Contacts of the helix formed by residues 450 - 456 (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 GLU 450 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C GLU* 3.4 13.3 - - - +
228C GLN* 2.7 48.2 + - - +
229C SER* 4.1 5.0 + - - -
331C VAL* 3.7 16.3 - - + +
428C TYR* 3.9 7.2 + - + +
430C PHE* 3.6 38.6 - - + -
448C GLY* 3.5 18.9 + - - -
449C TYR* 1.3 78.0 + - - +
451C ILE* 1.4 70.3 + - - +
452C GLU 3.4 1.1 - - - -
453C PHE* 2.9 16.0 + - - +
454C ILE* 3.0 18.8 + - + +
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Residues in contact with ILE 451 (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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86C TRP* 4.2 13.5 - - + -
117C TRP* 3.8 12.6 - - + -
132C VAL* 4.1 8.5 - - + +
133C TYR* 3.9 20.4 - - + +
202C GLU* 3.5 43.7 - - + +
228C GLN* 5.0 2.2 - - - +
448C GLY* 2.8 23.8 - - - +
449C TYR 3.5 0.2 - - - -
450C GLU* 1.4 80.3 - - + +
452C GLU* 1.3 68.7 - - - +
453C PHE 3.0 0.3 + - - -
454C ILE* 3.1 4.3 + - + +
455C PHE* 2.9 56.4 + - + +
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Residues in contact with GLU 452 (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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85C MET* 4.6 7.2 - - + +
86C TRP* 6.5 0.4 - - + -
132C VAL* 4.5 23.8 - - + +
434C ALA* 4.0 12.5 - - - +
436C THR* 3.9 9.7 + - - -
437C LEU* 4.7 3.5 - - - +
448C GLY 5.1 1.3 - - - +
449C TYR* 3.6 40.4 - - + +
451C ILE* 1.3 74.8 - - + +
453C PHE* 1.3 66.4 + - + +
455C PHE* 3.6 1.0 + - - -
456C GLY 3.1 2.4 + - - -
457C LEU* 3.0 35.0 + - + +
458C PRO* 4.4 1.6 - - - -
465C TYR* 2.6 38.4 + - + +
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Residues in contact with PHE 453 (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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430C PHE* 3.4 24.2 - + + -
432C HIS* 3.8 14.1 - + - -
434C ALA* 3.4 36.8 - - + -
449C TYR 3.8 15.5 - - - -
450C GLU 2.9 8.1 + - - +
452C GLU* 1.3 79.0 - - + +
454C ILE* 1.3 68.0 + - - +
456C GLY* 2.7 16.3 + - - -
458C PRO* 3.7 26.9 - - + -
465C TYR* 4.0 6.1 - + - -
469C GLU* 3.6 31.9 - - + -
472C PHE* 4.2 11.2 - + - -
473C ALA* 4.1 12.2 - - + +
476C LEU* 3.5 24.0 - - + -
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Residues in contact with ILE 454 (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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117C TRP* 6.4 0.2 - - + -
138C LEU* 3.5 19.2 - - + +
200C PHE* 4.1 17.7 - - + -
228C GLN* 4.0 20.4 - - - +
430C PHE* 5.5 0.4 - - + -
450C GLU* 3.0 23.5 + - + +
451C ILE* 3.9 5.2 - - + +
453C PHE* 1.3 71.8 - - - +
455C PHE* 1.3 65.5 + - + +
456C GLY 3.2 0.3 + - - -
476C LEU* 3.8 19.5 - - + +
477C MET* 4.0 8.1 - - - +
480C TRP* 3.2 73.4 - - + +
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Residues in contact with PHE 455 (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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117C TRP* 3.5 45.3 - + - -
132C VAL 3.3 25.1 - - - +
133C TYR* 3.8 20.6 - - - -
134C ASP 3.7 17.5 - - - +
135C GLY 4.2 0.2 - - - -
137C PHE* 3.5 21.1 - - - +
138C LEU* 3.5 22.3 + - + +
146C LEU* 3.9 25.6 - - + -
200C PHE* 3.5 24.5 - + - -
451C ILE* 2.9 30.8 + - + +
454C ILE* 1.3 76.4 - - + +
456C GLY* 1.3 59.7 + - - +
457C LEU* 3.6 11.7 - - + -
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Residues in contact with GLY 456 (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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137C PHE* 3.7 11.3 - - - -
452C GLU 3.1 0.8 + - - -
453C PHE 2.7 22.2 + - - -
455C PHE* 1.3 73.3 - - - +
457C LEU* 1.3 64.9 + - - +
458C PRO* 3.1 5.6 - - - -
459C LEU* 3.0 40.5 + - - +
473C ALA* 4.5 0.7 - - - -
477C MET* 3.9 7.6 - - - -
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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