Contacts of the helix formed by residues 46 - 55 (chain A) in PDB entry 2JPO
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP* 1.3 84.4 + - - +
47A LEU* 1.3 73.2 + - + +
48A ALA 3.2 2.7 - - - -
49A GLY* 3.1 13.7 + - - -
50A CYS* 3.1 18.7 + - - -
108A CYS* 3.5 6.5 - - + +
109A MET* 3.2 29.4 - - + -
112A ILE* 3.6 6.5 - - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER 5.6 0.9 - - - +
25A LEU* 3.3 26.1 - - + +
26A PRO* 3.8 28.7 - - + -
29A VAL* 3.8 17.9 - - + -
45A ASP* 3.0 16.0 + - - +
46A ARG* 1.3 83.7 - - + +
48A ALA* 1.3 56.2 + - - +
50A CYS* 3.1 21.0 + - + +
51A ALA 2.9 23.9 + - - -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.6 8.2 - - + +
32A ASP* 3.6 18.4 - - - +
33A LEU* 3.4 26.4 - - + +
43A MET* 3.4 30.3 - - + -
45A ASP* 4.7 4.3 - - + +
46A ARG* 3.2 1.8 - - - +
47A LEU* 1.3 76.8 - - - +
49A GLY* 1.3 57.3 + - - +
51A ALA* 3.1 5.7 + - - +
52A ILE* 2.9 28.9 + - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 4.3 0.2 - - - +
46A ARG 3.1 6.2 + - - -
48A ALA* 1.3 77.2 - - - +
50A CYS* 1.3 55.9 + - - +
52A ILE* 3.2 6.5 + - - +
53A ASN* 3.0 28.1 + - - -
108A CYS* 3.7 13.0 - - - -
111A THR* 3.7 12.0 - - - +
112A ILE* 3.5 29.9 - - - +
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.5 15.9 - - + +
25A LEU* 5.0 0.7 - - + -
46A ARG* 3.1 17.6 + - - -
47A LEU* 3.1 30.6 + - + +
49A GLY* 1.3 72.9 - - - +
51A ALA* 1.3 63.8 + - - +
53A ASN* 3.5 9.1 - - - +
54A CYS* 3.2 21.8 + - - +
108A CYS* 2.0 50.0 - - - -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 4.0 12.3 - - + -
19A CYS* 4.6 2.9 - - + -
23A LEU* 4.5 1.3 - - - -
25A LEU* 3.1 27.9 - - + +
33A LEU* 3.5 20.4 - - + -
47A LEU 2.9 6.7 + - - -
48A ALA 3.1 9.6 + - - +
50A CYS* 1.3 72.5 - - - +
52A ILE* 1.3 60.2 + - - +
54A CYS* 3.0 8.1 + - - +
55A LEU* 2.8 36.1 + - + +
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Residues in contact with ILE 52 (chain A).
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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33A LEU* 4.4 10.1 - - + -
37A TRP* 4.0 26.7 - - + -
43A MET* 3.9 28.0 - - + -
48A ALA 2.9 14.1 + - - +
49A GLY* 3.2 8.3 + - - +
51A ALA* 1.3 74.0 - - - +
53A ASN* 1.3 62.2 + - - +
54A CYS 3.1 0.7 + - - -
55A LEU* 3.1 12.0 + - - +
56A ALA* 3.0 20.7 + - - +
111A THR* 3.3 26.5 - - + +
112A ILE* 5.3 0.4 - - + -
115A ALA* 4.3 13.0 - - + -
138A VAL* 3.5 29.2 - - + -
139A LEU* 3.9 4.6 - - + +
142A VAL* 4.8 4.0 - - + -
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 5.4 1.0 - - - +
49A GLY 3.0 8.1 + - - +
50A CYS* 3.5 21.9 - - - +
52A ILE* 1.3 75.4 - - - +
54A CYS* 1.3 61.2 + - - +
56A ALA* 3.4 4.5 - - - +
57A THR* 3.3 22.2 + - - -
107A LYS* 2.7 57.3 + - + +
108A CYS* 3.8 4.8 - - - -
111A THR* 4.3 0.6 - - - +
142A VAL* 3.6 27.3 - - + +
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Residues in contact with CYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 4.8 0.2 - - - -
19A CYS* 2.0 52.9 - - + -
22A GLU* 5.1 3.4 - - - -
23A LEU* 3.7 19.1 - - + -
50A CYS 3.2 11.1 + - - +
51A ALA 3.0 6.8 + - - +
53A ASN* 1.3 79.5 + - - +
55A LEU* 1.3 63.8 + - - +
56A ALA 3.0 1.1 - - - -
57A THR* 2.9 30.5 + - - +
58A LYS* 3.3 18.6 + - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.1 17.7 - - + +
15A ALA* 3.4 31.6 - - + -
16A MET* 3.4 31.2 - - + +
19A CYS* 3.4 11.5 - - - -
33A LEU* 4.9 7.0 - - + -
51A ALA* 2.8 40.9 + - + +
52A ILE* 3.5 8.7 - - - +
54A CYS* 1.3 71.0 - - - +
56A ALA* 1.3 55.3 + - - +
58A LYS* 3.0 27.9 + - - +
59A LEU* 3.6 2.6 + - - +
62A VAL* 3.7 14.6 - - + +
135A ILE* 5.4 2.0 - - + -
139A LEU* 3.6 21.3 - - + -
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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