Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 2FX0
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 GLY 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.7 4.5 - - - -
45A SER* 3.0 25.4 + - - +
48A PHE* 3.3 2.0 - - - +
49A ASN* 1.3 78.8 - - - +
51A LYS* 1.3 65.9 + - - -
52A GLU 3.3 3.0 + - - -
53A ASN 3.4 2.3 + - - -
54A LEU* 3.0 23.6 + - - +
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Residues in contact with LYS 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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20A PHE* 4.1 15.7 - - + -
25A TYR* 2.8 53.2 + - + +
26A GLU* 4.0 9.5 + - - +
28A THR 2.9 26.3 + - - +
29A SER* 5.0 1.1 - - - +
30A ILE* 4.3 33.4 - - + +
33A ILE* 5.7 0.7 - - + -
50A GLY* 1.3 71.6 - - - -
52A GLU* 1.3 57.0 + - - +
54A LEU* 3.4 8.3 + - - +
55A TYR* 3.0 26.7 + - - +
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Residues in contact with GLU 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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25A TYR* 3.3 28.6 + - + +
50A GLY 3.3 1.0 - - - -
51A LYS* 1.3 78.5 - - - +
53A ASN* 1.3 63.7 + - - +
55A TYR* 3.3 5.0 + - - +
56A TYR* 2.4 64.5 + - + +
114A ARG* 4.3 8.0 - - - +
117A LYS* 3.3 16.1 + - - -
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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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48A PHE 3.0 21.3 - - - +
49A ASN* 3.1 34.9 + - - +
50A GLY 3.4 2.0 + - - -
52A GLU* 1.3 75.0 - - - +
54A LEU* 1.3 65.0 + - - +
56A TYR* 3.1 24.1 + - - +
57A GLU* 2.9 30.4 + - + +
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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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12A ILE* 3.9 13.9 - - + -
13A LEU* 3.8 21.5 - - + -
16A ALA* 3.9 15.9 - - + -
20A PHE* 4.4 4.0 - - + -
30A ILE* 3.6 27.4 - - + -
33A ILE* 4.0 30.5 - - + -
48A PHE* 3.8 32.6 + - + -
50A GLY 3.0 13.6 + - - +
51A LYS* 3.5 9.2 - - - +
53A ASN* 1.3 76.9 - - - +
55A TYR* 1.3 61.4 + - - +
57A GLU* 3.1 5.4 + - - +
58A VAL* 3.1 18.9 + - - +
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Residues in contact with TYR 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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20A PHE* 3.6 40.4 - + + -
25A TYR* 3.4 33.7 + + + +
51A LYS 3.0 14.0 + - - +
52A GLU 3.3 9.2 - - - +
53A ASN 3.2 0.2 - - - -
54A LEU* 1.3 77.6 - - - +
56A TYR* 1.3 71.3 + + - +
58A VAL* 3.1 19.8 + - + +
59A PHE* 3.3 35.2 - + - -
103A LEU* 3.7 23.4 - - + +
106A GLU* 4.9 2.3 - - - +
107A GLU* 2.8 41.7 + - - +
114A ARG* 3.8 17.0 - - - -
118A ILE* 4.5 4.0 - - + -
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Residues in contact with TYR 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 GLU* 2.4 53.9 + - + +
53A ASN* 3.1 26.3 + - - +
55A TYR* 1.3 84.6 - + - +
57A GLU* 1.3 60.0 + - - +
59A PHE* 3.2 6.1 + - - +
60A LYS* 2.9 28.8 + - - +
114A ARG* 3.4 29.4 - - + +
117A LYS* 3.5 41.9 + - + +
118A ILE* 3.5 25.4 - - + -
121A TYR* 4.9 7.2 - - + -
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Residues in contact with GLU 57 (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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9A MSE 5.9 3.1 - - + +
13A LEU* 3.7 20.7 - - + +
48A PHE* 3.9 22.7 - - + +
53A ASN* 2.9 20.5 + - + +
54A LEU 3.1 10.1 + - - +
56A TYR* 1.3 76.7 - - - +
58A VAL* 1.3 59.0 + - - +
60A LYS* 3.1 43.7 + - - +
61A LYS* 2.9 32.7 + - - +
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Residues in contact with VAL 58 (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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13A LEU* 3.8 12.8 - - + +
16A ALA* 3.8 28.7 - - + -
17A LYS* 4.0 22.9 - - + +
20A PHE* 4.2 11.4 - - + -
54A LEU 3.1 13.8 + - - +
55A TYR* 3.1 10.4 + - + +
57A GLU* 1.3 76.3 - - - +
59A PHE* 1.3 60.5 + - + +
61A LYS 3.3 0.3 + - - -
62A TYR* 2.9 48.3 + - + +
103A LEU* 4.7 16.6 - - + -
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Residues in contact with PHE 59 (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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55A TYR* 3.3 50.9 - + - -
56A TYR 3.2 7.4 + - - +
58A VAL* 1.3 78.2 - - + +
60A LYS* 1.3 59.1 + - - +
63A GLY* 2.8 36.7 + - - +
66A ASN* 5.1 0.5 + - - -
103A LEU* 3.9 42.4 - - + -
104A ALA* 5.7 1.1 - - - -
107A GLU* 4.3 7.4 - - + -
108A ILE* 6.4 0.4 - - + -
118A ILE* 3.9 30.5 - - + -
121A TYR* 4.2 24.3 - - + +
122A PHE* 4.8 16.4 - + + -
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Residues in contact with LYS 60 (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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56A TYR 2.9 17.1 + - - +
57A GLU* 3.1 40.4 + - - +
58A VAL 3.3 0.4 - - - -
59A PHE* 1.3 76.1 - - - +
61A LYS* 1.3 57.9 + - - +
66A ASN* 3.6 17.4 + - - -
121A TYR* 3.8 39.2 - - + +
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Residues in contact with LYS 61 (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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10A GLU* 5.0 22.4 + - + +
13A LEU* 4.4 17.9 - - + -
57A GLU* 2.9 17.9 + - - +
58A VAL 4.0 1.6 - - - +
60A LYS* 1.3 80.1 - - - +
62A TYR* 1.3 95.8 + - + +
63A GLY 3.6 3.4 - - - +
66A ASN* 5.2 1.6 + - - -
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Residues in contact with TYR 62 (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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10A GLU 4.6 1.9 + - - -
13A LEU* 3.9 24.3 - - + +
14A LYS* 3.3 29.9 + - - +
17A LYS* 3.7 44.6 - - + +
58A VAL* 2.9 33.2 + - + +
59A PHE* 5.1 0.2 - - - -
61A LYS* 1.3 109.2 - - + +
63A GLY* 1.3 66.0 + - - +
64A LEU* 3.5 3.8 + - - +
93A HIS* 4.5 15.2 + - - -
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Residues in contact with GLY 63 (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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59A PHE* 2.8 26.8 + - - +
61A LYS 3.6 1.9 - - - +
62A TYR* 1.3 79.0 + - - +
64A LEU* 1.3 60.5 + - - -
65A ALA 3.5 2.2 - - - -
66A ASN* 3.0 25.7 + - - +
121A TYR* 4.3 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