Contacts of the helix formed by residues 33 - 44 (chain C) in PDB entry 1ZZJ
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 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ILE* 3.2 32.4 - - - +
30C GLY 3.4 3.8 + - - -
31C LYS 3.1 2.2 + - - -
32C GLY* 1.3 75.9 - - - +
34C GLN* 1.3 56.6 + - - +
36C ILE* 3.4 7.9 - - - +
37C LYS* 3.2 26.9 + - - +
40C ARG* 4.9 1.4 + - - -
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Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE 3.3 0.6 + - - -
30C GLY* 5.5 0.2 - - - -
31C LYS 3.1 18.9 + - - +
32C GLY* 3.7 13.9 + - - +
33C GLY* 1.3 74.8 - - - +
35C ARG* 1.3 66.9 + - - +
37C LYS* 3.4 12.9 + - - +
38C GLN* 2.9 25.5 + - - +
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C SER 4.2 6.7 - - - +
28C ILE 3.3 17.0 - - - +
29C ILE 2.8 16.0 + - - +
30C GLY* 4.0 9.1 - - - +
34C GLN* 1.3 73.2 - - - +
36C ILE* 1.3 57.1 + - - +
38C GLN* 3.2 12.8 + - - +
39C ILE* 2.8 32.6 + - + +
80C SER* 4.4 7.9 - - - +
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 3.1 19.5 + - + +
29C ILE* 2.9 23.5 + - + +
33C GLY* 3.4 17.0 - - - +
35C ARG* 1.3 71.8 - - - +
37C LYS* 1.3 69.8 + - - +
39C ILE* 2.9 18.8 + - + -
40C ARG* 2.9 52.7 + - + +
47C ILE* 4.0 18.2 - - + +
49C ILE* 3.8 35.7 - - + +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLY 3.2 16.5 + - - +
34C GLN* 3.6 17.3 - - - +
36C ILE* 1.3 81.2 - - - +
38C GLN* 1.3 62.1 + - - +
40C ARG* 3.5 19.1 + - - +
41C HIS* 3.2 24.6 + - - +
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN 2.9 13.2 + - - +
35C ARG* 3.3 19.7 + - - +
37C LYS* 1.3 75.7 - - - +
39C ILE* 1.3 69.1 + - - +
41C HIS* 4.9 3.8 - - - -
42C GLU* 3.0 50.6 + - - +
76C LEU* 5.0 10.7 - - - +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE 4.2 8.7 - - - +
35C ARG 2.8 20.3 + - - +
36C ILE* 2.9 10.2 + - + +
38C GLN* 1.3 88.0 - - - +
40C ARG* 1.3 54.9 + - - +
43C SER* 3.0 32.4 + - - -
47C ILE* 3.3 22.7 - - + -
73C ALA* 4.2 8.7 - - - +
76C LEU* 3.6 42.1 - - + +
77C LEU* 3.9 20.9 - - + +
80C SER* 3.5 25.1 - - - +
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Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLY 4.9 1.0 + - - -
36C ILE* 2.9 51.2 + - + +
37C LYS* 3.9 18.3 - - - +
39C ILE* 1.3 76.6 - - - +
41C HIS* 1.3 56.4 + - - +
43C SER* 4.2 0.2 - - - -
44C GLY* 3.0 26.7 + - - -
45C ALA 3.5 17.8 - - - +
46C SER* 4.8 2.2 - - - +
47C ILE* 2.9 60.3 + - + +
48C LYS* 5.0 1.2 - - - +
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Residues in contact with HIS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LYS 3.2 16.8 + - - +
38C GLN* 4.2 4.3 - - - +
39C ILE 3.4 0.2 - - - -
40C ARG* 1.3 75.8 - - - +
42C GLU* 1.3 73.9 + - - +
44C GLY* 3.7 6.4 + - - -
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLN* 3.0 36.8 + - + +
41C HIS* 1.3 87.2 - - - +
43C SER* 1.3 61.4 + - - +
72C ASN* 4.0 8.5 - - - +
76C LEU* 3.4 29.2 - - + -
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Residues in contact with SER 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE 3.0 18.0 + - - -
40C ARG* 3.9 1.0 + - - -
42C GLU* 1.3 79.6 - - - +
44C GLY* 1.3 57.7 + - - +
45C ALA* 2.9 22.4 + - - +
47C ILE* 4.2 0.2 - - - +
69C GLN* 3.2 28.3 + - - +
72C ASN* 3.7 19.4 - - - +
73C ALA* 3.4 33.2 - - - +
76C LEU* 4.0 2.5 - - - -
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ARG 3.0 14.8 + - - -
41C HIS* 3.7 5.5 + - - -
42C GLU 3.3 3.0 + - - -
43C SER* 1.3 76.9 - - - +
45C ALA* 1.3 60.5 + - - +
46C SER 4.0 0.5 + - - -
64C THR 4.7 0.3 - - - +
69C GLN* 3.7 23.6 + - - +
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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