Contacts of the helix formed by residues 44 - 54 (chain A) in PDB entry 2JG0
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 LEU 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO* 2.8 29.9 + - + +
43A LEU* 1.3 84.3 - - + +
45A GLY* 1.3 68.2 + - - +
47A LEU* 3.0 22.5 + - + +
48A PHE* 3.0 12.5 + - + +
63A PHE* 4.6 13.0 - - + +
66A ALA* 5.5 3.8 - - + +
68A PRO* 4.3 14.1 - - + -
72A PRO* 4.0 26.5 - - + +
75A ILE* 5.1 2.2 - - + -
76A LEU* 3.3 19.1 - - + +
98A PHE* 3.8 38.8 - - + -
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Residues in contact with GLY 45 (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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41A ASP 3.2 21.5 + - - +
42A ILE* 3.3 9.4 + - - -
43A LEU 3.9 0.2 + - - -
44A LEU* 1.3 76.0 - - - +
46A PRO* 1.3 73.3 - - - +
48A PHE* 3.0 11.3 + - - +
49A ASN* 3.2 11.1 + - - +
76A LEU* 4.6 1.5 - - - +
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Residues in contact with PRO 46 (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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44A LEU 3.9 1.8 - - - +
45A GLY* 1.3 81.7 - - - +
47A LEU* 1.3 58.2 + - - +
49A ASN* 3.4 7.6 + - + +
50A ASP* 2.9 43.2 + - - +
76A LEU* 4.3 15.9 - - + -
79A TYR* 5.0 8.5 - - + -
83A GLN* 6.1 1.8 - - - +
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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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44A LEU* 3.0 13.7 + - + +
46A PRO* 1.3 83.3 - - - +
48A PHE* 1.3 64.3 + - - +
50A ASP* 3.2 0.6 + - - +
51A VAL* 2.9 46.9 + - + +
63A PHE* 5.1 1.6 - - + -
75A ILE* 3.6 30.7 - - + -
76A LEU* 3.7 14.1 - - + -
79A TYR* 3.7 43.5 - - + -
90A LEU* 4.0 7.0 - - + -
93A PHE* 3.9 13.0 - - + -
94A VAL* 5.1 0.9 - - + -
98A PHE* 3.8 20.4 - - + -
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Residues in contact with PHE 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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40A PRO* 3.6 40.4 - - + +
41A ASP* 3.5 20.0 - - + -
44A LEU* 3.0 13.0 + - + +
45A GLY 3.0 9.2 + - - +
47A LEU* 1.3 78.0 - - - +
49A ASN* 1.3 66.8 + - - +
51A VAL* 3.8 1.0 - - - +
52A GLN* 3.0 46.1 + - + +
63A PHE* 3.7 34.8 - + - -
64A ALA* 4.0 11.9 - - - -
278A PRO* 3.4 44.2 - - + -
281A TRP* 3.9 13.0 - + - -
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Residues in contact with ASN 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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45A GLY 3.2 8.0 + - - +
46A PRO* 3.7 9.5 + - + +
48A PHE* 1.3 79.0 - - - +
50A ASP* 1.3 78.6 + - - +
52A GLN* 3.4 0.3 + - - +
53A ASN* 2.8 53.7 + - - +
281A TRP* 3.0 44.7 + - + +
285A ILE* 4.6 3.1 - - - +
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Residues in contact with ASP 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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46A PRO* 2.9 28.5 + - - +
47A LEU 3.2 3.6 + - - +
49A ASN* 1.3 95.4 + - - +
51A VAL* 1.3 56.8 + - - +
53A ASN* 3.8 3.6 - - - +
54A ALA* 3.0 30.1 + - - +
79A TYR* 2.5 36.5 + - + +
83A GLN* 3.9 7.6 + - - -
90A LEU* 3.8 8.8 - - + +
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Residues in contact with VAL 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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47A LEU* 2.9 35.6 + - + +
50A ASP* 1.3 72.4 - - - +
52A GLN* 1.3 68.4 + - - +
54A ALA* 3.4 9.7 + - - +
55A LYS* 3.4 6.9 + - - -
56A LEU* 3.9 21.8 + - + -
57A PHE* 4.1 8.6 - - + -
63A PHE* 3.6 48.7 - - + -
90A LEU* 4.0 12.6 - - + -
94A VAL* 3.6 24.0 - - + -
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Residues in contact with GLN 52 (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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48A PHE* 3.0 46.6 + - + +
51A VAL* 1.3 78.3 - - - +
53A ASN* 1.3 58.4 + - - +
55A LYS 2.9 18.4 + - - -
57A PHE* 5.3 2.1 - - - +
59A ASP 5.2 0.5 - - - +
60A GLN* 2.8 68.9 + - - +
63A PHE* 3.4 23.9 - - + +
64A ALA 4.2 1.4 - - - +
278A PRO 2.9 21.4 + - - -
281A TRP* 3.5 17.3 - - + -
282A VAL* 3.3 5.4 - - - +
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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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49A ASN* 2.8 46.3 + - - +
50A ASP* 4.0 4.2 - - - +
52A GLN* 1.3 76.6 - - - +
54A ALA* 1.3 61.1 + - - +
55A LYS* 3.1 13.7 + - - +
281A TRP* 3.3 21.0 + - - -
282A VAL* 3.7 12.1 - - - +
285A ILE* 4.1 8.5 - - - +
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Residues in contact with ALA 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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50A ASP 3.0 18.0 + - - +
51A VAL 3.6 6.7 - - - +
52A GLN 3.1 0.6 - - - -
53A ASN* 1.3 75.0 - - - +
55A LYS* 1.3 69.6 + - - +
56A LEU* 3.2 23.4 + - + +
90A LEU* 3.9 13.5 - - + -
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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