Contacts of the helix formed by residues 56 - 68 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 1.3 80.9 - - - +
57B GLN* 1.3 65.1 + - - -
58B ASP 3.3 3.1 - - - -
59B ALA* 3.3 2.3 + - - +
60B GLU* 3.1 21.6 + - - +
1005B SO4 3.7 11.7 - - - -
1009B GOL 3.4 25.4 - - - -
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.0 36.5 + - + -
41A ILE* 3.7 12.8 - - + +
42A GLY* 3.3 26.6 + - - -
41B ILE* 6.0 0.2 - - - +
45B GLN* 4.8 6.3 + - - +
56B GLY* 1.3 72.3 - - - -
58B ASP* 1.3 67.9 + - - +
60B GLU* 3.9 12.1 - - - +
61B GLU* 2.9 30.4 + - - +
1005B SO4 2.9 35.7 + - - +
1009B GOL 3.3 1.7 + - - +
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 5.7 1.0 - - - +
40A ASP* 3.2 30.7 - - - +
72A ASP 3.6 5.3 - - - +
73A GLY* 3.5 18.0 - - - +
74A LYS* 3.9 28.3 - - + +
56B GLY 3.3 1.0 - - - -
57B GLN* 1.3 80.4 - - - +
59B ALA* 1.3 59.9 + - - +
62B LYS* 2.9 27.9 + - - +
1009B GOL 3.1 32.7 + - - +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.7 25.6 - - + -
56B GLY 3.3 8.3 + - - +
57B GLN 3.3 0.2 - - - -
58B ASP* 1.3 75.8 - - - +
60B GLU* 1.3 59.7 + - - +
62B LYS* 3.1 5.9 + - - +
63B ILE* 2.9 32.6 + - - +
155B PRO* 3.7 21.8 - - + +
1009B GOL 3.2 22.6 + - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ILE* 5.0 5.2 - - + -
44B LEU* 3.7 15.4 - - + +
45B GLN* 3.3 42.4 + - - +
48B LEU* 3.8 21.3 - - + +
53B ILE 5.2 0.3 - - - +
55B LEU* 3.6 39.6 + - + +
56B GLY 3.1 16.1 + - - +
57B GLN* 3.9 8.5 - - - +
59B ALA* 1.3 77.9 - - - +
61B GLU* 1.3 59.0 + - - +
63B ILE* 3.3 10.4 + - - +
64B PHE* 2.9 26.3 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.6 19.0 - - + +
61A GLU* 2.7 39.0 - - - +
64A PHE* 3.0 52.0 - - + -
73A GLY* 3.7 12.8 - - - +
41B ILE* 3.8 10.6 - - + +
57B GLN 2.9 20.4 + - - +
60B GLU* 1.3 74.4 - - - +
62B LYS* 1.3 60.9 + - - +
64B PHE* 3.2 2.6 + - - -
65B THR* 2.9 35.0 + - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS 3.5 24.5 - - - +
72A ASP* 3.8 10.2 - - + +
73A GLY* 3.6 10.5 - - - +
58B ASP 2.9 21.0 + - - +
59B ALA* 3.1 5.6 + - - +
61B GLU* 1.3 74.2 - - - +
63B ILE* 1.3 62.8 + - - +
65B THR* 3.1 6.6 + - - -
66B THR* 2.8 39.4 + - - +
155B PRO* 3.1 34.4 + - + +
156B VAL* 4.6 0.4 - - - +
157B THR* 4.2 9.5 - - - +
161B GLU* 3.0 35.2 + - - -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.7 13.5 - - + -
48B LEU* 5.2 4.9 - - + -
55B LEU* 3.9 17.3 - - + -
59B ALA 2.9 14.0 + - - +
60B GLU* 3.3 10.1 - - - +
62B LYS* 1.3 77.5 - - - +
64B PHE* 1.3 58.9 + - - +
66B THR* 3.7 1.7 - - - -
67B GLY* 2.9 27.0 + - - -
75B LEU* 5.1 7.0 - - + +
80B PHE* 6.0 4.9 - - + -
83B TYR* 3.4 49.1 - - + +
153B PHE* 3.5 36.1 - - + +
155B PRO* 3.8 6.7 - - + -
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Residues in contact with PHE 64 (chain B).
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 38.6 - - + +
65A THR* 4.1 3.6 - - + -
39B VAL 3.3 28.0 - - - -
40B ASP 3.5 3.6 - - - -
41B ILE* 3.4 30.7 - - + -
44B LEU* 3.8 17.5 - - + -
60B GLU 2.9 15.0 + - - +
61B GLU* 3.2 7.1 + - - +
63B ILE* 1.3 78.1 - - - +
65B THR* 1.3 56.7 + - - +
67B GLY 3.2 0.9 + - - -
68B ASP* 2.8 29.8 + - + +
73B GLY* 3.6 25.4 - - - -
74B LYS 3.9 2.9 - - - -
75B LEU* 3.7 29.9 - - + +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.9 6.7 - - + -
65A THR* 3.7 32.1 - - + -
68A ASP* 3.2 28.3 + - + +
71A LYS* 3.3 29.7 - - - +
61B GLU* 2.9 38.2 + - + +
62B LYS* 3.1 11.4 + - - -
64B PHE* 1.3 73.6 - - - +
66B THR* 1.3 67.0 + - - +
68B ASP* 3.7 5.7 + - - +
71B LYS* 4.0 8.8 + - - -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS* 3.8 25.4 + - + +
62B LYS* 2.8 30.5 + - - +
63B ILE 3.7 3.1 - - - -
65B THR* 1.3 78.6 + - - +
67B GLY* 1.3 61.2 + - - +
69B VAL* 4.3 12.0 + - - +
71B LYS* 5.4 0.5 + - - -
83B TYR* 3.7 27.3 - - + -
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE 2.9 16.4 + - - -
64B PHE 3.7 0.7 - - - -
66B THR* 1.3 78.0 - - - +
68B ASP* 1.3 57.6 + - - +
69B VAL* 2.8 15.8 + - - +
75B LEU* 3.4 14.1 - - - -
79B GLU* 3.3 25.2 - - - +
83B TYR* 4.3 20.4 - - - -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 3.1 26.4 + - + +
64B PHE* 2.8 20.0 + - + +
65B THR 3.7 1.5 + - - +
66B THR 3.4 1.0 - - - -
67B GLY* 1.3 71.6 - - - +
69B VAL* 1.3 54.1 + - - +
70B ASN* 2.9 6.8 - - - +
71B LYS* 2.5 34.3 + - - -
72B ASP* 2.8 8.0 + - - +
73B GLY* 2.7 29.1 + - - -
74B LYS 3.7 5.2 - - - -
75B LEU* 3.4 9.1 - - + +
79B GLU* 3.8 1.6 - - - -
1002B CA 2.4 30.1 - - - -
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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