Contacts of the helix formed by residues 79 - 85 (chain Y) in PDB entry 1YQV
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 PRO 79 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65Y ASN* 3.4 15.5 - - + +
78Y ILE* 1.3 99.2 - - + +
80Y CYS* 1.3 67.5 + - - +
81Y SER* 4.0 13.2 - - - +
82Y ALA* 2.9 30.5 + - + +
83Y LEU* 4.0 2.6 + - - +
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Residues in contact with CYS 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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53Y TYR* 3.6 29.9 - - + -
60Y SER* 3.7 8.3 - - - -
64Y CYS* 2.0 64.4 - - - -
65Y ASN 3.0 17.0 + - - -
66Y ASP* 3.6 14.4 - - + -
78Y ILE 3.5 1.0 + - - -
79Y PRO* 1.3 72.3 - - - +
81Y SER* 1.3 57.1 + - - +
83Y LEU* 2.8 30.0 + - - +
84Y LEU* 4.1 5.0 - - - +
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Residues in contact with SER 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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30H SER 4.8 12.1 - - - -
31H ASP* 4.7 13.0 + - - -
52H LEU* 4.4 17.5 - - - -
54H SER* 5.4 2.7 - - - -
53Y TYR* 4.8 1.0 - - - -
79Y PRO* 4.0 13.7 - - - +
80Y CYS* 1.3 77.7 - - - +
82Y ALA* 1.3 61.6 + - - +
83Y LEU 3.1 1.4 + - - -
84Y LEU* 3.4 29.2 + - - +
85Y SER 4.7 0.2 + - - -
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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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78Y ILE* 3.9 17.7 - - + -
79Y PRO* 2.9 30.9 + - + +
81Y SER* 1.3 79.8 + - - +
83Y LEU* 1.3 58.8 + - - +
84Y LEU 3.2 4.0 + - - -
85Y SER* 4.2 13.6 + - - -
90Y ALA* 3.4 18.0 - - + +
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Residues in contact with LEU 83 (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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40Y THR* 4.0 1.2 - - - +
53Y TYR* 4.5 10.5 - - + +
54Y GLY* 3.5 16.5 - - - -
55Y ILE* 4.6 0.5 + - - +
58Y ILE* 3.6 39.0 - - + -
64Y CYS* 3.8 25.4 - - + -
78Y ILE* 4.5 14.4 - - + -
79Y PRO 4.2 5.2 - - - +
80Y CYS 2.8 11.5 + - - +
82Y ALA* 1.3 79.1 - - - +
84Y LEU* 1.3 59.4 + - - +
85Y SER 3.6 2.7 + - - +
90Y ALA* 3.5 41.1 - - + +
91Y SER* 3.4 23.6 + - - +
94Y CYS* 4.6 1.1 - - + -
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Residues in contact with LEU 84 (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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52H LEU* 3.6 20.2 - - + -
54H SER* 3.6 35.3 - - - +
56H SER* 3.6 19.1 - - - +
40Y THR* 3.5 23.4 + - - +
41Y GLN* 4.2 11.2 - - + +
42Y ALA 4.0 6.3 - - - +
43Y THR* 4.1 5.2 - - + -
53Y TYR* 4.1 13.5 - - + -
54Y GLY 3.4 28.3 - - - +
80Y CYS 4.1 5.2 - - - +
81Y SER* 3.4 16.1 + - - +
82Y ALA 3.2 1.8 - - - -
83Y LEU* 1.3 79.9 - - - +
85Y SER* 1.3 65.3 + - - +
86Y SER 4.0 0.2 + - - -
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Residues in contact with SER 85 (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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40Y THR* 3.4 15.0 - - - +
81Y SER 4.7 0.6 + - - -
82Y ALA 4.2 11.4 + - - -
83Y LEU 3.6 2.7 - - - +
84Y LEU* 1.3 82.2 - - - +
86Y SER* 1.3 65.9 + - - +
87Y ASP* 2.9 36.8 + - - +
88Y ILE* 5.0 0.7 - - - -
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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