Contacts of the helix formed by residues 74 - 82 (chain Y) in PDB entry 2IY4
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 74 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25V VAL* 3.8 3.1 - - - -
29V GLN* 3.9 1.6 - - - +
86V GLU* 3.5 24.0 - - + -
87V ALA* 3.4 42.4 - - - +
88V PRO* 3.7 5.9 - - + +
73Y SER* 1.3 86.1 - - - +
75Y LEU* 1.3 63.7 + - - +
76Y LYS* 4.1 3.7 - - - +
77Y GLU* 2.8 36.8 + - - +
78Y PHE* 3.0 30.5 + - - -
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Residues in contact with LEU 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V ASN* 3.7 21.5 - - + +
22V VAL* 3.8 11.9 - - + -
25V VAL* 3.8 21.3 - - + -
75V LEU* 3.8 32.0 - - + +
78V PHE* 3.7 35.7 - - + -
79V LEU* 3.8 19.1 - - + -
86V GLU* 2.9 22.4 + - - +
74Y THR* 1.3 70.2 - - - +
76Y LYS* 1.3 64.1 + - - +
78Y PHE* 3.1 10.4 + - + +
79Y LEU* 2.9 27.5 + - - +
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Residues in contact with LYS 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V LEU* 3.5 17.1 - - + +
86V GLU* 3.1 18.4 + - - +
88V PRO* 5.8 10.7 - - + +
74Y THR* 4.2 4.7 - - - +
75Y LEU* 1.3 76.5 - - - +
77Y GLU* 1.3 62.0 + - + +
79Y LEU* 3.5 3.9 + - - +
80Y GLU* 3.1 48.7 + - + +
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Residues in contact with GLU 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88V PRO* 3.9 25.6 - - + +
89V TYR 4.8 1.4 + - - -
72Y PHE* 3.6 38.6 - - + -
73Y SER* 3.1 18.5 + - - -
74Y THR* 2.8 32.8 + - - +
76Y LYS* 1.3 77.1 - - + +
78Y PHE* 1.3 65.8 + - - +
80Y GLU* 3.4 16.2 + - - +
81Y ASN* 2.9 30.8 + - - +
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Residues in contact with PHE 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V VAL* 3.5 30.3 - - + -
32V TRP* 4.9 4.9 - + - -
75V LEU* 3.7 15.7 - - + -
17Y VAL* 4.0 5.8 - - + -
18Y ALA* 3.8 26.4 - - - +
21Y ASN* 3.4 43.5 - - + -
22Y VAL* 4.7 1.6 - - + -
72Y PHE* 3.4 40.8 - - + -
73Y SER* 3.9 1.6 - - - -
74Y THR 3.0 19.6 + - - -
75Y LEU* 3.1 13.6 + - + +
77Y GLU* 1.3 75.7 - - - +
79Y LEU* 1.3 58.4 + - - +
81Y ASN 3.2 0.9 + - - -
82Y ALA* 2.8 37.2 + - - +
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Residues in contact with LEU 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75V LEU* 3.9 14.4 - - + -
76V LYS* 3.8 32.3 - - + +
79V LEU* 4.1 19.5 - - + -
22Y VAL* 5.2 4.9 - - + -
75Y LEU 2.9 13.6 + - - +
76Y LYS* 3.8 4.5 - - - +
78Y PHE* 1.3 75.9 - - - +
80Y GLU* 1.3 62.8 + - - +
81Y ASN 3.3 0.3 + - - -
82Y ALA* 4.0 10.9 + - + +
86Y GLU* 3.3 33.0 - - + +
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Residues in contact with GLU 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Y LYS* 3.1 52.0 + - + +
77Y GLU* 3.5 23.9 - - - +
79Y LEU* 1.3 77.0 - - - +
81Y ASN* 1.3 67.3 + - - +
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Residues in contact with ASN 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y HIS* 2.8 31.0 + - + -
18Y ALA* 3.9 7.9 - - + -
72Y PHE* 3.3 45.2 - - + -
77Y GLU* 2.9 25.3 + - - +
80Y GLU* 1.3 88.4 + - - +
82Y ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y ALA* 3.8 10.0 - - - +
19Y ASN* 3.4 13.2 - - - +
22Y VAL* 3.5 26.9 - - + -
78Y PHE 2.8 21.7 + - - +
79Y LEU* 4.0 8.5 + - - +
80Y GLU 3.8 0.8 - - - +
81Y ASN* 1.3 74.8 - - - +
83Y SER* 1.3 59.9 + - - +
84Y VAL 3.8 10.4 - - - +
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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