Contacts of the strand formed by residues 70 - 75 (chain J) in PDB entry 2BX5
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 70 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J THR* 4.7 9.2 - - - +
23J CYS 3.6 3.8 - - - +
24J ARG* 3.1 41.8 + - - +
66J GLY* 3.5 3.3 - - - -
67J SER 3.0 28.5 + - - +
69J THR* 1.3 76.5 - - - +
71J PHE* 1.3 70.6 + - - +
72J THR* 4.7 6.3 + - - -
18K ARG* 4.0 19.3 + - - -
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Residues in contact with PHE 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J MET* 5.6 0.2 - - + -
22J THR* 3.8 1.6 - - - -
23J CYS* 3.0 39.0 + - + +
24J ARG* 5.5 0.4 - - - -
25J ALA* 5.3 1.8 - - + -
29J ILE* 3.6 39.9 - - + -
30J SER 4.2 3.8 - - - -
31J SER* 4.4 3.4 - - - -
33J LEU* 3.6 37.0 - - + -
35J TRP* 4.0 6.9 - - + +
51J ALA* 3.7 21.8 - - + +
65J SER 3.6 6.3 - - - +
66J GLY 3.3 16.4 - - - -
67J SER* 3.3 32.8 - - - -
68J GLY 4.2 1.8 - - - -
69J THR 4.2 5.8 - - - -
70J ASP* 1.3 89.0 - - - +
72J THR* 1.3 67.3 + - - +
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Residues in contact with THR 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J THR* 3.6 20.6 - - + -
21J ILE 2.8 22.0 + - - +
22J THR* 4.2 8.9 - - + +
35J TRP* 4.0 4.3 - - - -
63J SER 3.3 11.6 - - - +
64J GLY* 3.7 0.9 - - - -
65J SER* 2.7 40.7 + - - -
70J ASP* 4.7 6.8 + - - -
71J PHE* 1.3 79.3 + - - +
73J LEU* 1.3 70.9 + - - +
74J THR* 3.4 12.6 + - - +
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Residues in contact with LEU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J THR* 3.9 0.9 - - - -
21J ILE* 3.1 39.4 + - + +
35J TRP* 3.3 59.7 - - + -
47J LEU* 4.7 3.6 - - + -
48J ILE* 3.5 23.6 - - + -
62J PHE* 4.7 7.4 - - + -
63J SER 3.3 19.7 - - - +
72J THR* 1.3 75.6 - - - +
74J THR* 1.3 60.0 + - - +
75J ILE* 4.5 7.0 - - + -
86J TYR* 3.8 35.7 - - + -
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Residues in contact with THR 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ARG* 3.5 36.1 - - + +
19J VAL 3.8 8.7 - - - +
20J THR* 4.1 5.0 + - - +
61J ARG 3.4 3.8 - - - +
63J SER* 2.7 46.7 + - - -
65J SER* 4.9 3.1 + - - -
72J THR* 3.4 17.0 + - - +
73J LEU* 1.3 77.5 + - - +
75J ILE* 1.3 63.9 + - - +
76J SER* 3.7 3.5 + - - +
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Residues in contact with ILE 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ARG* 3.3 2.9 - - - +
19J VAL* 3.0 57.2 + - + +
21J ILE* 4.2 11.0 - - + -
61J ARG* 3.4 10.5 - - - +
62J PHE* 3.8 22.4 - - + +
73J LEU* 4.5 4.5 - - + -
74J THR* 1.3 72.8 - - - +
76J SER* 1.3 67.5 + - - +
77J SER* 3.2 9.9 + - - +
78J LEU* 4.2 13.5 - - + -
82J ASP* 3.8 21.3 - - - +
86J TYR* 4.0 35.4 - - + +
104J VAL* 5.2 0.2 - - + -
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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