Contacts of the helix formed by residues 43 - 47 (chain C) in PDB entry 1JB0
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 ARG 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASP* 2.9 55.2 + - - +
24C VAL* 3.3 21.7 + - - +
25C LEU 3.9 10.9 + - - -
26C GLU* 3.3 26.1 + - - +
42C PRO* 1.3 104.8 - - + +
44C THR* 1.3 57.2 + - - +
45C GLU* 3.1 22.4 - - - +
46C ASP* 3.0 23.4 + - - +
61D LYS* 4.4 9.0 - - - +
94D ILE* 4.7 11.4 + - - -
97D LYS* 3.9 30.8 - - + +
102D PRO* 4.4 2.8 - - - +
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Residues in contact with THR 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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1C ALA* 3.9 14.2 - - - +
2C HIS 3.7 14.9 + - - +
3C THR* 5.2 0.2 - - - -
4C VAL* 3.9 25.1 - - + +
24C VAL* 3.8 7.4 - - + -
41C SER* 3.7 35.7 + - - +
42C PRO 3.7 1.8 - - - -
43C ARG* 1.3 71.3 - - - +
45C GLU* 1.3 59.6 + - - +
46C ASP 2.9 6.1 - - - -
47C CYS* 2.8 26.1 + - - +
113D ASN* 4.3 6.3 + - - +
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Residues in contact with GLU 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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1C ALA* 4.3 13.6 - - + +
42C PRO 4.1 4.6 - - - +
43C ARG* 3.5 33.1 - - - +
44C THR* 1.3 81.5 + - - +
46C ASP* 1.3 65.3 + - - +
47C CYS 5.2 1.1 - - - +
72C THR* 5.0 1.9 + - - -
74C ARG* 3.4 48.1 - - - +
75C SER 5.2 0.5 + - - -
84D ARG* 4.7 5.9 + - - +
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 3.0 27.1 + - - +
24C VAL* 3.7 4.3 - - + -
43C ARG* 3.0 17.3 + - - +
44C THR 2.9 0.8 - - - -
45C GLU* 1.3 93.1 - - - +
47C CYS* 1.3 61.4 + - - +
48C VAL* 3.4 4.9 + - - +
74C ARG* 3.6 20.8 + - - +
61D LYS* 2.9 43.5 + - + +
84D ARG* 2.7 26.8 + - - -
94D ILE* 5.4 0.7 - - - +
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Residues in contact with CYS 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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1C ALA* 6.0 0.2 - - - +
2C HIS* 3.4 29.6 + - + -
4C VAL* 3.8 18.8 - - - -
24C VAL* 3.5 18.3 - - + +
44C THR* 2.8 25.2 + - - +
45C GLU 3.4 1.2 - - - +
46C ASP* 1.3 77.4 - - - +
48C VAL* 1.3 57.7 + - - +
49C GLY* 3.5 11.4 - - - -
66C VAL* 4.6 0.9 - - - -
75C SER* 3.5 15.0 - - - -
3002C SF4 2.3 35.4 - - - -
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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