Contacts of the strand formed by residues 48 - 52 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA* 4.6 2.8 - - - +
22B ARG 3.2 6.4 + - - +
23B LYS* 3.3 35.7 - - + +
24B ILE 3.1 23.7 + - - -
46B ALA* 3.9 3.5 - - - +
47B ASP* 1.3 79.2 - - - +
49B TYR* 1.3 67.4 + - - +
78B ASN* 2.9 39.0 + - + +
266C ASP* 5.3 0.2 - - - +
292C ARG* 3.0 32.7 + - - -
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.3 17.5 - - + +
26B ILE* 4.9 3.4 - - + -
37B ALA* 5.1 0.7 - - - -
40B LEU* 3.5 46.2 + - + +
41B ILE* 3.7 28.6 + - + +
44B GLY* 4.6 0.7 - - - -
45B VAL 4.0 0.9 + - - -
46B ALA* 3.2 50.2 + - + -
48B ASP* 1.3 77.4 - - - +
50B VAL* 1.3 63.3 + - - +
51B PHE* 4.0 27.1 - + + -
77B GLY* 4.2 11.7 - - - -
78B ASN 2.7 25.3 + - - +
79B ILE* 4.3 8.1 - - + -
80B VAL* 3.0 28.4 + - - +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 4.3 15.5 - - + +
24B ILE 3.0 7.9 + - - +
25B GLY* 4.1 0.9 - - - -
26B ILE 2.8 28.9 + - - +
48B ASP* 6.1 0.2 - - + -
49B TYR* 1.3 77.4 - - - +
51B PHE* 1.3 64.2 + - - +
52B ILE* 4.1 15.0 - - + +
80B VAL* 3.3 14.4 - - + +
83B ASP 3.6 24.7 - - - +
86B ALA* 3.8 26.5 - - + +
87B LEU* 3.6 28.0 - - + -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 3.7 26.7 - - + -
29B LEU* 4.1 25.1 - - + -
37B ALA* 3.7 20.9 - - + -
41B ILE* 4.3 4.7 - - + -
49B TYR* 4.0 16.6 - + + -
50B VAL* 1.3 79.9 - - - +
52B ILE* 1.3 54.6 + - - +
59B VAL* 3.6 17.8 - - + +
62B ASP* 4.7 0.7 - - + -
63B GLN* 4.5 14.1 - - - -
66B PHE* 3.7 26.2 - + - -
79B ILE* 3.5 32.8 - - + -
80B VAL 2.8 10.3 + - - -
81B ILE* 3.0 12.3 - - + +
82B ASN* 2.7 32.2 + - - +
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE 2.8 14.4 + - - +
27B ILE* 4.1 16.4 - - + +
28B GLY 2.6 33.8 + - - -
29B LEU* 4.2 1.5 + - - +
50B VAL* 4.1 13.9 - - + -
51B PHE* 1.3 77.7 - - - +
53B ASP* 1.3 61.6 + - - +
59B VAL* 4.4 0.9 - - - +
82B ASN* 3.1 20.4 - - - +
83B ASP 4.1 0.4 - - - +
84B TRP* 3.8 61.2 - - + +
87B LEU* 3.9 21.5 - - + -
330B NAD 4.6 4.7 - - + -
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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