Contacts of the helix formed by residues 93 - 99 (chain C) in PDB entry 1ADO
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 PHE 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ARG* 3.6 26.2 - - + -
59C ARG* 4.4 3.6 - - + -
60C GLN* 3.8 22.7 - - + -
63C LEU* 3.7 22.4 - - + -
64C THR* 5.2 0.7 - - + -
78C LEU* 4.7 3.1 - - + -
82C THR* 3.5 36.1 - - + +
85C GLN* 3.0 39.8 + - + -
86C LYS 3.9 10.8 - - - -
87C ALA* 3.6 31.0 - - + -
91C ARG 3.5 1.6 + - - -
92C PRO* 1.3 70.1 - - - +
94C PRO* 1.3 69.7 - - + +
96C VAL* 2.9 20.5 + - + +
97C ILE* 3.0 16.8 + - - +
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Residues in contact with PRO 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 5.0 0.9 - - + -
83C LEU* 3.5 40.4 - - + +
92C PRO* 3.4 13.5 - - + -
93C PHE* 1.3 92.5 - - + +
95C GLN* 1.3 63.4 + - + +
97C ILE* 3.6 1.3 + - + -
98C LYS* 2.9 34.8 + - + +
104C VAL* 3.6 22.8 - - + +
140C ASP 4.1 20.4 - - - +
141C GLY* 4.8 4.9 - - - -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ARG* 4.5 12.1 - - + -
92C PRO* 2.8 42.6 + - + +
94C PRO* 1.3 76.8 - - + +
96C VAL* 1.3 64.1 + - - +
98C LYS* 3.3 23.3 + - - +
99C SER* 2.9 26.3 + - - -
140C ASP 5.8 0.2 + - - -
141C GLY* 5.6 4.6 - - - -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 3.5 30.5 - - + +
64C THR* 4.1 12.6 - - + -
87C ALA* 4.2 19.1 - - + -
89C ASP* 4.9 0.2 - - - +
91C ARG* 3.8 37.9 - - + +
92C PRO 3.8 11.0 - - - +
93C PHE* 2.9 15.6 + - + +
95C GLN* 1.3 75.5 - - - +
97C ILE* 1.3 64.1 + - + +
99C SER* 2.7 22.7 + - - -
100C LYS* 3.2 19.4 + - + +
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 4.1 28.3 - - + +
76C VAL* 3.8 29.6 - - + -
78C LEU* 3.9 15.7 - - + -
93C PHE 3.0 12.1 + - - +
94C PRO 3.7 6.5 - - - +
96C VAL* 1.3 75.7 - - + +
98C LYS* 1.3 62.3 + - - +
100C LYS* 3.1 14.8 + - - +
101C GLY 3.4 0.3 + - - -
102C GLY* 3.1 41.8 + - - +
103C VAL 3.8 8.1 - - - +
104C VAL* 3.8 32.3 - - + -
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 6.3 0.4 - - - +
94C PRO 2.9 25.3 + - - +
95C GLN* 3.3 25.0 + - - +
97C ILE* 1.3 75.5 - - - +
99C SER* 1.3 58.5 + - - +
101C GLY* 3.0 18.7 + - - -
102C GLY 3.5 12.3 - - - +
103C VAL* 6.2 1.1 - - - +
104C VAL* 3.8 16.4 - - + +
141C GLY* 4.5 18.5 + - - +
143C ASP* 4.7 10.9 + - - -
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Residues in contact with SER 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASN* 4.8 1.7 + - - -
91C ARG* 2.8 28.4 + - - -
95C GLN 2.9 12.4 + - - -
96C VAL* 2.7 18.9 + - - -
98C LYS* 1.3 76.2 - - - +
100C LYS* 1.3 62.1 + - - +
101C GLY 3.2 2.8 + - - -
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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