Contacts of the helix formed by residues 23 - 32 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 5.1 4.9 - - - +
18E LEU* 3.4 30.1 - - + -
17J ARG* 3.8 10.4 - - - +
21J GLY 5.4 0.2 - - - +
22J MET* 1.3 74.2 - - - +
24J GLN* 1.3 63.6 + - - +
25J GLU* 3.4 18.0 + - - +
26J ASP* 2.8 38.5 + - - +
27J LEU 3.0 18.4 + - - -
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Residues in contact with GLN 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J LYS* 5.7 0.2 - - - +
17J ARG* 3.8 28.1 - - - +
23J THR* 1.3 70.7 - - - +
25J GLU* 1.3 63.4 + - - +
27J LEU* 3.3 2.9 + - - +
28J ALA* 2.8 34.4 + - - +
35J ARG* 5.1 5.4 - - + +
38J ILE* 4.0 16.5 - - + +
39J SER* 3.6 40.5 + - - +
42J GLU* 2.9 31.1 + - - +
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Residues in contact with GLU 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR* 4.5 16.3 - - - +
23J THR* 3.4 13.6 + - - +
24J GLN* 1.3 87.8 + - - +
26J ASP* 1.3 59.4 + - - +
28J ALA* 3.2 2.6 + - - +
29J TYR* 2.8 30.9 + - - +
35J ARG* 3.7 37.7 - - + +
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Residues in contact with ASP 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J GLY 4.3 2.4 - - - +
22J MET* 3.5 24.0 - - + +
23J THR* 2.8 46.6 + - - +
25J GLU* 1.3 78.3 - - - +
27J LEU* 1.3 58.1 + - - +
29J TYR* 3.4 8.6 + - - +
30J LYS* 3.0 32.8 + - + +
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Residues in contact with LEU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE* 4.0 21.8 - - + -
17J ARG* 3.9 20.2 - - + -
22J MET* 3.7 8.0 - - + +
23J THR 3.0 12.4 + - - +
24J GLN 3.6 7.0 - - - +
25J GLU 3.3 0.2 - - - -
26J ASP* 1.3 73.8 - - - +
28J ALA* 1.3 64.8 + - - +
30J LYS 3.3 0.3 + - - -
31J SER* 2.9 42.9 + - - +
38J ILE* 4.2 20.9 - - + -
42J GLU* 4.7 0.2 - - - +
56J ILE* 4.0 10.5 - - + +
59J GLY* 3.9 19.1 - - - +
60J LEU* 3.8 33.7 - - + +
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J GLN 2.8 17.4 + - - +
25J GLU 3.5 7.6 - - - +
27J LEU* 1.3 70.8 - - - +
29J TYR* 1.3 64.1 + - - +
31J SER* 3.2 1.7 + - - -
32J ASN* 3.1 4.7 + - - -
33J LEU 3.1 43.4 + - - +
34J ASP 3.9 2.2 - - - +
35J ARG* 3.6 35.4 - - + +
38J ILE* 4.0 10.7 - - + +
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Residues in contact with TYR 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J GLU 2.8 17.2 + - - +
26J ASP* 3.6 6.3 - - - +
28J ALA* 1.3 77.0 - - - +
30J LYS* 1.3 89.9 + - + +
31J SER 3.4 0.2 + - - -
32J ASN* 3.5 12.0 + - - +
35J ARG* 5.8 0.2 - - - +
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Residues in contact with LYS 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J MET* 3.8 15.0 - - + -
26J ASP* 3.0 20.7 + - + +
27J LEU 3.9 2.2 - - - +
28J ALA 3.3 0.2 - - - -
29J TYR* 1.3 99.3 - - + +
31J SER* 1.3 59.0 + - - +
32J ASN* 3.5 4.3 + - - -
58J LYS* 4.7 9.0 + - - +
59J GLY* 3.7 31.3 + - - +
61J GLU* 4.2 23.0 + - - +
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Residues in contact with SER 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J LEU* 2.9 38.4 + - - +
28J ALA 3.8 3.1 - - - -
30J LYS* 1.3 76.6 - - - +
32J ASN* 1.3 73.9 + - - +
33J LEU* 3.9 26.2 - - - +
38J ILE* 5.1 0.4 - - - -
55J LEU* 3.6 42.3 + - - +
56J ILE* 3.7 5.8 - - - +
58J LYS* 5.9 1.1 - - - -
59J GLY* 3.9 0.7 - - - -
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Residues in contact with ASN 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ALA 3.1 5.6 + - - -
29J TYR 3.5 8.3 + - - +
30J LYS 3.5 5.9 + - - -
31J SER* 1.3 82.4 + - - +
33J LEU* 1.3 66.0 + - - +
55J LEU* 5.5 6.3 - - + +
58J LYS* 4.9 12.3 - - - +
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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