Contacts of the helix formed by residues 18 - 26 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TYR* 4.1 24.0 - + + -
71C LEU 3.6 23.8 - - - -
72C GLY* 4.7 2.0 - - - -
73C ILE* 3.9 27.1 - - + -
292C ARG* 3.6 17.3 - - - -
297C ASN* 3.4 22.9 - - - -
15D ASP* 2.9 26.6 + - + +
17D LEU* 1.3 74.4 - - - +
19D GLY* 1.3 64.1 + - - +
20D ILE 3.2 0.2 - - - -
21D LYS* 3.2 35.9 + - + +
22D GLN* 3.3 16.4 + - - +
37D ILE* 4.0 10.3 - - + -
904D MAE 3.5 24.9 - - - -
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Residues in contact with GLY 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO* 4.5 8.3 - - - -
15D ASP* 2.9 24.2 + - - +
18D PHE* 1.3 78.8 - - - +
20D ILE* 1.3 59.0 + - - +
22D GLN* 3.2 18.8 - - - +
23D ARG* 3.1 35.1 + - - +
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Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA 3.6 21.0 + - - +
17D LEU* 3.1 9.8 + - - +
19D GLY* 1.3 76.9 - - - +
21D LYS* 1.3 57.3 + - - +
23D ARG* 3.4 24.6 - - - +
24D TYR* 2.9 28.1 + - - +
34D ASP* 4.5 5.6 - - - +
36D GLY* 4.4 16.8 - - - -
37D ILE 5.4 0.9 - - - +
380D TYR* 3.8 31.3 - - + -
381D LEU 3.1 25.4 - - - +
382D VAL* 3.8 23.3 - - + -
383D ALA 5.2 0.7 - - - +
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TYR* 2.9 34.8 + - + +
71C LEU* 3.3 22.4 + - - +
72C GLY* 3.9 4.3 - - - +
17D LEU 3.5 1.8 + - - -
18D PHE* 3.2 33.0 + - + +
19D GLY 3.2 0.2 - - - -
20D ILE* 1.3 80.1 - - - +
22D GLN* 1.3 62.0 + - - +
24D TYR* 3.8 7.4 - - - +
25D GLY* 3.3 17.7 + - - -
34D ASP* 5.6 6.3 - - - +
37D ILE* 4.3 19.0 - - + +
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO* 4.5 13.0 - - - +
18D PHE 3.3 7.3 + - - +
19D GLY* 3.2 23.6 - - - +
21D LYS* 1.3 77.6 - - - +
23D ARG* 1.3 65.4 + - + +
25D GLY* 3.3 2.1 + - - -
26D GLN* 3.0 49.5 + - + +
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA 5.7 0.4 + - - -
19D GLY* 3.1 30.7 + - - +
20D ILE* 3.4 30.1 - - - +
22D GLN* 1.3 76.5 - - + +
24D TYR* 1.3 66.0 + - - +
26D GLN* 3.2 15.2 + - - +
27D ASP* 3.2 17.5 + - - +
374D GLU* 2.9 41.2 + - - +
380D TYR* 3.7 16.6 + - + +
381D LEU 4.9 3.2 + - - -
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ILE 2.9 20.8 + - - +
21D LYS* 3.8 7.4 - - - +
23D ARG* 1.3 76.5 - - - +
25D GLY* 1.3 63.9 + - - +
27D ASP* 3.3 12.0 - - - +
32D LYS* 3.1 63.4 + - + +
33D VAL 3.6 4.9 - - - -
34D ASP* 3.4 53.4 + - + +
380D TYR* 3.7 35.1 - + + -
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Residues in contact with GLY 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS 3.3 12.0 + - - -
22D GLN* 3.3 4.9 + - - -
23D ARG 3.2 0.6 - - - -
24D TYR* 1.3 86.4 - - - +
26D GLN* 1.3 59.9 + - - +
27D ASP 3.4 0.4 - - - +
32D LYS* 3.8 11.5 + - - -
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Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLN* 3.0 36.6 + - + +
23D ARG* 3.2 16.9 + - - +
25D GLY* 1.3 75.1 - - - +
27D ASP* 1.3 65.4 + - - +
28D GLN* 3.2 16.3 + - - +
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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