Contacts of the helix formed by residues 14 - 27 (chain A) in PDB entry 1I4A
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 ASN 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 4.1 12.1 + - - +
12A GLY 3.4 4.6 + - - +
13A PHE* 1.3 80.1 - - - +
15A ALA* 1.3 65.7 + - - +
16A ALA* 3.4 15.2 - - - +
17A GLU* 2.6 66.1 + - + +
18A ASP* 3.0 25.8 + - - +
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Residues in contact with ALA 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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13A PHE* 4.0 23.9 - - + -
14A ASN* 1.3 72.8 - - - +
16A ALA* 1.3 57.5 + - - +
18A ASP* 3.3 2.3 + - - +
19A ALA* 2.8 28.8 + - - +
50A GLU* 3.6 37.7 - - + +
51A ILE* 4.3 8.1 - - - +
54A ALA* 3.6 9.5 - - + +
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Residues in contact with ALA 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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14A ASN* 3.2 12.0 - - - +
15A ALA* 1.3 79.4 - - - +
17A GLU* 1.3 62.0 + - + +
19A ALA* 3.1 4.3 + - - +
20A GLN* 2.7 33.4 + - - +
54A ALA* 3.7 12.9 - - + +
58A THR* 4.3 12.8 - - - +
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Residues in contact with GLU 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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10A ALA* 5.6 1.9 + - - +
11A SER* 3.9 20.5 + - - -
14A ASN* 2.6 48.0 + - + +
16A ALA* 1.3 70.4 - - - +
18A ASP* 1.3 68.2 + - - +
20A GLN* 3.1 13.1 + - + +
21A THR* 3.0 25.0 + - - -
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Residues in contact with ASP 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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13A PHE* 3.3 18.2 - - - -
14A ASN 3.0 15.1 + - - +
15A ALA 3.6 7.4 - - - +
17A GLU* 1.3 78.0 - - - +
19A ALA* 1.3 63.4 + - - +
21A THR* 3.2 7.8 + - - -
22A LEU* 2.9 31.8 + - - +
39A VAL* 3.8 12.3 - - + +
43A ARG* 2.7 44.9 + - - -
51A ILE* 3.5 20.0 - - + +
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Residues in contact with ALA 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 ALA 2.8 14.0 + - - +
16A ALA* 3.1 15.5 - - - +
18A ASP* 1.3 77.7 - - - +
20A GLN* 1.3 68.6 + - - +
22A LEU* 3.4 3.8 + - - +
23A ARG* 3.0 24.4 + - - +
51A ILE* 4.5 7.6 - - - +
54A ALA* 4.1 1.6 - - + -
55A TYR* 3.7 43.4 - - + +
58A THR* 4.8 0.9 - - + -
59A ILE* 4.8 1.1 - - + +
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Residues in contact with GLN 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 ALA* 2.7 27.4 + - - +
17A GLU* 3.1 14.8 + - + +
19A ALA* 1.3 80.6 - - - +
21A THR* 1.3 62.1 + - - +
23A ARG* 3.2 6.0 + - - +
24A LYS* 2.9 26.0 + - - +
58A THR* 2.7 43.8 + - - +
59A ILE* 4.2 5.9 - - - +
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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 GLU 3.0 12.9 + - - -
18A ASP* 3.5 10.9 + - - -
20A GLN* 1.3 77.8 - - - +
22A LEU* 1.3 57.0 + - + +
24A LYS* 3.5 6.6 + - - +
25A ALA* 3.0 26.9 + - - +
35A ALA* 4.4 16.7 - - + +
39A VAL* 3.7 26.6 - - + +
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Residues in contact with LEU 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 ASP 2.9 28.9 + - - +
19A ALA* 3.8 4.9 - - - +
21A THR* 1.3 74.8 - - + +
23A ARG* 1.3 64.8 + - - +
25A ALA* 3.2 8.0 + - - +
26A MET* 3.1 33.0 + - + +
36A ILE* 5.2 14.1 - - + +
39A VAL* 3.6 37.9 - - + -
40A LEU* 4.1 23.1 - - + -
51A ILE* 3.9 26.2 - - + -
55A TYR* 4.6 7.0 - - + -
63A LEU* 4.0 21.8 - - + -
67A LEU* 5.7 2.2 - - + -
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Residues in contact with ARG 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 ALA 3.0 17.2 + - - +
20A GLN* 3.7 4.5 - - - +
22A LEU* 1.3 77.5 - - - +
24A LYS* 1.3 63.8 + - - +
26A MET* 3.1 12.9 + - - +
27A LYS* 3.0 45.1 + - + +
55A TYR* 3.6 27.4 + - + -
59A ILE* 3.9 22.4 - - + +
61A ARG* 3.0 47.0 - - - +
66A ASP* 3.6 3.4 + - - +
450A SO4 2.5 42.6 + - - +
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Residues in contact with LYS 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 GLN 2.9 17.3 + - - +
21A THR* 3.6 6.7 - - - +
23A ARG* 1.3 76.2 - - - +
25A ALA* 1.3 66.5 + - - +
27A LYS* 3.1 25.6 + - + +
32A ASP* 6.0 2.0 - - + +
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Residues in contact with ALA 25 (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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21A THR 3.0 18.1 + - - +
22A LEU* 3.2 7.6 + - - +
24A LYS* 1.3 81.4 - - - +
26A MET* 1.3 58.9 + - - +
27A LYS 3.7 2.6 + - - +
31A THR* 3.6 5.2 - - - +
32A ASP* 2.9 53.0 + - + +
35A ALA* 3.7 15.9 - - + -
36A ILE* 4.0 12.6 - - + +
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Residues in contact with MET 26 (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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22A LEU* 3.1 21.9 + - + +
23A ARG* 3.1 13.0 + - - +
25A ALA* 1.3 76.9 - - - +
27A LYS* 1.3 63.9 + - - +
28A GLY 4.2 0.3 - - - +
31A THR* 4.4 2.7 - - + -
36A ILE* 4.3 15.0 - - + -
55A TYR* 3.3 33.2 - - + +
63A LEU* 4.0 15.7 - - + -
66A ASP* 3.8 22.7 - - + +
67A LEU* 3.9 15.5 - - + -
70A GLU* 3.3 52.6 - - + +
401A CA 3.4 5.9 - - - -
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Residues in contact with LYS 27 (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 ARG* 3.0 42.8 + - + +
24A LYS* 3.1 21.1 + - + +
25A ALA 4.2 2.8 - - - +
26A MET* 1.3 79.6 - - - +
28A GLY* 1.3 72.8 + - - +
29A LEU 4.6 1.2 - - - +
30A GLY 4.1 5.2 - - - +
450A SO4 3.0 40.3 + - - +
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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