Contacts of the strand formed by residues 48 - 52 (chain A) in PDB entry 1HYH
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 4.8 2.4 - - - +
22A ARG 3.1 6.5 + - - +
23A LYS* 3.2 34.0 - - + +
24A ILE 3.0 24.1 + - - -
46A ALA* 4.0 2.4 - - - +
47A ASP* 1.3 77.3 - - - +
49A TYR* 1.4 65.5 + - - +
50A VAL* 6.0 0.2 - - + -
78A ASN* 2.8 39.1 + - + +
292D ARG* 2.8 35.1 + - - -
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Residues in contact with TYR 49 (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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24A ILE* 3.2 15.0 - - + +
26A ILE* 5.1 3.6 - - + -
37A ALA 5.1 0.4 - - - -
40A LEU* 3.5 45.3 + - + -
41A ILE* 3.5 26.9 + - + -
44A GLY* 4.6 1.0 - - - -
45A VAL 4.0 1.0 + - - -
46A ALA* 3.3 50.3 + - + -
48A ASP* 1.4 76.4 - - - +
50A VAL* 1.3 67.9 + - - +
51A PHE* 3.8 26.2 - + + -
77A GLY* 4.1 13.5 - - - -
78A ASN 2.7 23.7 + - - +
79A ILE* 3.4 11.4 - - + -
80A VAL* 3.0 25.1 + - - +
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Residues in contact with VAL 50 (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 LYS* 4.5 13.2 - - + +
24A ILE 2.9 9.6 + - - +
25A GLY* 3.4 1.1 - - - -
26A ILE 2.8 31.0 + - - +
48A ASP* 6.0 0.2 - - + -
49A TYR* 1.3 79.8 - - - +
51A PHE* 1.3 61.7 + - - +
52A ILE* 4.1 15.2 - - + +
80A VAL* 3.4 17.5 - - + +
83A ASP 3.7 24.5 - - - +
86A ALA* 3.8 29.2 - - + +
87A LEU* 3.9 22.4 - - + -
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Residues in contact with PHE 51 (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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26A ILE* 3.6 14.6 - - + -
29A LEU* 3.6 24.7 - - + -
37A ALA* 3.6 29.8 - - + -
41A ILE* 4.2 10.1 - - + -
49A TYR* 3.8 21.5 - + + -
50A VAL* 1.3 78.9 - - - +
52A ILE* 1.3 61.0 + - - +
59A VAL* 3.5 20.0 - - + -
62A ASP* 4.6 4.0 - - + -
63A GLN* 4.6 11.7 - - - -
66A PHE* 3.6 28.5 - + - -
79A ILE* 3.8 24.2 - - + -
80A VAL 2.8 7.7 + - - -
81A ILE* 3.1 10.1 - - + +
82A ASN* 2.8 24.1 + - - +
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Residues in contact with ILE 52 (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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26A ILE 2.9 13.1 + - - +
27A ILE* 4.4 15.7 - - + -
28A GLY* 2.7 32.2 + - - -
29A LEU* 4.0 2.1 - - - +
50A VAL* 4.1 16.2 - - + +
51A PHE* 1.3 80.1 - - - +
53A ASP* 1.3 63.9 + - - +
59A VAL* 4.5 1.1 - - - -
82A ASN* 3.2 20.4 - - - +
83A ASP 4.4 7.2 - - - +
84A TRP* 3.8 56.5 - - + +
87A LEU* 4.0 17.7 - - + -
330A NAD 4.2 4.4 + - + -
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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