Contacts of the helix formed by residues 40 - 51 (chain C) 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 ASP 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C ASN* 5.5 2.1 + - - -
36C ASP* 5.5 0.7 - - - +
38C VAL 4.1 1.0 - - - -
39C VAL* 1.3 78.1 - - - +
41C ILE* 1.3 61.0 + - + +
42C GLY* 3.5 5.2 + - - +
43C GLU* 2.9 52.0 + - - +
44C LEU* 2.9 23.7 + - - +
64C PHE* 3.5 8.1 - - - -
73C GLY 4.3 3.8 - - - +
74C LYS* 3.4 33.7 + - + +
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Residues in contact with ILE 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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40C ASP* 1.3 74.8 - - + +
42C GLY* 1.3 67.2 + - - +
44C LEU* 3.2 14.0 + - + -
45C GLN* 2.9 44.5 + - + +
57C GLN 5.8 0.2 - - - +
60C GLU* 4.3 11.9 - - + +
61C GLU* 4.6 6.3 - - + -
64C PHE* 3.3 40.9 - - + -
73C GLY 4.7 2.2 + - - +
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Residues in contact with GLY 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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40C ASP* 3.3 5.6 + - - -
41C ILE* 1.3 84.6 - - - +
43C GLU* 1.3 57.8 + - - +
45C GLN* 3.0 13.0 + - - +
46C GLU* 2.9 42.0 + - - +
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Residues in contact with GLU 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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31C LEU* 3.7 17.7 - - - +
32C ASP* 3.8 0.6 - - - +
33C ARG* 4.0 16.8 - - + +
34C ASN* 2.8 27.4 + - - +
38C VAL 3.1 3.3 - - - +
39C VAL* 3.2 6.9 - - + -
40C ASP* 2.9 43.2 + - - +
42C GLY* 1.3 74.8 - - - +
44C LEU* 1.3 58.8 + - - +
46C GLU* 4.7 4.7 - - - -
47C GLY* 2.9 27.4 + - - +
1001C CA 2.3 31.8 - - - -
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Residues in contact with LEU 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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31C LEU* 3.7 27.1 - - + -
39C VAL* 3.8 9.8 - - + +
40C ASP 2.9 13.2 + - - +
41C ILE* 3.5 14.6 - - + +
42C GLY 3.1 0.2 - - - -
43C GLU* 1.3 76.8 - - - +
45C GLN* 1.3 57.5 + - - +
48C LEU* 2.9 58.5 + - + +
60C GLU* 3.9 29.8 - - + +
63C ILE* 4.5 15.5 - - + -
64C PHE* 3.9 20.4 - - + -
75C LEU* 5.1 5.8 - - + -
80C PHE* 5.2 5.2 - - + -
153C PHE* 5.8 2.2 - - + -
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Residues in contact with GLN 45 (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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41C ILE* 2.9 34.5 + - + +
42C GLY* 3.5 11.5 - - - +
44C LEU* 1.3 76.9 - - - +
46C GLU* 1.3 72.2 + - + +
48C LEU* 3.3 2.5 + - - +
49C ARG* 2.9 24.9 + - - +
57C GLN* 4.9 5.7 + - - +
60C GLU* 2.7 44.1 + - + +
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Residues in contact with GLU 46 (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 ARG* 6.5 0.7 - - - -
42C GLY* 2.9 26.1 + - - +
43C GLU* 4.6 3.1 - - - +
45C GLN* 1.3 79.2 - - - +
47C GLY* 1.3 57.0 + - - +
49C ARG* 3.3 17.0 + - - +
50C ASN* 2.9 44.7 + - - +
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Residues in contact with GLY 47 (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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30C ALA 5.3 2.5 - - - -
31C LEU* 3.8 21.1 - - - -
43C GLU 2.9 21.4 + - - -
46C GLU* 1.3 77.5 - - - +
48C LEU* 1.3 56.1 + - - +
50C ASN* 3.0 8.0 + - - +
51C LEU* 2.9 32.6 + - - +
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Residues in contact with LEU 48 (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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31C LEU* 3.9 11.6 - - + +
44C LEU* 2.9 45.3 + - + +
45C GLN* 3.8 3.1 - - - +
47C GLY* 1.3 75.3 - - - +
49C ARG* 1.3 59.3 + - - +
51C LEU* 3.5 3.3 + - + +
52C GLY 3.3 2.6 + - - -
53C ILE* 2.9 68.2 + - + +
55C LEU* 3.6 35.0 - - + -
60C GLU* 5.0 6.7 - - + +
63C ILE* 5.2 0.9 - - + -
153C PHE* 3.9 26.0 - - + -
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Residues in contact with ARG 49 (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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45C GLN 2.9 17.1 + - - +
46C GLU* 3.6 16.6 + - - +
47C GLY 3.1 0.2 - - - -
48C LEU* 1.3 76.7 - - - +
50C ASN* 1.3 68.5 + - - +
52C GLY* 3.5 10.6 + - - -
53C ILE 4.6 3.8 - - - +
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Residues in contact with ASN 50 (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 ARG* 5.7 5.5 - - - +
46C GLU* 2.9 29.9 + - - +
47C GLY* 3.0 6.8 + - - +
49C ARG* 1.3 84.7 - - - +
51C LEU* 1.3 64.4 + - + +
52C GLY 3.3 1.3 + - - -
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Residues in contact with LEU 51 (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 LEU* 4.2 14.1 - - + -
30C ALA* 3.8 28.3 - - + -
31C LEU* 3.8 22.2 - - + -
47C GLY* 2.9 19.5 + - - +
48C LEU* 3.5 3.1 + - + +
49C ARG 3.3 0.4 - - - -
50C ASN* 1.3 80.7 - - + +
52C GLY* 1.3 61.5 + - - +
53C ILE* 3.4 29.8 - - + +
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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