Contacts of the helix formed by residues 45 - 52 (chain C) in PDB entry 4Z0R
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 SER 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LYS* 4.3 2.9 - - - -
43C LEU 4.0 1.4 + - - -
44C LEU* 1.3 73.5 - - - +
46C SER* 1.3 59.6 + - - +
47C GLU* 3.6 8.7 + - - +
48C ASP* 3.0 31.8 + - - +
49C SER* 2.7 33.1 + - - -
63C ASN* 5.4 0.6 + - - -
64C THR* 4.5 2.7 + - - -
65C ASP* 5.9 5.9 - - - +
1002C UNX 3.6 13.0 - - - -
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Residues in contact with SER 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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30A TRP* 4.6 2.3 + - - -
78A ARG* 6.1 4.7 - - - -
26C VAL* 2.6 45.1 + - - +
27C ASN 3.9 9.4 - - - -
28C LYS* 3.5 21.7 - - - +
45C SER* 1.3 72.5 - - - +
47C GLU* 1.3 63.5 + - - +
49C SER 3.4 0.2 + - - -
50C ALA* 3.2 19.1 + - - +
1002C UNX 3.0 14.4 - - - -
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Residues in contact with GLU 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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37B ASN* 3.6 28.1 + - - +
45C SER* 3.6 8.7 + - - +
46C SER* 1.3 80.8 - - - +
48C ASP* 1.3 65.9 + - - +
50C ALA* 3.3 3.5 + - - +
51C LYS* 3.1 55.8 + - + +
64C THR* 6.0 1.9 - - - +
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Residues in contact with ASP 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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44C LEU* 3.9 23.2 - - + +
45C SER* 3.0 18.9 + - - +
47C GLU* 1.3 81.4 - - - +
49C SER* 1.3 57.6 + - - +
51C LYS* 3.8 15.9 + - - +
52C VAL* 3.0 32.2 + - - +
62C MET 5.2 3.6 - - - -
63C ASN* 3.7 7.5 - - - +
64C THR* 2.5 55.5 + - - +
65C ASP 4.2 0.5 + - - -
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Residues in contact with SER 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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71B CYS 4.2 0.2 - - - +
72B SER* 3.6 21.9 - - - +
26C VAL* 4.5 0.2 - - - -
27C ASN 3.2 21.0 + - - -
29C VAL* 3.1 36.3 + - - +
44C LEU* 3.3 15.3 - - - +
45C SER 2.7 23.1 + - - -
46C SER 3.8 2.0 - - - -
47C GLU 3.3 0.2 - - - -
48C ASP* 1.3 76.9 - - - +
50C ALA* 1.3 62.3 + - - +
52C VAL* 3.5 15.5 - - - +
54C HIS* 4.7 1.2 + - - -
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Residues in contact with ALA 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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35B ASN* 4.1 5.6 - - - +
37B ASN* 3.2 31.1 - - + +
38B CYS* 4.0 1.3 - - + +
40B LYS* 2.9 24.3 + - - -
71B CYS* 3.8 32.1 - - + -
26C VAL* 4.1 2.8 - - + +
46C SER 3.2 13.2 + - - +
47C GLU* 3.7 8.1 - - - +
48C ASP 3.2 0.2 - - - -
49C SER* 1.3 76.3 - - - +
51C LYS* 1.4 60.8 + - - +
52C VAL 3.7 0.7 + - - +
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Residues in contact with LYS 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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37B ASN* 3.3 41.3 + - + +
47C GLU* 3.1 42.7 + - + +
48C ASP* 3.2 15.1 + - - +
50C ALA* 1.4 75.5 - - - +
52C VAL* 1.3 66.2 + - - +
53C ASP* 3.3 5.4 + - - +
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Residues in contact with VAL 52 (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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40B LYS* 4.5 3.6 + - - -
29C VAL* 5.3 2.9 - - + -
31C VAL* 4.8 11.4 - - + -
44C LEU* 4.4 11.7 - - + -
48C ASP 3.0 13.9 + - - +
49C SER* 3.5 21.1 - - - +
50C ALA 3.5 5.1 - - - +
51C LYS* 1.3 77.9 - - - +
53C ASP* 1.3 69.0 + - - +
54C HIS* 3.4 40.0 + - + +
58C TRP* 3.5 37.5 - - + +
62C MET* 5.7 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