Contacts of the helix formed by residues 23 - 33 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ASN* 4.9 6.1 + - - -
22D CYS* 1.3 76.5 - - - +
24D PHE* 1.3 63.6 + - - +
25D CGU 3.3 9.8 + - - +
26D CGU 2.8 44.4 + - - +
27D ALA* 3.0 20.5 + - - +
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Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASP* 1.3 75.9 - - - +
25D CGU 1.3 60.0 + - - +
27D ALA* 3.1 11.2 + - + +
28D LYS* 2.8 65.5 + - + +
31D PHE* 5.1 9.4 - + - -
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Residues in contact with CGU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU* 3.0 5.6 - - - -
87B ARG* 2.9 41.4 - - - +
146B PHE* 4.9 2.9 - - + -
7D CGU 6.1 0.2 - - - -
23D ASP* 3.3 8.3 + - - +
24D PHE* 1.3 76.9 + - - +
26D CGU 1.3 63.2 + - - +
28D LYS* 3.2 25.7 + - + -
29D CGU 2.9 49.9 + - - +
32D GLN* 5.3 1.6 - - - -
34D MG 2.1 50.1 - - - -
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Residues in contact with CGU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA* 2.8 27.5 - - - +
2D ASN* 3.1 22.1 - - - +
7D CGU 2.8 3.8 - - - -
16D CGU 2.9 7.4 - - + -
17D CYS* 5.0 0.4 - - - -
22D CYS* 3.3 15.4 - - + -
23D ASP* 2.8 48.7 + - - +
25D CGU 1.3 77.5 + - - +
27D ALA* 1.3 63.7 + - - +
29D CGU 2.8 9.1 + - - +
30D ILE* 3.2 26.2 + - - +
35D CA 2.4 25.8 - - - -
36D CA 2.4 29.5 - - - -
37D CA 2.4 35.0 - - - -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D CYS* 4.6 2.6 - - - -
22D CYS* 4.6 11.0 - - - -
23D ASP 3.0 13.2 + - - +
24D PHE* 3.1 16.1 + - + +
26D CGU 1.3 79.7 + - - +
28D LYS* 1.3 61.8 + - - +
30D ILE* 2.9 25.5 + - - +
31D PHE* 3.0 39.0 + - + -
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Residues in contact with LYS 28 (chain D).
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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24D PHE* 2.8 69.7 + - + +
25D CGU 3.2 24.5 + - - +
27D ALA* 1.3 71.4 - - - +
29D CGU 1.3 62.5 + - - +
31D PHE* 3.2 13.2 + - + +
32D GLN* 3.0 34.8 + - - +
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Residues in contact with CGU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLN 5.1 2.3 - - - -
86B GLU* 3.0 12.5 - - - +
11D SER* 3.5 8.4 + - - -
25D CGU 2.9 31.2 + - - +
26D CGU 2.8 11.4 - - - +
27D ALA 3.1 0.2 - - - -
28D LYS* 1.3 77.0 + - - +
30D ILE* 1.3 60.0 + - - +
32D GLN* 4.5 8.8 - - - +
33D ASN* 2.9 44.5 + - - +
34D MG 2.1 50.2 - - - -
35D CA 2.5 25.1 - - - -
36D CA 2.4 34.5 - - - -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 3.8 10.8 - - - +
12D SER* 3.7 5.6 - - - +
13D LEU* 3.7 46.4 - - + +
16D CGU 3.8 18.8 - - + -
17D CYS* 3.0 37.7 - - - -
26D CGU 3.2 12.6 + - - +
27D ALA* 2.9 9.7 + - - +
29D CGU 1.3 74.4 + - - +
31D PHE* 1.3 75.6 + - + +
33D ASN* 3.0 21.7 + - - +
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Residues in contact with PHE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 5.6 6.3 - - + -
17D CYS* 6.6 0.2 - - - -
24D PHE* 5.1 7.4 - + - -
27D ALA* 3.0 45.0 + - + -
28D LYS* 3.2 16.3 + - + +
30D ILE* 1.3 89.5 - - + +
32D GLN* 1.3 61.8 + - - +
33D ASN 3.4 2.9 + - - +
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D CGU 5.3 1.4 - - - -
28D LYS* 3.0 25.2 + - - +
29D CGU 4.5 11.4 - - - +
30D ILE 3.2 0.2 - - - -
31D PHE* 1.3 78.0 - - - +
33D ASN* 1.3 73.9 + - - +
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Residues in contact with ASN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D HIS* 3.1 33.3 + - + +
11D SER* 3.5 16.2 + - - +
29D CGU 2.9 38.9 + - - +
30D ILE 3.0 15.0 + - - +
31D PHE 4.5 2.3 - - - +
32D GLN* 1.3 93.6 + - - +
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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