Contacts of the helix formed by residues 16 - 26 (chain A) in PDB entry 1A4Y
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 ASP 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A SER* 1.3 69.5 - - - +
17A ALA* 1.3 56.0 + - - +
19A TRP* 3.8 14.7 - - + +
20A ALA* 3.1 26.7 + - - +
43A ARG* 3.7 19.5 + - - +
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Residues in contact with ALA 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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15A SER* 2.7 13.1 + - - +
16A ASP* 1.3 72.8 - - - +
18A ARG* 1.3 62.3 + - - +
20A ALA* 3.4 11.5 + - - +
21A GLU* 3.1 23.0 - - - +
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Residues in contact with ARG 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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9A ILE* 5.6 5.7 - - + +
12A GLU* 5.7 2.7 - - - +
14A LEU* 3.1 42.4 - - + +
15A SER* 2.7 8.5 + - - +
17A ALA* 1.3 74.5 - - - +
19A TRP* 1.3 62.2 + - - +
21A GLU* 3.0 55.5 + - - +
22A LEU* 3.0 32.8 + - + +
25A LEU* 6.0 2.8 - - - +
3D ASP* 4.3 13.5 + - - -
5D GLN* 3.7 19.8 - - - +
28D GLN* 3.6 24.4 + - - +
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Residues in contact with TRP 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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14A LEU* 3.2 36.7 - - + +
15A SER 2.7 17.0 + - - +
16A ASP* 3.9 15.0 - - - +
18A ARG* 1.3 79.2 - - - +
20A ALA* 1.3 63.0 + - - +
22A LEU* 3.4 8.0 + - + -
23A LEU* 3.1 41.5 + - + +
26A LEU* 4.2 11.0 - - + -
34A LEU* 4.5 10.8 - - + -
39A LEU* 3.7 20.0 - - + -
43A ARG* 3.5 50.7 - - + +
46A ASP* 2.7 32.6 + - + -
47A ILE* 3.8 21.8 - - + -
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Residues in contact with ALA 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 ASP 3.1 19.7 + - - +
17A ALA* 3.5 8.1 - - - +
18A ARG 3.1 0.2 - - - -
19A TRP* 1.3 79.6 - - - +
21A GLU* 1.3 62.3 + - + +
23A LEU* 3.5 11.6 + - - +
24A PRO* 3.4 16.1 - - - +
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Residues in contact with GLU 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 ALA* 3.1 21.4 - - - +
18A ARG* 3.0 39.3 + - - +
20A ALA* 1.3 76.5 - - + +
22A LEU* 1.3 56.8 + - - +
24A PRO* 3.0 20.0 - - - +
25A LEU* 3.3 13.1 - - - +
28D GLN* 5.4 3.5 + - - +
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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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7A LEU* 5.0 15.4 - - + +
9A ILE* 5.2 6.7 - - + -
14A LEU* 5.1 6.5 - - + -
18A ARG* 3.0 27.2 + - + +
19A TRP* 3.9 16.6 - - + +
20A ALA 3.3 0.2 - - - -
21A GLU* 1.3 78.5 - - - +
23A LEU* 1.3 62.4 + - - +
25A LEU* 3.0 27.8 + - - +
26A LEU* 3.4 11.4 + - + +
34A LEU* 6.2 1.1 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TRP* 3.1 41.1 + - + +
20A ALA* 3.7 10.8 - - - +
22A LEU* 1.3 74.9 - - - +
24A PRO* 1.3 68.1 - - + +
26A LEU* 3.1 42.1 + - + +
27A GLN* 3.4 14.3 + - - +
46A ASP* 3.5 40.6 - - + +
50A ALA* 4.0 5.6 - - + +
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Residues in contact with PRO 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 ALA 3.4 8.5 - - - +
21A GLU* 3.0 19.7 - - - +
23A LEU* 1.3 94.3 - - + +
25A LEU* 1.3 66.0 + - + +
27A GLN* 3.1 31.0 + - + +
28A GLN* 3.3 17.7 - - - +
21D GLU* 5.5 6.5 - - - +
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Residues in contact with LEU 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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5A GLN* 5.3 2.9 - - - +
6A SER 5.9 0.4 - - - +
7A LEU* 4.5 15.7 - - + -
18A ARG* 6.0 2.9 - - - +
21A GLU 3.3 23.1 - - - +
22A LEU* 3.0 14.4 + - - +
24A PRO* 1.3 77.0 - - + +
26A LEU* 1.3 55.9 - - - +
27A GLN 2.9 5.2 - - - -
28A GLN* 2.7 37.8 + - - +
29A CYS* 3.0 30.9 + - - -
5D GLN* 3.2 32.3 - - - +
25D LEU* 5.2 19.1 - - + -
28D GLN* 5.8 4.7 - - - +
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Residues in contact with LEU 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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7A LEU* 3.8 20.9 - - + -
19A TRP* 4.2 19.5 - - + -
22A LEU* 3.7 8.7 - - + +
23A LEU* 3.2 37.2 - - + +
25A LEU* 1.3 78.3 - - - +
27A GLN* 1.3 50.2 + - - +
28A GLN 3.3 0.2 - - - -
32A VAL* 3.7 35.1 - - + +
34A LEU* 4.2 7.9 - - + -
47A ILE* 4.4 19.3 - - + -
50A ALA* 3.9 10.8 - - + +
51A LEU* 4.0 13.9 - - + +
54A ASN* 2.6 29.4 + - - +
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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