Contacts of the helix formed by residues 34 - 46 (chain J) in PDB entry 5GAG
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 ASN 34 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28J LEU* 4.3 0.5 - - - +
32J GLY 4.2 0.6 + - - -
33J VAL* 1.3 85.6 - - - +
35J ILE* 1.3 62.3 + - - +
36J MET* 4.8 1.8 - - + +
37J GLU* 3.3 39.3 + - + +
38J PHE* 3.5 13.3 - - - +
65J ARG* 3.7 18.0 - - - +
66J SER* 4.8 2.9 - - - -
67J PHE* 3.9 7.2 - - + -
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Residues in contact with ILE 35 (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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19J ASN* 3.2 35.7 - - - +
24J VAL* 4.9 2.9 - - + -
25J GLY* 3.2 40.6 - - - +
28J LEU* 3.5 25.1 - - + -
29J GLY* 3.7 13.0 - - - -
33J VAL 3.4 3.3 + - - +
34J ASN* 1.3 74.6 - - - +
36J MET* 1.3 64.2 + - + +
38J PHE* 3.8 2.9 + - - +
39J CYS* 2.9 32.9 + - - -
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Residues in contact with MET 36 (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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19J ASN* 4.3 10.8 - - - +
34J ASN* 5.8 2.0 - - + -
35J ILE* 1.3 81.2 - - + +
37J GLU* 1.3 63.8 + - + +
39J CYS* 3.7 8.8 - - + +
40J LYS* 3.0 45.8 + - + +
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Residues in contact with GLU 37 (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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34J ASN* 3.3 38.4 + - + +
35J ILE 3.6 0.2 - - - -
36J MET* 1.3 80.8 - - + +
38J PHE* 1.3 58.5 + - - +
40J LYS* 5.4 0.4 - - - -
41J ALA* 3.0 36.1 + - + +
67J PHE* 4.0 12.8 - - + -
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Residues in contact with PHE 38 (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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11J LEU* 3.4 24.9 - - + -
13J VAL* 4.9 2.5 - - + -
24J VAL* 4.1 8.7 - - + -
28J LEU* 3.3 27.6 - - + -
34J ASN 3.5 12.3 + - - +
35J ILE 3.8 2.4 + - - +
36J MET 3.4 0.2 - - - -
37J GLU* 1.3 76.2 - - - +
39J CYS* 1.3 63.0 + - - +
41J ALA* 4.8 1.6 - - - -
42J PHE* 2.9 52.8 + + + +
57J VAL* 3.3 47.6 - - + -
59J ILE* 3.3 25.8 - - + -
67J PHE* 3.4 21.4 - - + -
69J PHE* 4.0 10.5 - + - -
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Residues in contact with CYS 39 (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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18J ALA* 3.5 10.9 - - + +
19J ASN* 3.1 50.7 - - + +
24J VAL* 4.8 9.0 - - - -
35J ILE* 2.9 28.7 + - - +
36J MET* 3.7 8.7 - - - +
37J GLU 3.4 0.4 - - - -
38J PHE* 1.3 78.0 - - - +
40J LYS* 1.3 74.3 + - - +
42J PHE* 3.8 1.0 - - - +
43J ASN* 2.9 37.9 + - - +
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Residues in contact with LYS 40 (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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18J ALA 4.0 12.9 + - - -
19J ASN* 4.7 6.0 - - - +
36J MET* 3.0 34.4 + - + +
37J GLU* 4.7 0.9 - - - +
39J CYS* 1.3 90.3 - - + +
41J ALA* 1.3 62.1 + - - +
43J ASN* 3.4 33.3 - - - +
44J ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 41 (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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37J GLU* 3.0 23.9 + - + +
40J LYS* 1.3 76.2 - - - +
42J PHE* 1.3 57.7 + - - +
44J ALA* 3.9 4.1 - - - +
45J LYS* 3.0 34.2 + - + +
67J PHE* 6.0 0.2 - - + -
69J PHE* 3.6 20.9 - - + -
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Residues in contact with PHE 42 (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 VAL* 3.5 49.1 - - + -
14J ALA 3.7 11.2 - - - -
17J MET 3.9 2.2 - - - -
18J ALA* 4.7 4.0 - - + -
38J PHE* 2.9 35.5 + + + +
39J CYS 4.6 0.7 - - - -
41J ALA* 1.3 75.7 - - - +
43J ASN* 1.3 64.0 + - - +
45J LYS* 4.4 1.1 - - - +
46J THR* 2.4 57.6 + - + +
55J ILE* 3.7 19.3 - - + -
57J VAL* 3.4 27.8 - - + -
69J PHE* 3.6 9.1 - - + -
71J THR* 3.2 22.4 - - + -
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Residues in contact with ASN 43 (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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15J ALA 4.2 1.3 - - - +
16J GLY* 3.9 16.3 + - - +
17J MET* 2.9 30.0 + - - +
18J ALA* 3.4 18.2 - - - +
39J CYS 2.9 23.2 + - - +
40J LYS* 3.4 30.9 - - - +
42J PHE* 1.3 80.7 - - - +
44J ALA* 1.3 58.4 + - - +
46J THR* 3.8 4.5 - - - -
47J ASP* 2.9 30.2 + - - +
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Residues in contact with ALA 44 (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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40J LYS 3.0 20.4 + - - +
41J ALA* 4.1 5.4 - - - +
43J ASN* 1.3 77.0 - - - +
45J LYS* 1.3 58.2 + - - +
47J ASP* 2.9 21.7 - - - +
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Residues in contact with LYS 45 (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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41J ALA* 3.0 20.2 + - + +
42J PHE* 4.2 5.4 - - - +
44J ALA* 1.3 77.5 - - - +
46J THR* 1.3 63.1 + - + +
47J ASP* 3.5 2.5 + - - +
48J SER* 3.5 16.3 + - - -
69J PHE* 3.8 37.4 + - + -
71J THR* 4.0 16.2 + - - +
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Residues in contact with THR 46 (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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15J ALA* 2.2 41.8 + - - +
42J PHE* 2.4 58.5 + - + +
45J LYS* 1.3 76.1 - - - +
47J ASP* 1.3 58.6 + - - +
48J SER 3.0 6.6 + - - +
49J ILE* 3.2 26.9 + - - +
55J ILE* 3.4 23.1 - - + -
71J THR* 3.7 9.9 - - + -
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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