Contacts of the helix formed by residues 18 - 25 (chain A) in PDB entry 1YAA
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASP* 3.0 27.7 + - + +
17A LEU* 1.3 78.2 - - + +
19A GLY* 1.3 59.9 + - - +
20A ILE 3.4 0.2 - - - -
21A LYS* 3.2 39.1 - - - +
22A GLN* 3.3 28.7 + - - +
37A ILE* 3.9 17.5 - - + -
901A MAE 3.6 14.4 - - - -
70B TYR* 4.3 12.8 - + + -
71B LEU 3.8 14.8 - - - -
72B GLY* 4.9 1.1 - - - -
73B ILE* 4.1 24.9 - - + +
292B ARG* 3.5 30.1 - - - -
297B ASN* 3.6 24.5 - - - -
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Residues in contact with GLY 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 PRO* 4.7 8.1 - - - -
15A ASP* 2.9 21.9 + - - +
18A PHE* 1.3 77.1 - - - +
20A ILE* 1.3 64.4 + - - +
21A LYS 3.2 0.4 - - - -
22A GLN* 3.1 16.2 + - - +
23A ARG* 3.0 36.6 + - - +
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Residues in contact with ILE 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 3.4 23.8 - - - +
17A LEU* 3.1 10.3 + - - +
19A GLY* 1.3 75.6 - - - +
21A LYS* 1.3 59.2 + - - +
23A ARG* 3.6 23.9 - - - +
24A TYR* 2.8 35.2 + - - +
34A ASP* 4.2 8.3 - - - +
36A GLY* 4.2 14.6 - - - -
37A ILE 5.4 0.2 - - - +
380A TYR* 3.7 33.2 - - + -
381A LEU 3.9 6.1 - - - +
382A VAL* 3.6 42.0 - - + +
383A ALA 5.2 0.7 - - - +
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Residues in contact with LYS 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 LEU 3.6 1.2 + - - -
18A PHE* 3.2 50.9 - - - +
19A GLY 3.2 0.2 - - - -
20A ILE* 1.3 81.1 - - - +
22A GLN* 1.3 57.8 + - + +
24A TYR* 3.9 9.8 - - + +
25A GLY* 3.0 24.3 + - - -
34A ASP* 5.3 5.8 - - - +
37A ILE* 3.7 23.1 - - + +
70B TYR* 3.9 17.7 + - - +
71B LEU 3.9 11.2 + - - -
72B GLY* 5.2 5.2 - - - -
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Residues in contact with GLN 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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14A PRO* 4.4 12.3 - - - +
15A ASP 5.4 0.7 + - - -
18A PHE* 3.3 19.0 - - - +
19A GLY* 3.1 15.9 + - - +
21A LYS* 1.3 76.8 - - + +
23A ARG* 1.3 62.0 + - + +
25A GLY* 2.9 4.0 + - - -
26A GLN* 2.8 40.2 + - + +
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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 GLY* 3.0 17.5 + - - +
20A ILE* 3.6 32.1 - - - +
22A GLN* 1.3 76.7 - - + +
24A TYR* 1.3 60.8 + - - +
26A GLN* 3.7 8.8 + - - +
27A ASP* 3.7 11.3 + - - +
371A LYS* 5.4 4.8 - - - +
374A GLU* 2.9 42.8 + - - +
380A TYR* 3.5 17.7 + - + -
381A LEU 5.1 3.0 + - - -
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Residues in contact with TYR 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 ILE 2.8 20.5 + - - +
21A LYS* 3.9 8.5 - - + +
23A ARG* 1.3 74.5 - - - +
25A GLY* 1.3 67.9 + - - +
27A ASP* 3.1 10.6 - - - +
32A LYS* 3.1 71.2 + - + +
33A VAL 4.1 0.4 - - - -
34A ASP* 3.4 51.3 + - + +
380A TYR* 3.6 34.5 - + + -
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Residues in contact with GLY 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 LYS 3.0 13.4 + - - -
22A GLN* 2.9 7.2 + - - -
24A TYR* 1.3 78.8 - - - +
26A GLN* 1.3 64.0 + - - +
27A ASP 3.1 14.0 + - - +
32A LYS* 4.2 5.5 + - - -
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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