Contacts of the helix formed by residues 45 - 52 (chain C) in PDB entry 6B0Z
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 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C GLN 3.6 3.4 + - - -
15C GLY 3.9 10.1 - - - -
16C ASP* 3.2 12.8 - - - -
43C ASP* 2.8 17.0 + - - -
44C LEU* 1.3 77.7 - - - +
46C ILE* 1.3 61.1 + - - -
47C GLU* 3.1 12.3 - - - -
48C ASN* 2.9 7.8 + - - -
49C ARG* 2.8 23.6 + - - +
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ASP* 2.9 15.7 + - - +
45C GLY* 1.3 71.4 - - - -
47C GLU* 1.3 66.2 + - - +
49C ARG* 3.3 31.2 - - + +
50C ASP* 2.9 28.8 + - - +
76C ILE* 4.0 26.5 - - + -
78C PRO* 4.5 14.6 - - + -
82C ARG* 4.9 1.6 - - + -
86C PHE* 3.9 36.8 - - + -
88C LEU* 3.6 37.8 - - + +
92C TRP* 5.1 3.4 - - + -
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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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16C ASP* 4.3 4.9 - - - +
20C ARG* 5.9 0.9 + - - -
43C ASP* 5.1 2.6 - - - +
45C GLY* 3.5 17.1 - - - -
46C ILE* 1.3 90.3 - - + +
48C ASN* 1.3 56.3 + - - +
50C ASP* 3.2 6.7 + - - +
51C ALA* 2.8 32.2 + - - +
86C PHE* 4.5 16.7 - - + -
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Residues in contact with ASN 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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43C ASP* 2.8 49.4 + - - +
45C GLY 2.9 8.6 + - - +
47C GLU* 1.3 77.6 + - - +
49C ARG* 1.3 50.4 + - - +
51C ALA* 3.9 8.1 - - - +
52C THR* 2.6 46.4 + - - +
56C VAL* 3.4 17.9 - - - +
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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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16C ASP* 2.4 36.4 + - - -
44C LEU* 2.4 33.1 + - - +
45C GLY 2.8 10.0 + - - +
46C ILE* 3.3 33.1 - - + +
47C GLU 3.2 0.2 - - - -
48C ASN* 1.3 75.7 - - - +
50C ASP* 1.3 60.4 + - - +
52C THR* 4.0 3.4 - - - -
53C ASN 3.0 5.2 + - - -
54C ASP* 2.4 55.8 + - - +
56C VAL* 4.1 5.2 - - + -
57C THR* 3.9 9.0 - - - +
75C THR* 3.8 1.7 - - - -
76C ILE* 2.7 33.1 + - - +
78C PRO* 4.6 8.1 - - - +
92C TRP* 4.3 6.8 - - + +
93C LYS 5.0 0.4 + - - -
95C PRO* 3.3 29.8 - - - +
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Residues in contact with ASP 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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46C ILE 2.9 17.7 + - - +
47C GLU* 3.5 5.4 - - - +
49C ARG* 1.3 77.2 - - - +
51C ALA* 1.3 58.7 + - - +
53C ASN* 2.9 27.4 + - - +
86C PHE 4.9 2.4 - - - +
87C LYS 4.2 1.6 - - - +
88C LEU* 3.5 22.5 - - + +
89C LYS* 3.0 55.3 + - - +
92C TRP* 3.2 22.0 + - - +
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Residues in contact with ALA 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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47C GLU 2.8 21.9 + - - +
48C ASN* 4.4 7.0 - - - +
50C ASP* 1.3 73.8 - - - +
52C THR* 1.3 62.2 + - + +
53C ASN* 3.5 4.0 + - - -
89C LYS* 5.6 4.5 - - - +
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Residues in contact with THR 52 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ASN* 2.6 42.0 + - - +
50C ASP 3.1 0.2 - - - -
51C ALA* 1.3 81.7 - - + +
53C ASN* 1.3 71.3 + - - +
54C ASP 3.7 1.2 + - - -
55C GLN* 3.0 21.6 + - - +
56C VAL* 3.3 28.8 + - + +
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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