Contacts of the strand formed by residues 85 - 90 (chain O) 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 THR 85 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O TYR 4.0 0.5 - - - +
37O GLN* 3.6 0.5 - - - -
38O GLN* 2.6 53.5 + - - +
40O PRO* 5.7 5.8 - - - +
84O ALA* 1.3 70.4 - - - +
86O TYR* 1.3 60.1 + - - +
87O TYR* 3.2 35.0 - - + +
101O GLY* 4.5 1.1 - - - -
102O THR 4.2 4.3 - - - +
103O LYS* 3.2 49.5 - - + +
104O VAL 4.3 0.2 - - - +
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Residues in contact with TYR 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O GLN* 3.2 11.1 + - - +
21O ILE* 3.9 22.2 - - + -
35O TRP* 4.7 2.9 - + + -
36O TYR 3.9 1.8 - - - +
37O GLN* 2.6 55.0 + - + -
47O LEU* 4.1 4.5 - - + -
62O PHE* 3.5 25.2 - + - -
73O LEU* 3.9 28.3 - - + -
75O ILE* 4.6 9.7 - - + +
78O LEU* 6.1 1.6 - - + +
82O ASP* 3.0 24.2 + - - +
84O ALA* 3.1 29.2 - - + -
85O THR* 1.3 72.1 - - - +
87O TYR* 1.3 60.7 + - - +
102O THR* 2.9 33.3 + - - +
104O VAL* 4.4 10.8 - - + -
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Residues in contact with TYR 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O GLN* 3.8 4.3 - - - -
35O TRP* 2.9 13.7 - - - -
36O TYR* 2.8 47.0 + - + +
38O GLN* 4.8 13.5 - - + -
44O PRO* 6.2 1.1 - - + -
85O THR* 3.2 34.9 - - + +
86O TYR* 1.3 74.6 - - - +
88O CYS* 1.3 62.7 + - - +
98O PHE* 4.2 17.7 - + + -
99O GLY 3.5 31.4 - - - -
100O GLN 4.4 5.3 + - - -
101O GLY* 4.1 10.3 - - - -
103O LYS* 6.0 1.9 - - - -
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Residues in contact with CYS 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O MET* 4.2 16.4 - - - -
6O GLN* 3.4 8.4 + - - -
23O CYS* 2.0 48.5 - - - -
33O LEU* 3.8 15.3 - - + -
34O ASN 2.8 17.3 - - - +
35O TRP* 3.6 15.3 - - + -
36O TYR* 4.7 1.6 - - - +
87O TYR* 1.3 74.5 - - - +
89O GLN* 1.3 61.3 + - - +
98O PHE* 3.2 9.7 - - - -
99O GLY 2.8 22.9 + - - -
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Residues in contact with GLN 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O MET* 4.2 5.8 - - - -
33O LEU* 3.3 4.5 - - - +
34O ASN* 2.4 67.9 + - + +
36O TYR* 3.7 27.8 + - + -
88O CYS* 1.3 77.9 - - - +
90O GLN* 1.3 60.7 + - - +
91O SER* 3.3 17.8 - - - +
96O ASN* 3.3 23.6 + - - +
97O THR 2.9 24.7 - - - +
98O PHE* 3.2 32.7 - - + -
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Residues in contact with GLN 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O ILE* 3.8 20.3 - - + +
4O MET* 3.4 20.7 - - + +
29O ILE* 4.1 9.6 - - + -
32O TYR 3.0 11.9 - - - +
89O GLN* 1.3 78.8 - - - +
91O SER* 1.3 53.4 + - - +
92O TYR* 2.6 32.4 + - + -
93O SER* 3.2 22.8 + - - +
95O PRO 3.1 13.2 - - - +
96O ASN* 3.5 5.9 - - - -
97O THR* 2.5 51.7 + - - +
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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