Contacts of the helix formed by residues 46 - 56 (chain A) in PDB entry 5J3V
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 PHE 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.8 32.5 - - + -
37A LEU* 3.9 33.0 - - + -
40A LEU* 3.2 48.9 - - + +
41A ASN* 3.8 11.4 - - - -
43A TYR* 3.5 17.2 + - + +
44A PRO 3.6 0.4 - - - -
45A ASP* 1.3 74.2 - - - +
47A ASN* 1.3 64.6 + - - +
48A ASN 3.0 4.5 - - - -
49A TYR* 3.2 23.2 + + - +
50A LEU* 3.8 27.3 + - + +
71A ILE* 5.3 1.3 - - + -
75A ASN* 3.8 23.6 - - - -
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Residues in contact with ASN 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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41A ASN* 3.4 24.0 + - - -
43A TYR 4.9 2.6 + - - -
44A PRO 5.3 3.0 + - - -
45A ASP* 3.4 0.6 - - - +
46A PHE* 1.3 77.7 - - - +
48A ASN* 1.3 63.5 + - - +
49A TYR 3.1 1.5 + - - -
50A LEU* 3.5 17.4 + - - +
51A ILE* 3.5 15.8 + - - +
72A LEU* 3.3 22.2 - - + +
75A ASN* 3.3 32.4 + - - +
83A PHE* 3.5 30.6 - - + -
87A VAL* 4.3 9.6 - - + +
91A ILE* 4.4 2.4 - - + +
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Residues in contact with ASN 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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8A ASP* 4.6 12.8 - - - +
45A ASP* 3.3 31.9 + - + +
46A PHE 3.0 0.2 - - - -
47A ASN* 1.3 79.4 - - - +
49A TYR* 1.3 67.9 + - - +
51A ILE* 3.5 12.6 - - - +
52A PHE* 3.3 17.0 - - - +
87A VAL* 4.4 14.2 - - + +
90A PHE* 3.3 32.1 - - + -
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Residues in contact with TYR 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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8A ASP* 3.4 44.9 + - + +
11A GLY* 5.1 5.4 - - - -
12A LEU* 4.0 33.0 - - + -
15A ILE* 3.6 34.3 - - + -
45A ASP* 3.2 34.7 + - - -
46A PHE* 3.2 15.2 + - - +
47A ASN 3.1 0.2 - - - -
48A ASN* 1.3 85.2 - - - +
50A LEU* 1.3 60.6 + - + +
51A ILE 3.3 0.4 - - - -
52A PHE* 3.0 6.3 + - - +
53A VAL* 2.9 38.6 + - + +
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Residues in contact with LEU 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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15A ILE* 4.7 12.6 - - + -
19A LEU* 5.1 5.8 - - + -
37A LEU* 6.2 0.7 - - + -
46A PHE* 3.8 43.1 - - + +
47A ASN* 3.5 22.8 + - - +
49A TYR* 1.3 77.4 - - - +
51A ILE* 1.3 59.8 + - - +
53A VAL* 3.6 1.5 + - + -
54A LEU* 3.4 9.9 + - - +
68A SER* 3.3 51.5 + - - +
69A GLY* 4.2 0.3 + - - -
71A ILE* 4.0 10.3 - - + -
72A LEU* 3.7 34.1 - - + +
75A ASN* 3.9 4.9 - - - +
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Residues in contact with ILE 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 ASN 3.5 9.7 + - - +
48A ASN* 3.5 14.6 - - - +
50A LEU* 1.3 77.7 - - - +
52A PHE* 1.3 65.4 + - - +
54A LEU* 3.5 24.1 + - + -
55A THR* 3.0 37.9 + - + -
72A LEU* 3.8 15.8 - - + +
90A PHE* 3.9 24.2 - - + -
91A ILE* 4.0 22.7 - - + -
94A GLU* 3.8 21.8 - - + -
95A CYS* 4.0 23.6 - - - -
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Residues in contact with PHE 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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8A ASP* 4.9 14.1 - - - -
12A LEU* 3.6 34.5 - - + -
48A ASN* 3.3 16.4 - - - +
49A TYR* 3.0 12.7 + - - +
51A ILE* 1.3 81.1 - - - +
53A VAL* 1.3 65.9 + - + +
55A THR* 4.6 2.2 - - - -
56A LYS* 3.0 71.9 + - + -
57A LEU* 3.1 25.2 + - + -
90A PHE* 5.2 8.3 - + + -
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Residues in contact with VAL 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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12A LEU* 5.7 4.0 - - + -
15A ILE* 5.8 3.6 - - + -
16A LEU* 3.8 26.5 - - + -
19A LEU* 4.3 11.2 - - + -
49A TYR* 2.9 25.3 + - + +
50A LEU* 4.0 1.3 - - + +
51A ILE 3.4 0.2 - - - -
52A PHE* 1.3 81.7 - - + +
54A LEU* 1.3 61.6 + - - +
55A THR 3.6 0.2 + - - -
57A LEU* 3.5 34.0 - - + +
60A GLU* 4.7 4.0 - - - +
64A THR 4.5 1.3 - - - +
65A ARG* 3.4 28.5 - - + +
68A SER* 3.5 22.7 - - - +
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Residues in contact with LEU 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 LEU 3.4 14.5 + - - +
51A ILE* 3.8 16.8 - - + +
52A PHE 3.2 0.4 - - - -
53A VAL* 1.3 79.4 - - - +
55A THR* 1.3 61.6 + - + +
65A ARG* 3.1 55.4 + - - +
66A SER* 4.4 0.7 - - - -
68A SER* 3.8 0.8 + - - +
69A GLY* 4.0 9.0 - - - -
106A ILE* 3.9 22.1 - - + +
109A THR* 3.9 20.2 - - + -
110A VAL* 4.0 16.6 - - + -
113A LEU* 3.6 30.1 - - + -
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Residues in contact with THR 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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51A ILE* 3.0 29.2 + - + +
54A LEU* 1.3 96.3 - - + +
56A LYS* 1.3 67.8 + - - +
57A LEU 3.6 0.7 - - - -
58A LYS* 3.6 28.7 - - - +
65A ARG* 4.6 0.7 - - - +
94A GLU* 3.4 27.8 + - + +
95A CYS* 5.4 0.2 - - - -
98A ASN* 3.3 38.9 + - + +
106A ILE* 6.0 0.2 - - + -
110A VAL* 4.7 4.3 - - + -
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Residues in contact with LYS 56 (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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52A PHE* 3.0 49.9 + - + +
55A THR* 1.3 88.1 + - - +
57A LEU* 1.3 60.9 + - - +
58A LYS* 3.1 10.1 + - - +
90A PHE* 4.6 14.6 - - + -
94A GLU* 4.2 15.3 - - - +
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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