Contacts of the strand formed by residues 81 - 86 (chain A) in PDB entry 1U4A
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASN 3.6 2.5 + - - +
19A LEU* 3.4 14.0 - - + +
20A LYS* 3.1 24.8 + - - +
61A PHE* 3.3 24.8 - - + -
77A MET* 3.3 46.5 - - - +
78A GLU* 3.8 10.4 + - - +
79A ASP 3.2 9.5 + - - +
80A GLU* 1.3 89.3 + - - +
82A THR* 1.3 62.9 + - - +
83A ILE* 3.7 2.4 - - - +
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Residues in contact with THR 82 (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 LYS* 3.6 33.0 - - + +
61A PHE* 3.1 23.4 - - - -
62A ASP 5.3 1.4 + - - -
81A ASP* 1.3 72.7 - - - +
83A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 83 (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 LEU* 3.6 36.1 - - + -
20A LYS 3.1 10.9 + - - +
21A VAL* 3.5 31.0 - - + -
22A ALA* 2.7 29.2 + - - +
59A PHE* 4.1 23.6 - - + -
60A ARG 3.1 31.2 - - - +
61A PHE* 3.9 21.3 - - + -
66A ILE* 4.7 2.9 - - + -
77A MET* 5.7 0.9 - - + -
81A ASP 3.7 4.3 - - - +
82A THR* 1.3 81.0 - - - +
84A ASP* 1.3 66.6 + - - +
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Residues in contact with ASP 84 (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 VAL* 4.4 0.4 - - - -
22A ALA* 3.1 23.6 - - - +
60A ARG* 2.8 47.4 + - + +
62A ASP 5.6 2.6 + - - -
82A THR 5.9 0.4 - - - -
83A ILE* 1.3 83.4 - - - +
85A VAL* 1.3 63.6 + - - +
86A PHE* 3.3 26.4 - - + -
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Residues in contact with VAL 85 (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 VAL* 3.6 16.2 - - + +
22A ALA 3.0 3.3 + - - +
23A GLY* 3.4 13.7 - - - -
24A GLN* 3.0 26.4 + - - +
46A TYR* 3.2 39.5 - - + +
50A GLN* 5.0 0.9 - - - +
52A LEU* 4.9 8.5 - - + -
57A ILE* 4.2 12.8 - - + -
58A ARG 3.7 4.9 - - - +
59A PHE* 3.5 30.1 - - + -
84A ASP* 1.3 70.6 - - - +
86A PHE* 1.3 66.4 + - - +
87A GLN* 5.8 1.1 - - + -
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Residues in contact with PHE 86 (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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22A ALA 5.4 0.7 - - - -
24A GLN* 3.2 40.2 - - + -
57A ILE* 4.0 0.7 - - - -
58A ARG* 2.8 35.2 + - + +
60A ARG* 3.8 29.8 - - + -
84A ASP* 3.3 46.9 - - + -
85A VAL* 1.3 77.3 - - - +
87A GLN* 1.3 66.9 + - - +
88A GLN* 3.1 31.9 - - - +
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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