Contacts of the strand formed by residues 66 - 71 (chain H) in PDB entry 1BGX
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 ILE 66 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H MET* 3.8 40.2 - - + +
59H ASN* 3.4 26.7 + - + +
62H LEU 3.4 21.2 + - - +
63H LYS* 3.7 18.2 - - - +
64H SER 5.1 0.2 - - - -
65H ARG* 1.3 78.3 - - - +
67H SER* 1.3 68.4 + - - +
68H ILE* 4.5 4.7 - - + -
79H LEU* 3.9 30.1 - - + -
80H GLN 3.8 4.0 - - - +
81H LEU* 4.1 22.6 - - + +
388T GLU* 5.8 1.9 - - - +
392T ARG* 4.1 8.8 + - - -
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Residues in contact with SER 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ASN* 5.8 0.4 - - - +
65H ARG 3.9 1.0 + - - -
66H ILE* 1.3 79.7 + - - +
68H ILE* 1.3 64.9 + - - +
69H THR* 4.2 5.7 + - - -
79H LEU* 3.8 3.6 - - - +
80H GLN* 2.9 53.0 + - - +
82H ASN* 3.8 12.4 + - - -
392T ARG* 3.4 26.9 - - - +
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Residues in contact with ILE 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 4.9 9.4 - - + +
48H MET 3.5 25.1 - - - +
49H GLY* 3.9 2.5 - - - -
50H TYR 3.5 37.5 - - - +
51H ILE* 4.0 23.6 - - + -
55H THR* 4.2 14.0 - - - +
57H ASP* 4.0 12.5 - - - +
59H ASN* 3.8 12.3 - - - +
66H ILE* 4.5 4.0 - - + -
67H SER* 1.3 76.6 - - - +
69H THR* 1.3 68.3 + - - +
77H PHE* 5.7 0.7 - - + -
78H PHE 4.0 11.0 - - - +
79H LEU* 4.1 17.0 - - + -
392T ARG* 4.9 13.2 + - - +
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Residues in contact with THR 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ILE* 3.9 7.4 - - - +
55H THR* 5.5 1.8 - - - -
67H SER* 5.3 5.3 + - - -
68H ILE* 1.3 78.8 - - - +
70H ARG* 1.3 65.2 + - - +
77H PHE* 3.7 4.5 - - - +
78H PHE* 2.9 44.9 + - - +
79H LEU* 4.9 0.3 + - - -
80H GLN* 5.7 4.5 - - - +
392T ARG* 6.2 2.2 - - - +
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Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ILE* 2.9 40.6 + - + +
30H THR* 5.1 2.4 - - - +
51H ILE* 3.7 24.9 - - + +
52H THR 3.0 35.6 + - - -
53H SER 3.2 19.2 + - - -
54H GLY* 3.6 14.0 + - - +
55H THR* 5.9 1.1 - - + -
69H THR* 1.3 79.6 - - - +
71H ASP* 1.3 61.6 + - - +
72H THR* 3.6 22.5 - - + +
76H GLN 3.8 10.8 - - - +
77H PHE* 4.1 8.3 - - + +
78H PHE* 4.2 6.2 - - - +
383T SER* 5.6 6.2 - - - -
728T ARG* 4.8 7.1 - - - +
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Residues in contact with ASP 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ILE* 4.5 0.2 - - - -
70H ARG* 1.3 73.5 - - - +
72H THR* 1.3 58.2 + - - +
73H SER* 3.4 11.1 + - - -
74H LYS* 3.1 42.7 + - - +
75H ASN 3.2 5.7 + - - -
76H GLN* 3.0 38.4 + - + +
78H PHE* 3.9 22.5 - - + -
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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