Contacts of the helix formed by residues 54 - 66 (chain A) in PDB entry 1X57
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.5 4.6 + - - -
52A ILE* 3.3 12.4 + - + +
53A PRO* 1.3 75.5 - - - +
55A ASN* 1.3 75.4 + - - +
56A GLN* 3.1 14.0 - - + +
57A VAL* 3.0 16.4 + - + +
58A LEU* 2.9 29.3 + - - +
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Residues in contact with ASN 55 (chain A).
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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54A ASN* 1.3 83.1 + - - +
56A GLN* 1.3 62.4 + - - +
58A LEU* 3.9 13.6 - - - +
59A GLY* 2.9 24.5 + - - -
70A ARG* 3.8 28.5 + - - +
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASN* 4.8 13.6 - - - +
55A ASN* 1.3 85.7 - - - +
57A VAL* 1.3 69.6 + - + +
59A GLY* 3.2 3.6 + - - -
60A LYS* 3.1 32.2 + - + +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 3.9 23.8 - - + -
38A GLU* 3.8 25.8 - - + +
42A VAL* 5.6 1.6 - - + -
46A TYR* 3.3 33.0 - - + +
52A ILE 6.2 0.2 - - - +
54A ASN* 3.0 12.6 + - + +
56A GLN* 1.3 79.6 - - + +
58A LEU* 1.3 65.7 + - - +
60A LYS* 3.0 14.5 + - - +
61A ILE* 2.9 23.3 + - + +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.9 20.9 - - + -
46A TYR* 3.7 27.7 + - + +
53A PRO* 4.1 15.5 - - + +
54A ASN 2.9 28.9 + - - +
55A ASN* 3.9 6.5 - - - +
57A VAL* 1.3 73.9 - - - +
59A GLY* 1.3 55.5 + - - +
61A ILE* 3.1 9.7 + - + +
62A GLU* 2.9 31.7 + - - +
69A LEU* 4.0 24.7 - - + +
70A ARG* 3.9 34.3 - - + +
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN 2.9 17.3 + - - -
56A GLN 3.2 5.4 + - - -
57A VAL 3.2 0.4 - - - -
58A LEU* 1.3 74.8 - - - +
60A LYS* 1.3 60.5 + - - +
62A GLU* 3.3 30.7 + - - +
63A ARG* 3.5 13.2 + - - +
70A ARG* 4.5 5.5 - - - +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS 5.6 0.2 - - - +
36A ILE* 2.7 50.5 + - + +
37A ASN* 4.0 5.5 + - - +
38A GLU* 2.8 28.3 + - - -
56A GLN* 3.1 18.2 + - + +
57A VAL* 3.0 24.2 + - - +
59A GLY* 1.3 73.6 - - - +
61A ILE* 1.3 63.9 + - - +
63A ARG* 3.2 17.7 + - - +
64A ALA 3.1 15.1 + - - -
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.7 27.4 - - + -
32A LEU* 4.3 11.4 - - + -
36A ILE* 3.6 22.4 - - + -
43A ILE* 4.7 5.8 - - + -
46A TYR* 3.9 37.2 - - + -
57A VAL* 2.9 22.2 + - + +
58A LEU* 3.1 9.8 + - + +
60A LYS* 1.3 71.9 - - - +
62A GLU* 1.3 65.4 + - - +
64A ALA* 3.0 21.8 + - + +
65A ILE* 3.4 13.3 + - + +
69A LEU* 3.7 21.1 - - + -
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU 2.9 20.9 + - - +
59A GLY* 3.5 13.4 - - - +
60A LYS 3.2 0.4 - - - -
61A ILE* 1.3 76.0 - - - +
63A ARG* 1.3 53.6 + - + +
66A GLY* 2.8 36.0 + - - -
67A LEU 3.2 20.7 + - - +
68A LYS* 3.5 28.8 + - - +
69A LEU* 3.8 16.2 + - + +
70A ARG* 4.0 21.7 + - - +
78A ILE* 3.5 19.6 - - + +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 5.8 0.5 - - - -
35A LYS* 5.0 3.1 - - - +
59A GLY 3.5 13.6 + - - +
60A LYS* 3.2 14.7 + - - +
62A GLU* 1.3 79.0 - - + +
64A ALA* 1.3 63.1 + - - +
65A ILE 3.2 1.2 + - - -
66A GLY* 3.5 7.3 + - - -
78A ILE* 4.1 12.6 - - + -
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Residues in contact with ALA 64 (chain A).
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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25A LYS* 3.8 5.4 - - - -
27A LEU* 3.6 20.1 - - - +
32A LEU* 3.6 35.7 - - + -
35A LYS* 3.6 26.4 - - + +
36A ILE* 3.9 7.2 - - + -
60A LYS 3.1 9.1 + - - +
61A ILE* 3.0 14.6 + - - +
63A ARG* 1.3 80.1 - - - +
65A ILE* 1.3 58.2 + - + +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.4 34.3 - - + +
18A ILE* 4.3 7.2 - - + +
21A GLY* 3.5 34.2 - - - +
22A ARG* 3.6 4.7 - - - +
25A LYS* 3.6 23.7 + - - +
27A LEU* 4.8 1.1 - - + -
32A LEU* 4.1 17.5 - - + -
61A ILE* 3.6 13.9 - - + +
62A GLU 4.0 0.2 - - - +
63A ARG 4.2 0.2 - - - -
64A ALA* 1.3 81.7 - - + +
66A GLY* 1.3 62.7 + - - +
67A LEU* 3.8 21.0 + - + +
69A LEU* 3.9 22.7 - - + -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU 2.8 13.4 + - - -
63A ARG 3.5 6.2 + - - -
65A ILE* 1.3 78.7 - - - +
67A LEU* 1.3 59.4 + - - +
77A PRO* 3.4 8.8 - - - +
78A ILE* 3.1 36.0 + - - +
80A LYS 4.4 5.3 - - - +
81A GLY* 5.1 1.6 - - - -
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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