Contacts of the strand formed by residues 86 - 92 (chain C) in PDB entry 2BHT
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 ARG 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C GLY 5.1 2.6 - - - +
62C ASP 2.9 11.1 + - - +
63C VAL* 3.2 31.3 - - + +
64C LEU 2.8 29.4 + - - +
85C TYR* 1.3 70.8 - - - +
87C MET* 1.3 64.4 + - - +
88C LYS* 3.5 2.8 + - + +
107C GLY 5.0 10.1 + - - -
109C GLU* 4.0 29.5 + - + +
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Residues in contact with MET 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 5.7 0.2 - - - -
64C LEU* 3.7 44.9 - - + +
65C ILE 4.5 7.0 - - - +
76C LEU* 3.6 31.6 - - + +
77C ALA* 3.5 26.5 - - + +
80C ALA* 3.7 20.4 - - + -
85C TYR 3.6 2.8 + - - -
86C ARG* 1.3 74.7 - - - +
88C LYS* 1.3 60.2 + - - +
89C LEU* 3.6 27.8 - - + -
107C GLY 5.7 0.6 + - - -
108C ALA* 3.7 18.6 - - + +
109C GLU* 3.0 28.6 + - - +
138C LEU* 4.9 1.1 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B HIS* 4.1 9.0 - - - -
63C VAL* 3.8 23.1 - - + +
64C LEU 2.7 16.1 + - - +
65C ILE* 3.2 12.9 - - + +
66C GLU 3.2 23.7 + - - -
86C ARG* 6.1 2.2 - - + +
87C MET* 1.3 73.5 - - - +
89C LEU* 1.3 64.2 + - - +
109C GLU* 3.9 29.4 - - + +
111C ILE* 4.2 10.8 - - + -
129C MET* 3.7 16.2 - - + -
134C GLU* 2.8 55.3 + - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 3.6 9.6 - - + +
68C THR* 4.2 6.5 - - + -
73C GLY* 3.3 40.4 - - - +
76C LEU* 5.0 0.7 - - + -
87C MET* 3.6 31.0 - - + -
88C LYS* 1.3 87.4 - - - +
90C LEU* 1.3 59.8 + - - +
103C MET* 3.3 29.4 - - + -
108C ALA* 4.1 13.0 - - + -
109C GLU 3.0 15.5 + - - +
110C LEU* 3.4 12.2 - - + +
111C ILE* 2.8 34.7 + - - +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ILE* 4.3 8.3 - - + -
66C GLU 2.8 14.2 + - - +
67C ALA* 3.1 9.7 - - + +
68C THR* 2.5 37.5 + - - +
89C LEU* 1.3 73.6 - - - +
91C MET* 1.3 55.9 + - - +
111C ILE* 3.5 24.0 - - + +
113C VAL* 3.8 10.1 - - + -
122C ALA* 3.1 35.4 - - + +
125C LEU* 3.5 26.2 - - + -
126C ALA* 4.1 13.2 - - + +
129C MET* 3.7 26.9 - - - -
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Residues in contact with MET 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR* 2.8 20.0 - - + +
70C GLY* 4.0 19.1 - - - -
89C LEU 4.2 0.4 - - - -
90C LEU* 1.3 73.1 - - - +
92C PRO* 1.3 67.0 - - - +
95C MET* 3.4 36.6 - - + -
99C ARG* 4.2 4.0 - - + -
100C ARG* 3.5 33.2 - - + +
103C MET* 3.4 31.4 - - + +
110C LEU* 4.4 6.2 - - + +
111C ILE 3.4 5.3 + - - -
112C LEU* 2.8 37.5 - - + +
113C VAL* 3.5 11.7 + - - +
122C ALA* 4.9 0.8 - - - +
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Residues in contact with PRO 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR 3.4 10.5 - - - +
91C MET* 1.3 93.3 - - + +
93C ASP* 1.3 65.4 + - - +
94C ASN* 3.2 16.2 - - - +
95C MET* 3.1 41.1 + - + +
112C LEU* 4.2 1.6 - - - +
113C VAL* 3.4 17.0 - - + -
114C THR 4.3 0.9 - - - +
118C GLY* 3.7 23.3 - - - +
119C MET* 3.7 27.8 - - + +
122C ALA* 4.6 2.0 - - + -
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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