Contacts of the helix formed by residues 23 - 32 (chain C) in PDB entry 3JTC
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 ASP 23 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ASN* 5.1 4.9 + - - -
21C ILE 4.3 0.2 + - - -
22C CYS* 1.3 77.3 - - - +
24C PHE* 1.3 65.9 + - - +
25C CGU 3.3 10.8 + - - +
26C CGU 2.9 43.3 + - - +
27C ALA* 3.0 21.1 + - - +
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Residues in contact with PHE 24 (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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23C ASP* 1.3 76.5 - - - +
25C CGU 1.3 59.4 + - - +
27C ALA* 3.1 10.4 + - + -
28C LYS* 2.9 65.1 + - + +
31C PHE* 5.1 9.9 - + - -
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Residues in contact with CGU 25 (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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86A GLU* 2.8 10.2 - - - -
87A ARG* 2.9 37.3 - - - +
146A PHE* 5.0 2.6 - - + -
23C ASP* 3.3 8.7 + - - +
24C PHE* 1.3 74.1 + - - +
26C CGU 1.3 71.1 + - - +
28C LYS* 3.2 27.6 + - + +
29C CGU 2.9 40.6 + - - +
34C MG 2.1 49.2 - - - -
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Residues in contact with CGU 26 (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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1C ALA* 2.8 32.7 - - - +
2C ASN* 3.0 23.5 - - - +
7C CGU 2.9 5.2 - - - -
16C CGU 3.0 9.3 - - + -
21C ILE 3.9 0.2 - - - -
22C CYS* 3.3 10.2 - - + -
23C ASP* 2.9 47.0 + - - +
25C CGU 1.3 80.3 + - - +
27C ALA* 1.4 61.9 + - - +
29C CGU 3.2 16.3 + - - +
30C ILE* 3.3 18.0 + - - +
35C CA 2.4 25.4 - - - -
36C CA 2.4 28.8 - - - -
37C CA 2.4 39.2 - - - -
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Residues in contact with ALA 27 (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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17C CYS* 4.6 1.3 - - - -
22C CYS* 4.1 14.5 - - - -
23C ASP 3.0 12.4 + - - +
24C PHE* 3.1 15.5 + - + +
26C CGU 1.4 77.2 + - - +
28C LYS* 1.4 56.9 + - - +
30C ILE* 2.9 29.9 + - - +
31C PHE* 3.0 40.0 + - + -
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Residues in contact with LYS 28 (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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24C PHE* 2.9 68.0 + - + +
25C CGU 3.2 25.5 + - + +
27C ALA* 1.4 72.5 - - - +
29C CGU 1.3 62.6 + - - +
31C PHE* 3.9 12.1 - - + -
32C GLN* 3.0 24.6 + - - -
33C ASN 4.7 0.9 + - - -
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Residues in contact with CGU 29 (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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85A GLN 5.2 2.3 - - - -
86A GLU* 2.9 12.2 - - - +
7C CGU 2.9 0.9 - - - -
11C SER* 3.5 15.9 + - - -
25C CGU 2.9 31.9 + - - +
26C CGU 3.1 10.1 - - - +
27C ALA 3.2 0.2 - - - -
28C LYS* 1.3 78.1 + - - +
30C ILE* 1.3 59.5 + - - +
32C GLN* 3.1 36.8 + - - +
34C MG 2.0 51.0 - - - -
35C CA 2.5 25.8 - - - -
36C CA 2.6 33.3 - - - -
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Residues in contact with ILE 30 (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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11C SER* 3.8 24.6 + - - +
12C SER* 3.9 4.0 - - - +
13C LEU* 3.7 42.0 - - + +
16C CGU 3.9 7.0 - - + -
17C CYS* 3.7 29.6 - - - -
26C CGU 3.3 13.7 + - - +
27C ALA* 2.9 8.8 + - - +
29C CGU 1.3 78.0 + - - +
31C PHE* 1.3 78.5 + - + +
32C GLN* 3.3 6.2 + - - +
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Residues in contact with PHE 31 (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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13C LEU* 5.1 11.2 - - + -
17C CYS* 6.5 0.2 - - - -
24C PHE* 5.1 10.3 - + - -
27C ALA* 3.0 42.2 + - + -
28C LYS* 3.2 13.4 + - + +
30C ILE* 1.3 90.1 - - + +
32C GLN* 1.3 71.0 + - - +
33C ASN* 3.3 16.5 + - + +
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Residues in contact with GLN 32 (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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28C LYS 3.0 13.3 + - - -
29C CGU 3.1 45.5 + - - +
30C ILE 4.1 4.5 - - - +
31C PHE* 1.3 79.5 - - - +
33C ASN* 1.3 62.6 + - - +
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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