Contacts of the helix formed by residues 11 - 24 (chain A) in PDB entry 1FR2
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 THR 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 1.3 77.9 - - - +
12A GLU* 1.3 64.6 + - - +
13A ALA* 3.6 8.9 + - - +
14A GLU* 2.9 43.8 + - - +
15A PHE* 3.0 17.7 + - - +
83A PHE* 4.1 0.2 - - - -
84A LYS* 3.4 21.2 - - - +
85A GLN* 3.4 40.8 - - + +
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Residues in contact with GLU 12 (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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11A THR* 1.3 73.2 - - - +
13A ALA* 1.3 57.9 + - - +
15A PHE* 3.3 2.6 + - - +
16A LEU* 2.8 28.8 + - + +
68A VAL* 4.0 17.3 - - + +
72A LYS* 2.7 41.5 + - - +
83A PHE* 3.7 35.1 - - + +
84A LYS 4.3 1.2 + - - -
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Residues in contact with ALA 13 (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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11A THR* 3.2 8.1 + - - +
12A GLU* 1.3 80.7 - - - +
14A GLU* 1.3 57.9 - - + +
16A LEU* 3.3 12.5 + - + +
17A GLN* 3.0 26.9 + - - +
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Residues in contact with GLU 14 (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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3A LEU* 5.5 5.9 - - - +
9A ASP 3.8 6.8 - - - +
10A TYR* 3.6 23.9 - - + -
11A THR* 2.9 45.8 + - - +
13A ALA* 1.3 77.2 - - + +
15A PHE* 1.3 62.6 + - - +
17A GLN* 3.2 13.7 + - - +
18A LEU* 3.1 17.8 + - - +
84A LYS* 4.6 3.0 + - - -
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Residues in contact with PHE 15 (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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7A ILE* 4.7 5.2 - - + -
10A TYR* 3.6 20.5 - + + -
11A THR 3.0 8.9 + - - +
12A GLU 3.6 5.2 - - - +
14A GLU* 1.3 72.7 - - - +
16A LEU* 1.3 60.6 + - - +
18A LEU* 3.1 27.7 + - + +
19A VAL* 2.9 39.3 + - + +
40A PHE* 3.7 16.6 - + - -
43A MET* 4.4 17.9 - - + -
44A THR* 3.7 24.2 - - + -
68A VAL* 4.0 14.6 - - + -
71A VAL* 4.2 22.4 - - + -
83A PHE* 3.5 36.3 - + + -
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Residues in contact with LEU 16 (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 GLU* 2.8 17.9 + - + +
13A ALA* 3.5 11.4 - - - +
15A PHE* 1.3 77.6 - - - +
17A GLN* 1.3 56.9 + - - +
20A THR* 2.8 47.4 + - - +
64A PRO* 3.9 21.1 - - + -
65A SER* 4.0 11.7 - - - +
68A VAL* 3.8 28.4 - - + +
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Residues in contact with GLN 17 (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 ALA 3.0 13.8 + - - +
14A GLU* 3.3 15.9 - - - +
15A PHE 3.2 0.2 - - - -
16A LEU* 1.3 77.6 - - - +
18A LEU* 1.3 56.5 + - - +
20A THR* 3.4 6.0 + - - -
21A THR* 2.9 38.7 + - - +
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Residues in contact with LEU 18 (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 TYR* 3.9 24.2 - - + +
14A GLU 3.1 7.8 + - - +
15A PHE* 3.1 35.1 + - + +
17A GLN* 1.3 78.1 - - - +
19A VAL* 1.3 63.8 + - + +
21A THR* 3.3 5.6 + - - -
22A ILE* 3.0 38.0 + - + +
36A LEU* 3.9 33.0 - - + +
39A HIS* 4.0 14.4 - - + +
40A PHE* 4.7 12.8 - - + -
43A MET* 5.3 0.2 - - + -
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Residues in contact with VAL 19 (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 PHE* 2.9 34.0 + - + +
16A LEU 3.8 3.6 - - - +
18A LEU* 1.3 75.5 - - + +
20A THR* 1.3 57.7 + - - +
22A ILE* 3.2 7.8 + - - +
23A CYS* 2.9 37.6 + - - -
40A PHE* 3.8 30.5 - - + -
53A ILE* 5.4 2.5 - - + -
64A PRO* 3.8 30.5 - - + +
67A ILE* 4.0 15.5 - - + -
68A VAL* 4.0 10.3 - - + -
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Residues in contact with THR 20 (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 LEU* 2.8 34.9 + - - +
17A GLN* 3.7 7.2 - - - -
19A VAL* 1.3 70.6 - - - +
21A THR* 1.3 65.3 + - - +
23A CYS* 3.3 0.7 + - - +
24A ASN* 3.0 43.8 + - - +
64A PRO* 3.4 28.9 - - + +
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Residues in contact with THR 21 (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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17A GLN* 2.9 26.7 + - - +
18A LEU* 3.5 8.6 - - - -
19A VAL 3.3 0.2 - - - -
20A THR* 1.3 78.5 - - - +
22A ILE* 1.3 60.8 + - - +
24A ASN* 3.4 0.4 + - - +
25A ALA* 3.1 2.8 + - - -
26A ASP* 2.9 64.0 + - + +
27A THR* 4.3 1.1 - - + -
32A GLU* 5.5 0.9 - - - +
33A LEU* 4.7 0.2 - - - +
36A LEU* 3.6 26.2 - - + -
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Residues in contact with ILE 22 (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 LEU* 3.0 24.3 + - + +
19A VAL* 3.6 7.2 - - - +
21A THR* 1.3 75.3 - - - +
23A CYS* 1.3 58.6 + - - +
25A ALA* 2.9 20.1 + - - +
33A LEU* 3.9 12.1 - - + +
36A LEU* 3.7 44.4 - - + +
37A VAL* 3.7 13.7 - - + -
40A PHE* 3.9 20.6 - - + -
53A ILE* 3.9 25.1 - - + -
54A TYR* 3.4 25.4 + - - +
74B SER 4.9 2.8 - - - +
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Residues in contact with CYS 23 (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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19A VAL* 2.9 29.4 + - - +
20A THR 3.3 4.4 + - - +
22A ILE* 1.3 73.8 - - - +
24A ASN* 1.3 60.0 + - - +
53A ILE* 4.3 5.8 - - - -
62A ASP 4.5 2.5 - - - -
64A PRO* 4.0 24.5 - - + -
67A ILE* 3.7 27.8 - - - -
73B PRO 4.3 0.3 - - - +
74B SER* 3.4 33.1 - - - +
77B SER* 2.8 22.5 + - - -
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Residues in contact with ASN 24 (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 THR* 3.0 38.1 + - - +
21A THR 3.9 3.1 - - - +
23A CYS* 1.3 79.9 - - - +
25A ALA* 1.3 70.8 + - - +
26A ASP* 3.1 16.2 + - + +
77B SER* 3.7 11.8 + - - -
81B LYS* 4.1 9.4 - - - -
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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