Contacts of the helix formed by residues 45 - 55 (chain C) in PDB entry 4JQ0
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 THR 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ASN 4.8 3.8 - - - +
44C PRO* 1.3 76.8 - - - +
46C GLU* 1.3 63.6 + - - +
47C ALA* 3.2 11.3 + - - +
48C GLU* 2.8 44.3 + - - +
49C LEU* 3.0 24.8 + - - +
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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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30C THR* 6.0 0.3 - - - +
45C THR* 1.3 74.4 - - - +
47C ALA* 1.3 57.8 + - - +
49C LEU* 3.3 11.4 + - - +
50C GLN* 2.9 30.8 + - - +
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Residues in contact with ALA 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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45C THR* 3.2 9.7 + - - +
46C GLU* 1.3 79.1 - - - +
48C GLU* 1.3 56.7 + - + +
50C GLN* 3.2 7.8 + - - +
51C ASP* 2.9 28.8 + - - +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASN 4.5 0.9 - - - +
44C PRO* 3.2 24.9 - - + +
45C THR* 2.8 40.0 + - + +
47C ALA* 1.3 76.1 - - + +
49C LEU* 1.3 58.9 + - - +
51C ASP* 3.5 7.8 + - - +
52C MET* 2.9 35.1 + - + +
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Residues in contact with LEU 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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30C THR* 3.3 33.4 - - - +
33C LEU* 4.0 22.2 - - + +
34C GLY* 3.6 16.2 - - - +
37C MET* 4.1 6.1 - - + -
44C PRO* 3.7 26.9 - - + +
45C THR 3.0 19.0 + - - +
46C GLU* 3.6 12.6 - - - +
47C ALA 3.2 0.2 - - - -
48C GLU* 1.3 74.8 - - - +
50C GLN* 1.3 59.8 + - - +
51C ASP 3.1 0.2 - - - -
52C MET* 3.1 21.7 + - - +
53C ILE* 2.9 34.4 + - - +
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Residues in contact with GLN 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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30C THR* 5.1 8.9 - - + +
46C GLU 2.9 17.6 + - - +
47C ALA* 3.7 6.3 - - - +
49C LEU* 1.3 76.7 - - - +
51C ASP* 1.3 57.4 + - - +
53C ILE* 3.9 5.5 - - - +
54C ASN* 2.8 44.9 + - - +
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Residues in contact with ASP 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 ALA 2.9 14.1 + - - +
48C GLU* 3.5 11.7 - - - +
50C GLN* 1.3 74.8 - - - +
52C MET* 1.3 65.4 + - + +
53C ILE 3.0 2.8 + - - -
54C ASN* 3.1 4.9 + - - +
55C GLU* 3.1 27.7 + - - +
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Residues in contact with MET 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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33C LEU* 4.0 23.6 - - + -
37C MET* 3.5 33.0 - - + +
42C GLN* 5.5 1.1 - - - +
44C PRO* 5.3 3.8 - - - -
48C GLU* 2.9 21.1 + - + +
49C LEU* 3.4 25.1 - - - +
51C ASP* 1.3 75.6 - - + +
53C ILE* 1.3 61.2 + - - +
55C GLU* 5.0 0.8 - - - +
56C VAL* 3.4 25.1 - - - +
64C ILE* 6.1 1.0 - - - +
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Residues in contact with ILE 53 (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 5.2 0.9 - - - +
29C THR 4.8 0.9 - - - -
30C THR* 3.4 35.7 - - + +
33C LEU* 3.4 27.4 - - + -
49C LEU 2.9 10.3 + - - +
50C GLN* 3.9 4.7 - - - +
52C MET* 1.3 77.4 - - - +
54C ASN* 1.3 65.9 + - - +
56C VAL* 2.9 5.1 + - - +
57C ASP* 2.7 61.4 + - + +
62C GLY* 3.7 24.7 - - - +
63C THR 5.6 0.4 - - - +
64C ILE* 5.3 13.5 - - + -
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Residues in contact with ASN 54 (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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50C GLN* 2.8 37.4 + - - +
51C ASP* 3.1 5.2 + - - +
53C ILE* 1.3 84.6 - - - +
55C GLU* 1.3 62.5 + - - +
56C VAL 3.4 0.2 + - - -
57C ASP* 3.8 16.4 + - - +
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Residues in contact with GLU 55 (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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51C ASP 3.1 15.0 + - - +
52C MET* 5.0 0.9 - - - +
54C ASN* 1.3 77.6 - - - +
56C VAL* 1.3 66.3 + - + +
57C ASP 5.1 0.6 - - - +
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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