Contacts of the strand formed by residues 43 - 48 (chain D) in PDB entry 1Y8Q
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 HIS 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ALA 3.2 17.5 + - - -
17D GLY* 4.6 7.2 - - - -
18D GLY 3.4 19.1 + - - +
19D ARG* 3.4 18.5 - - + +
20D VAL* 2.9 26.0 + - - +
41D PHE* 3.7 0.9 - - - +
42D SER* 1.3 94.2 + - - +
44D ILE* 1.3 62.5 + - - +
45D ASP* 5.0 0.4 - - - -
88D ASN* 3.5 33.4 + - + +
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Residues in contact with ILE 44 (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 VAL* 3.5 20.9 - - + -
22D VAL* 4.1 11.2 - - + -
33D LEU* 3.9 26.7 - - + -
36D LEU* 3.7 22.7 - - + -
37D VAL* 3.7 30.5 - - + -
41D PHE* 4.0 9.2 - - + +
42D SER 3.8 1.5 + - - -
43D HIS* 1.3 84.6 - - - +
45D ASP* 1.3 80.1 + - - +
46D LEU* 5.2 0.4 - - + -
88D ASN 3.1 7.4 + - - +
89D ILE* 3.1 17.9 - - + +
90D VAL 3.0 22.2 + - - -
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Residues in contact with ASP 45 (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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19D ARG* 2.8 37.3 + - - +
20D VAL 2.8 6.6 + - - +
21D LEU* 3.4 8.6 - - + +
22D VAL* 2.9 27.0 + - - -
44D ILE* 1.3 81.5 + - - +
46D LEU* 1.3 59.8 + - - +
88D ASN 5.4 0.2 - - - +
90D VAL* 3.4 15.2 - - - +
92D TYR* 2.5 33.4 + - + -
109D PHE* 3.5 29.3 - - + -
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Residues in contact with LEU 46 (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 VAL* 3.5 20.0 - - + +
24D GLY 3.8 9.9 - - - +
25D ALA* 3.7 26.7 - - + -
29D GLY 6.0 1.8 - - - +
33D LEU* 3.6 38.6 - - + -
44D ILE 4.2 0.2 - - - -
45D ASP* 1.3 73.9 - - - +
47D ILE* 1.3 76.5 + - - +
48D ASP* 5.0 0.2 - - + -
73D ALA* 4.2 12.0 - - - +
76D ALA* 3.6 20.0 - - + -
77D LYS 4.8 1.6 - - - +
89D ILE* 4.7 10.1 - - + -
90D VAL 2.9 12.7 + - - +
91D ALA* 3.4 4.6 - - + -
92D TYR* 2.8 30.2 + - - +
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Residues in contact with ILE 47 (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 LEU* 4.3 8.1 - - + -
22D VAL 3.2 12.8 + - - +
23D VAL* 3.8 17.3 - - + -
24D GLY* 2.8 31.2 + - - -
46D LEU* 1.3 78.9 - - - +
48D ASP* 1.3 64.1 + - - +
92D TYR* 3.4 16.2 - - + +
94D ASP 3.4 13.9 - - - +
95D SER 3.8 2.5 - - - -
96D ILE* 3.7 39.9 - - + +
101D TYR* 3.7 41.3 - - + +
105D PHE* 6.0 0.9 - - + -
801D ATP 4.1 4.3 - - + -
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Residues in contact with ASP 48 (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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24D GLY 3.6 0.7 - - - -
25D ALA* 2.6 40.1 + - + +
47D ILE* 1.3 76.3 - - - +
49D LEU* 1.3 58.7 + - - +
50D ASP* 2.9 22.2 + - - +
72D LYS* 3.7 11.5 - - + +
73D ALA* 4.2 14.1 - - + +
92D TYR 3.1 5.5 + - - +
93D HIS* 3.3 13.2 + - - -
94D ASP 3.0 18.5 + - - -
801D ATP 2.6 50.4 + - - -
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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