Contacts of the helix formed by residues 83 - 93 (chain R) in PDB entry 6Y5D
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 83 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q GLN* 3.2 28.9 - - + +
89Q ALA* 3.7 3.8 - - - -
79R ARG* 3.8 21.2 + - - +
81R THR* 3.9 7.2 - - + +
82R VAL* 1.3 77.4 - - - +
84R ALA* 1.3 65.6 + - - +
85R MET* 3.5 14.0 + - - +
86R ASP* 2.7 39.3 + - - +
87R VAL* 3.3 11.8 + - - +
84T TYR* 4.2 2.4 + - - -
105U G 6.5 0.7 - - - -
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Residues in contact with ALA 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q GLN* 3.0 10.4 + - - +
88Q SER* 3.4 33.0 - - - +
89Q ALA* 3.8 13.2 - - - +
92Q ALA* 4.8 1.2 - - + +
83R THR* 1.3 71.8 - - - +
85R MET* 1.3 59.4 + - + +
87R VAL* 3.1 5.3 + - - +
88R VAL* 2.9 31.4 + - - +
101R PHE* 4.3 22.0 - - + +
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Residues in contact with MET 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R THR* 3.1 11.1 + - - +
84R ALA* 1.3 80.0 - - + +
86R ASP* 1.3 56.9 + - - +
88R VAL* 3.3 15.7 + - + +
89R TYR* 2.8 63.5 + - + +
101R PHE 4.0 19.3 - - - +
84T TYR* 4.2 13.2 - - + +
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Residues in contact with ASP 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ALA* 3.6 25.3 - - - +
73R TYR* 3.8 11.1 - - + +
74R THR* 3.3 11.8 + - - +
79R ARG* 3.0 20.5 + - - -
82R VAL* 4.1 4.9 - - + -
83R THR* 2.7 37.6 + - - +
85R MET* 1.3 73.8 - - - +
87R VAL* 1.3 60.6 + - - +
89R TYR* 3.5 7.4 + - - +
90R ALA* 3.0 27.0 + - - +
84T TYR* 2.6 29.0 + - - -
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Residues in contact with VAL 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q ALA* 3.7 24.5 - - + +
92Q ALA* 3.8 19.5 - - + -
93Q LEU* 3.6 36.6 - - + +
66R VAL* 4.3 0.4 - - + -
70R ALA* 3.9 17.5 - - + -
82R VAL* 4.1 4.9 - - + -
83R THR 3.8 10.5 - - - +
84R ALA 3.1 7.6 + - - +
86R ASP* 1.3 76.2 - - - +
88R VAL* 1.3 59.4 + - - +
90R ALA* 3.2 2.7 + - - +
91R LEU* 2.8 41.4 + - + +
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Residues in contact with VAL 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q ALA* 5.2 0.4 - - + -
84R ALA 2.9 19.2 + - - +
85R MET* 3.3 24.0 + - + +
87R VAL* 1.3 78.1 - - + +
89R TYR* 1.3 60.4 + - + +
91R LEU* 3.3 7.7 + - - +
92R LYS* 2.8 33.0 + - + +
98R LEU* 4.3 32.5 + - + +
101R PHE* 3.5 32.1 - - + +
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Residues in contact with TYR 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R TYR* 3.5 29.9 + + + -
85R MET* 2.8 51.4 + - + +
86R ASP* 3.8 4.3 - - - +
87R VAL 3.3 0.2 - - - -
88R VAL* 1.3 77.1 - - + +
90R ALA* 1.3 64.0 + - - +
92R LYS* 3.2 31.1 + - + +
93R ARG* 3.3 19.1 + - - +
80T ARG* 4.7 23.3 - - + -
83T HIS* 6.1 0.9 - - - -
84T TYR* 3.4 55.3 - + + +
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Residues in contact with ALA 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R VAL* 3.1 33.9 - - + +
69R ASP* 3.5 20.9 - - + -
70R ALA* 3.6 3.1 - - - +
73R TYR* 3.8 2.6 - - - -
86R ASP 3.0 14.8 + - - +
87R VAL* 3.3 10.1 - - - +
89R TYR* 1.3 77.5 - - - +
91R LEU* 1.3 61.4 + - - +
93R ARG* 3.3 16.8 - - - +
94R GLN* 3.4 17.2 + - - +
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Residues in contact with LEU 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Q ALA 4.1 1.1 - - - +
93Q LEU* 5.3 0.9 - - + -
96Q ALA* 3.5 35.4 - - + -
62R PHE* 4.0 8.1 - - + -
66R VAL* 3.6 32.5 - - + -
87R VAL* 2.8 31.3 + - + +
88R VAL* 3.7 3.8 - - - +
90R ALA* 1.3 74.1 - - - +
92R LYS* 1.3 68.1 + - - +
94R GLN* 2.9 17.0 + - - +
96R ARG* 3.1 35.3 - - + +
98R LEU* 3.6 29.4 - - + -
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Residues in contact with LYS 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P ASP* 4.7 13.3 + - - +
72P GLU* 2.8 35.3 + - - -
73P ARG* 6.0 0.4 - - - +
88R VAL* 2.8 22.4 + - + +
89R TYR* 3.4 26.3 - - + +
91R LEU* 1.3 75.9 - - - +
93R ARG* 1.3 60.8 + - + +
95R GLY* 3.0 19.6 + - - -
96R ARG 3.2 17.3 + - - -
97R THR* 4.0 18.2 + - + +
80T ARG* 5.0 14.7 - - - +
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Residues in contact with ARG 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R ASP* 3.1 31.3 + - - +
73R TYR* 3.3 30.5 + - - +
89R TYR 3.4 8.1 - - - +
90R ALA 3.3 13.7 - - - +
92R LYS* 1.3 81.2 - - + +
94R GLN* 1.3 60.5 + - + +
95R GLY 3.2 2.5 + - - -
77T GLU* 3.3 23.7 + - - +
101T LEU* 2.6 45.8 + - - +
102T LEU* 3.8 11.9 - - - +
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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