Contacts of the helix formed by residues 745 - 752 (chain C) in PDB entry 1RR8
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 ASN 745 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741C GLU 4.9 2.2 - - - -
743C ILE 4.1 1.0 + - - -
744C TYR* 1.3 74.3 - - - +
746C LYS* 1.3 58.8 + - - +
747C THR* 3.2 25.8 + - - +
748C GLN* 3.0 44.2 + - - +
749C ARG* 2.9 34.6 + - - +
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Residues in contact with LYS 746 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B T 5.4 5.5 + - - -
745C ASN* 1.3 77.6 - - + +
747C THR* 1.3 74.8 + - + +
749C ARG* 3.5 25.5 + - - +
750C GLU* 3.4 41.1 + - - +
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Residues in contact with THR 747 (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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721C LEU* 5.6 3.1 - - - +
745C ASN* 3.2 13.5 + - - +
746C LYS* 1.3 91.7 - - + +
748C GLN* 1.3 64.2 + - - +
750C GLU* 3.3 17.3 + - - +
751C LYS* 3.3 20.4 + - - +
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Residues in contact with GLN 748 (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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720C LYS* 3.6 22.7 - - - +
721C LEU* 3.3 40.2 - - + +
743C ILE 3.9 0.8 + - - -
744C TYR* 3.3 28.7 - - + +
745C ASN* 3.0 49.2 + - - +
747C THR* 1.3 75.6 - - - +
749C ARG* 1.3 59.7 + - - +
751C LYS* 3.2 7.1 + - - +
752C PHE* 2.9 41.1 + - + +
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Residues in contact with ARG 749 (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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740C ILE* 4.6 14.7 - - + +
741C GLU* 3.8 29.5 + - - +
744C TYR* 3.4 31.1 + - + +
745C ASN* 2.9 22.6 + - - +
746C LYS* 3.5 23.8 + - - +
747C THR 3.3 0.2 - - - -
748C GLN* 1.3 76.2 - - - +
750C GLU* 1.3 59.6 + - + +
752C PHE 4.0 0.4 - - - -
753C ALA* 3.2 25.8 + - - +
756C ILE* 3.5 27.3 - - + +
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Residues in contact with GLU 750 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349C ARG* 3.4 26.7 + - - -
430C ASN* 5.6 1.9 - - - +
432C SER* 3.3 31.1 - - - +
746C LYS* 3.4 32.8 - - + +
747C THR* 3.3 18.6 + - - +
748C GLN 3.2 0.4 - - - -
749C ARG* 1.3 77.6 - - + +
751C LYS* 1.3 62.6 + - - +
752C PHE 3.4 0.4 - - - -
753C ALA* 3.6 17.1 - - - +
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Residues in contact with LYS 751 (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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431C PRO* 3.7 46.9 - - + +
432C SER* 4.3 3.2 - - - +
437C GLY* 5.4 0.5 - - - -
440C ASP* 3.7 22.0 + - - +
721C LEU* 2.8 49.6 + - + +
722C ASN* 4.5 7.7 + - - -
747C THR 3.3 10.0 + - - +
748C GLN* 3.2 9.3 + - - +
750C GLU* 1.3 79.3 - - - +
752C PHE* 1.3 74.9 + - + +
753C ALA 3.4 0.7 - - - -
754C TRP* 3.4 21.1 + - - -
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Residues in contact with PHE 752 (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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440C ASP* 4.1 10.1 - - - -
444C TYR* 5.2 1.6 - - - -
720C LYS 3.5 25.8 - - - -
721C LEU* 4.0 20.2 - - + -
724C LEU 4.7 5.6 - - - -
726C PRO* 3.6 36.1 - - + -
744C TYR* 3.7 34.3 - + + -
748C GLN* 2.9 28.1 + - + +
751C LYS* 1.3 106.3 - - + +
753C ALA* 1.3 63.2 + - - +
754C TRP* 3.2 11.0 - - - +
755C ALA* 3.1 13.4 + - - +
756C ILE* 3.1 24.7 + - + +
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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