Contacts of the helix formed by residues 23 - 34 (chain J) in PDB entry 4UJ3
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 GLY 23 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21J GLY 3.2 1.2 - - - -
22J VAL* 1.3 80.5 - - - +
24J LYS* 1.3 67.3 + - - +
26J ASN* 3.1 4.2 + - - +
27J LEU* 2.8 28.3 + - - +
124J ASN* 3.7 2.9 + - - -
200J GNP 2.9 41.6 + - - -
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Residues in contact with LYS 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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16J LEU* 3.7 32.3 - - + +
17J ILE* 3.6 25.4 - - - +
18J GLY 3.1 22.1 + - - +
19J ASP 3.3 7.3 + - - -
22J VAL* 3.7 11.6 - - + +
23J GLY* 1.3 74.5 - - - +
25J SER* 1.3 57.7 + - - +
27J LEU* 2.8 29.8 + - - +
28J LEU* 2.8 14.6 + - - +
66J ASP* 4.1 8.5 - - - +
67J THR 3.6 19.3 - - - -
69J GLY* 3.4 5.5 - - - -
90J VAL* 4.2 11.0 - - + -
200J GNP 2.8 45.6 + - - +
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Residues in contact with SER 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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24J LYS* 1.3 75.7 - - - +
26J ASN* 1.3 58.8 + - - +
28J LEU* 3.4 6.7 - - - +
29J SER* 3.0 25.5 + - - -
40J SER* 5.4 3.4 - - - -
41J LYS 5.7 1.1 - - - -
43J THR* 2.4 14.2 + - - +
66J ASP* 3.0 16.0 + - - -
200J GNP 2.6 18.4 + - - -
201J MG 2.2 32.2 - - - -
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Residues in contact with ASN 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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23J GLY 3.1 7.2 + - - +
24J LYS 3.1 0.8 - - - -
25J SER* 1.3 76.2 - - - +
27J LEU* 1.3 61.2 + - - +
28J LEU 3.1 1.1 - - - -
29J SER* 3.1 6.8 + - - -
30J ARG* 2.8 32.9 + - - +
35J GLU 4.2 0.3 - - - +
36J PHE* 3.3 15.2 - - + -
37J ASN* 2.8 39.5 + - - +
40J SER* 3.2 23.6 + - - -
155J ALA* 3.9 16.6 - - + +
200J GNP 2.7 34.8 + - + +
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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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16J LEU* 5.0 7.6 - - + -
23J GLY 2.8 17.4 + - - +
24J LYS* 2.8 10.4 + - - +
26J ASN* 1.3 74.1 - - - +
28J LEU* 1.3 63.1 + - - +
30J ARG* 3.8 2.5 - - - +
31J PHE* 3.1 25.5 + - - +
88J LEU* 5.8 2.5 - - + -
90J VAL* 3.6 39.3 - - + -
122J VAL* 4.4 11.7 - - + -
124J ASN* 3.7 14.1 - - - +
153J THR* 3.5 23.1 - - + +
155J ALA* 4.0 10.1 - - + +
161J VAL* 4.0 17.7 - - + +
165J PHE* 3.6 16.0 - - + -
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Residues in contact with LEU 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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16J LEU* 3.9 10.0 - - + +
24J LYS 2.8 10.8 + - - +
25J SER* 3.4 9.6 - - - +
27J LEU* 1.3 78.5 - - - +
29J SER* 1.3 63.7 + - - +
31J PHE* 3.9 0.5 - - - +
32J THR* 3.1 42.5 + - + +
33J ARG* 5.4 3.8 - - - +
47J GLU* 4.5 12.1 - - + +
48J PHE* 5.2 2.0 - - - -
49J ALA* 4.0 14.6 - - + +
64J ILE* 3.5 42.0 - - + +
66J ASP* 3.6 33.0 - - + +
165J PHE* 4.7 4.0 - - - -
755L VAL* 5.7 2.2 - - + -
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Residues in contact with SER 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 SER 3.0 12.5 + - - -
26J ASN* 3.1 21.0 + - - -
28J LEU* 1.3 76.5 - - - +
30J ARG* 1.3 64.2 + - - +
32J THR* 4.0 5.6 - - - -
33J ARG* 3.1 47.0 + - - +
34J ASN 3.2 5.5 + - - -
35J GLU* 2.6 33.2 + - - -
36J PHE* 4.3 0.3 - - - -
37J ASN* 5.0 0.7 + - - +
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Residues in contact with ARG 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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26J ASN 2.8 19.7 + - - +
27J LEU* 3.8 4.7 - - - +
29J SER* 1.3 77.5 + - - +
31J PHE* 1.3 58.1 + - - +
34J ASN* 2.8 74.0 + - - +
35J GLU 3.4 6.9 - - - +
36J PHE* 3.0 34.5 - - + +
155J ALA* 3.0 23.7 + - + +
156J LEU 3.3 14.3 + - - -
158J SER* 3.3 24.8 + - - -
161J VAL* 3.6 32.1 - - + -
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Residues in contact with PHE 31 (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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27J LEU 3.1 8.9 + - - +
28J LEU 3.9 2.2 - - - +
30J ARG* 1.3 80.0 - - - +
32J THR* 1.3 73.4 + - + +
34J ASN 4.5 0.9 + - - -
51J ARG* 2.9 78.7 + - + +
53J ILE* 4.3 13.7 - - + -
62J ALA* 4.8 7.4 - - + -
64J ILE* 4.5 10.3 - - + -
161J VAL* 4.4 4.7 - - + -
162J GLU* 3.6 22.2 - - - -
165J PHE* 3.2 69.5 - + + -
166J GLN* 5.0 2.0 - - + -
169J LEU* 4.5 5.4 - - + -
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Residues in contact with THR 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 LEU* 3.1 26.8 + - + +
31J PHE* 1.3 93.1 - - + +
33J ARG* 1.3 90.4 + - - +
34J ASN 3.7 0.2 - - - -
49J ALA* 3.6 31.7 - - + +
50J THR 4.3 18.3 - - - +
51J ARG* 4.7 10.5 - - + +
64J ILE* 5.0 2.0 - - + -
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Residues in contact with ARG 33 (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 LEU* 5.4 4.2 - - - +
29J SER* 3.1 29.5 + - - +
32J THR* 1.3 91.5 + - - +
34J ASN* 1.3 71.2 + - - +
35J GLU* 2.9 42.3 + - + +
49J ALA* 4.8 4.9 - - - +
755L VAL* 3.6 33.0 - - - +
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Residues in contact with ASN 34 (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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30J ARG* 2.8 58.1 + - - +
31J PHE 4.4 1.0 + - - +
32J THR 3.7 0.8 - - - -
33J ARG* 1.3 78.8 - - - +
35J GLU* 1.3 60.1 + - - +
158J SER* 4.5 2.3 + - - -
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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