Contacts of the helix formed by residues 80 - 85 (chain C) in PDB entry 1C2O
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 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C TYR* 3.2 25.9 + - + +
78C PRO 3.2 1.8 + - - +
79C GLY* 1.3 75.6 - - - +
81C GLU* 1.3 61.5 + - - +
82C GLY* 3.1 24.2 - - - -
83C THR* 3.0 26.7 + - + -
84C GLU* 2.8 28.8 + - - +
348C LYS* 2.9 39.9 - - + -
438C THR* 3.2 39.7 - - + -
439C TRP* 3.7 29.6 - + - -
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Residues in contact with GLU 81 (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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79C GLY 3.6 4.9 + - - -
80C PHE* 1.3 74.1 - - - +
82C GLY* 1.3 63.5 + - - +
84C GLU* 4.4 5.6 - - - -
85C MET* 2.9 46.7 + - + +
436C THR* 4.5 7.5 - - - +
437C LEU* 5.6 0.3 - - - -
438C THR* 3.2 35.8 + - + +
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Residues in contact with GLY 82 (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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80C PHE* 3.1 27.6 + - - -
81C GLU* 1.3 79.3 - - - +
83C THR* 1.3 56.3 + - - +
85C MET* 3.5 4.1 - - - +
86C TRP* 3.0 23.2 + - - -
438C THR* 3.5 10.3 + - - -
439C TRP* 3.5 15.8 - - - -
449C TYR* 3.0 11.9 + - - -
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Residues in contact with THR 83 (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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74C ASP* 3.9 17.6 - - - +
75C THR 5.0 0.9 - - - -
76C LEU* 4.8 0.7 - - + -
77C TYR* 3.1 30.8 + - + -
80C PHE* 3.0 20.3 + - + -
82C GLY* 1.3 73.8 - - - +
84C GLU* 1.3 69.9 + - - +
85C MET 3.2 2.0 - - - -
86C TRP* 2.9 25.1 + - - +
87C ASN* 3.7 7.3 + - - -
337C TYR* 4.9 1.3 - - - +
341C TYR* 3.2 27.8 - - + +
439C TRP* 3.7 22.2 - - + -
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP 4.7 4.6 - - - +
75C THR 5.8 0.2 - - - -
77C TYR 3.8 2.0 - - - +
78C PRO* 3.5 9.5 - - - +
79C GLY* 2.7 28.6 + - - +
80C PHE 2.8 31.0 + - - +
81C GLU* 4.3 3.1 - - - +
83C THR* 1.3 79.7 + - - +
85C MET* 1.3 52.2 + - - +
86C TRP 2.6 13.9 + - - -
87C ASN* 2.6 51.0 + - - +
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Residues in contact with MET 85 (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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81C GLU* 2.9 42.2 + - + +
82C GLY* 3.5 12.1 - - - +
84C GLU* 1.3 73.8 - - - +
86C TRP* 1.3 93.1 + - + +
87C ASN 3.5 1.3 - - - -
130C LEU* 3.8 20.1 - - - +
131C ASP* 5.5 1.9 + - - +
132C VAL* 3.7 31.8 + - + +
449C TYR* 3.5 31.6 - - + -
452C GLU* 4.6 9.0 - - + +
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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