.3 12.0 - - + +
91N ARG* 3.5 16.0 + - - -
175N LEU* 3.6 24.0 - - + +
178N THR* 4.4 16.5 + - + +
179N LEU* 4.2 6.5 - - + -
184N ILE* 3.2 44.0 - - + -
185N GLU* 2.6 26.2 + - + -
186N LEU* 3.2 17.5 + - - -
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Residues in contact with GLY 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67N ALA 2.6 15.5 + - - -
69N TYR* 1.3 74.1 - - - +
71N TRP* 1.3 63.0 + - - +
72N GLU* 3.3 4.5 + - - +
171N HIS* 2.9 20.7 + - - -
175N LEU* 4.8 4.0 - - - -
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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