Contacts of the helix formed by residues 23 - 32 (chain N) in PDB entry 3G5G
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 THR 23 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17N ARG* 3.6 9.9 - - - +
21N GLY 5.6 0.9 - - - +
22N MET* 1.3 76.4 - - - +
24N GLN* 1.3 60.0 + - - +
25N GLU* 3.2 21.5 - - + +
26N ASP* 2.8 52.3 + - - +
27N LEU 3.0 7.3 + - - -
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Residues in contact with GLN 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J LYS* 5.0 11.3 - - - +
17N ARG* 3.6 29.1 - - - +
23N THR* 1.3 74.0 - - - +
25N GLU* 1.3 64.7 + - - +
27N LEU* 3.3 3.8 + - - +
28N ALA* 2.8 30.0 + - - +
35N ARG* 4.7 4.9 - - + +
38N ILE* 3.9 15.5 - - + +
39N SER* 3.7 31.6 + - - +
42N GLU* 2.7 37.2 + - - +
43N ARG* 5.7 2.6 - - - +
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Residues in contact with GLU 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J LYS* 5.4 8.0 + - - -
23N THR* 3.2 24.9 + - + +
24N GLN* 1.3 75.9 - - - +
26N ASP* 1.3 58.3 + - - +
28N ALA* 3.7 0.7 - - - +
29N TYR* 2.8 32.4 + - - +
35N ARG* 3.7 38.8 + - + +
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Residues in contact with ASP 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N GLY 4.3 2.6 - - - +
22N MET* 3.4 22.0 - - + +
23N THR* 2.8 45.1 + - - +
25N GLU* 1.3 75.2 - - - +
27N LEU* 1.3 64.6 + - - +
29N TYR* 3.9 4.9 - - - +
30N LYS* 3.1 30.5 + - + +
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Residues in contact with LEU 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N ILE* 4.1 21.3 - - + -
17N ARG* 3.8 23.1 - - - -
22N MET* 3.7 7.8 - - + +
23N THR 3.0 8.4 + - - +
24N GLN 3.3 7.4 + - - +
26N ASP* 1.3 77.2 - - - +
28N ALA* 1.3 63.3 + - - +
30N LYS* 3.1 1.4 + - - -
31N SER* 2.4 49.7 + - - +
38N ILE* 4.2 21.5 - - + -
56N ILE* 4.0 12.6 - - + +
59N GLY 4.1 4.5 - - - -
60N LEU* 3.8 45.1 - - + +
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Residues in contact with ALA 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N GLN 2.8 17.4 + - - +
25N GLU 3.7 4.5 - - - +
27N LEU* 1.3 76.8 - - - +
29N TYR* 1.3 64.2 + - - +
31N SER* 4.3 1.3 - - - -
32N ASN* 3.1 15.4 + - - -
33N LEU 3.0 30.7 + - - +
34N ASP 3.9 2.2 - - - +
35N ARG* 3.7 33.7 - - + +
38N ILE* 4.0 10.0 - - + +
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Residues in contact with TYR 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLU 2.8 18.6 + - - +
26N ASP* 3.9 5.2 - - - +
28N ALA* 1.3 79.9 - - - +
30N LYS* 1.3 85.9 + - + +
31N SER 3.5 0.3 + - - -
32N ASN* 3.7 10.3 + - - +
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Residues in contact with LYS 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N MET* 3.7 14.1 - - + -
26N ASP 3.1 18.3 + - - +
27N LEU 3.1 4.3 + - - +
29N TYR* 1.3 97.9 - - + +
31N SER* 1.3 58.7 - - - +
32N ASN* 3.5 6.2 + - - -
58N LYS* 4.8 10.1 + - - +
59N GLY* 3.8 31.7 + - - +
61N GLU* 4.1 26.7 + - - +
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Residues in contact with SER 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N LEU* 2.4 42.7 + - - +
28N ALA* 3.3 0.6 + - - -
30N LYS* 1.3 74.7 - - - +
32N ASN* 1.3 72.9 + - - +
33N LEU* 3.4 26.9 + - - -
38N ILE* 4.6 0.7 - - - +
55N LEU* 3.9 41.7 + - - +
56N ILE* 4.4 3.8 - - - +
58N LYS* 5.7 1.6 - - - -
59N GLY* 4.6 0.6 - - - -
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Residues in contact with ASN 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ALA 3.1 6.7 + - - -
29N TYR 3.7 7.4 + - - -
30N LYS 3.5 8.3 + - - -
31N SER* 1.3 82.6 + - - +
33N LEU* 1.3 64.5 + - - +
55N LEU* 5.3 7.4 - - + +
58N LYS* 4.6 13.9 - - - +
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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