Contacts of the helix formed by residues 56 - 68 (chain A) in PDB entry 4ZCU
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 1.3 76.3 - - - +
57A GLN* 1.3 65.3 + - - -
58A ASP 3.3 3.1 - - - -
59A ALA* 3.3 7.2 + - - +
60A GLU* 3.1 23.1 + - - +
1005A SO4 3.2 15.7 - - - -
1008A GOL 3.6 19.8 - - - -
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Residues in contact with GLN 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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41A ILE* 6.0 0.2 - - - +
45A GLN* 4.9 6.0 + - - +
55A LEU 4.1 0.2 + - - -
56A GLY* 1.3 71.5 - - - -
58A ASP* 1.3 67.1 + - - +
60A GLU* 3.9 13.2 + - - +
61A GLU* 2.9 31.1 + - - +
1005A SO4 2.5 32.9 + - - +
1008A GOL 3.4 3.3 + - - +
40B ASP* 3.0 35.8 + - + -
41B ILE* 3.8 12.0 - - + +
42B GLY* 3.3 27.2 + - - -
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Residues in contact with ASP 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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57A GLN* 1.3 80.3 - - - +
59A ALA* 1.3 59.7 + - - +
61A GLU* 5.6 0.2 - - - +
62A LYS* 2.9 29.9 + - - +
1008A GOL 3.2 30.4 + - - +
38B VAL* 5.7 1.0 - - - +
40B ASP* 3.2 31.7 - - - +
72B ASP 3.6 5.1 - - - +
73B GLY* 3.6 17.3 - - - +
74B LYS* 3.8 30.0 - - + +
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Residues in contact with ALA 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 LEU* 4.2 14.1 - - + -
56A GLY 3.3 10.9 + - - +
58A ASP* 1.3 75.9 - - - +
60A GLU* 1.3 59.3 + - - +
62A LYS* 3.1 5.2 + - - +
63A ILE* 2.9 32.9 + - - +
155A PRO* 3.7 28.1 - - + +
1008A GOL 3.4 22.6 - - - +
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Residues in contact with GLU 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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41A ILE* 5.0 6.1 - - + -
44A LEU* 3.7 14.5 - - + +
45A GLN* 3.3 44.7 + - - +
48A LEU* 3.7 22.4 - - + +
53A ILE 5.3 0.2 - - - +
55A LEU* 3.6 37.0 + - + +
56A GLY 3.1 16.2 + - - +
57A GLN* 3.9 9.1 - - - +
59A ALA* 1.3 78.5 - - - +
61A GLU* 1.3 58.6 + - - +
63A ILE* 3.3 10.0 + - - +
64A PHE* 2.9 26.3 + - - +
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Residues in contact with GLU 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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41A ILE* 3.9 7.3 - - - +
57A GLN 2.9 19.5 + - - +
58A ASP 4.2 0.2 - - - +
60A GLU* 1.3 73.5 - - - +
62A LYS* 1.3 60.5 + - - +
64A PHE* 4.2 2.7 - - - -
65A THR* 2.9 36.3 + - + +
41B ILE* 3.5 21.3 - - + +
61B GLU* 2.7 38.9 - - - +
64B PHE* 2.9 51.2 - - + +
73B GLY* 3.6 13.9 - - - +
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Residues in contact with LYS 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 ASP 2.9 21.2 + - - +
59A ALA* 3.1 6.2 + - - +
61A GLU* 1.3 75.1 - - - +
63A ILE* 1.3 62.2 + - - +
65A THR* 3.0 7.1 + - - -
66A THR* 2.8 38.4 + - - +
155A PRO* 3.2 35.4 + - + +
156A VAL* 4.6 0.8 - - - +
157A THR* 4.4 9.0 - - - -
161A GLU* 3.0 35.1 + - - -
71B LYS 3.5 24.5 - - - +
72B ASP* 3.8 16.6 - - - +
73B GLY* 3.6 4.2 - - - -
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Residues in contact with ILE 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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44A LEU* 4.6 14.4 - - + -
48A LEU* 5.1 6.1 - - + -
55A LEU* 3.8 18.4 - - + -
59A ALA 2.9 14.3 + - - +
60A GLU* 3.3 10.3 - - - +
62A LYS* 1.3 77.3 - - - +
64A PHE* 1.3 58.8 + - - +
66A THR* 3.7 2.1 - - - -
67A GLY* 2.9 27.0 + - - -
75A LEU* 5.1 7.7 - - + +
80A PHE* 6.1 4.7 - - + -
83A TYR* 3.5 48.7 - - + +
153A PHE* 3.7 33.7 - - + +
155A PRO* 3.9 6.7 - - + -
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Residues in contact with PHE 64 (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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39A VAL 3.5 26.5 - - - -
40A ASP* 3.7 2.7 - - - -
41A ILE* 3.6 26.9 - - + -
44A LEU* 3.9 16.2 - - + -
60A GLU 2.9 12.9 + - - +
61A GLU* 3.2 9.1 + - - +
63A ILE* 1.3 79.5 - - - +
65A THR* 1.3 57.7 + - - +
67A GLY 3.2 0.5 + - - -
68A ASP* 2.8 30.8 + - + +
73A GLY* 3.5 26.7 - - - -
74A LYS 3.8 3.1 - - - -
75A LEU* 3.8 31.3 - - + +
61B GLU* 3.0 39.9 - - + +
65B THR* 3.9 4.3 - - + -
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Residues in contact with THR 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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61A GLU* 2.9 37.7 + - + +
62A LYS* 3.0 15.2 + - - -
64A PHE* 1.3 75.7 - - - +
66A THR* 1.3 60.7 + - - +
68A ASP 3.8 2.1 + - - +
71A LYS* 3.8 12.5 + - - -
64B PHE* 4.1 2.5 - - + -
65B THR* 3.7 30.3 - - + -
68B ASP* 3.1 33.6 + - + +
71B LYS* 3.2 31.2 - - - +
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Residues in contact with THR 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 LYS* 2.8 28.5 + - - +
63A ILE 3.7 3.1 - - - -
65A THR* 1.3 80.7 + - - +
67A GLY* 1.3 59.7 + - - +
68A ASP 4.7 0.2 - - - -
69A VAL* 4.3 11.8 + - - +
71A LYS* 5.3 0.7 + - - -
83A TYR* 3.7 28.5 - - + -
71B LYS* 3.9 23.9 + - + +
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Residues in contact with GLY 67 (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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63A ILE 2.9 15.9 + - - -
64A PHE 3.7 0.9 - - - -
66A THR* 1.3 77.5 - - - +
68A ASP* 1.3 58.0 + - - +
69A VAL* 2.8 16.0 + - - +
75A LEU* 3.5 14.1 - - - -
79A GLU* 3.2 24.1 - - - +
82A LYS* 5.5 0.2 - - - -
83A TYR* 4.3 19.5 - - - -
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Residues in contact with ASP 68 (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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64A PHE* 2.8 23.1 + - + +
65A THR 3.8 1.5 + - - +
66A THR 3.5 1.2 - - - -
67A GLY* 1.3 68.3 - - - +
69A VAL* 1.3 54.5 + - - +
70A ASN* 2.9 7.3 - - - +
71A LYS* 2.4 41.6 + - - -
72A ASP* 2.9 9.1 + - - +
73A GLY* 2.7 28.7 + - - -
74A LYS 3.7 4.9 - - - -
75A LEU* 3.5 9.3 - - + +
79A GLU* 3.8 2.7 - - - -
1002A CA 2.4 30.3 - - - -
65B THR* 3.2 20.5 + - + +
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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