Contacts of the strand formed by residues 39 - 46 (chain C) in PDB entry 1BI8
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 PHE 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C VAL* 4.3 11.0 - - + -
29C LYS* 3.9 29.4 - - + -
30C ALA 3.1 14.4 - - - -
31C ARG* 3.4 36.3 - - + -
38C ARG* 1.3 81.6 - - - +
40C VAL* 1.3 61.7 + - - +
80C PHE* 6.1 0.5 - - - -
99C GLU* 5.6 0.3 - - - -
100C HIS* 4.1 21.7 + - + +
102C ASP* 3.9 22.9 - - - +
47D GLN 4.0 7.6 - - - -
48D VAL* 5.3 1.1 - - + -
51D PHE* 3.3 37.7 - + - -
80D ASP* 3.5 13.5 - - + -
83D ARG* 3.4 14.9 - - - +
84D THR* 5.0 4.3 - - + -
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Residues in contact with VAL 40 (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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13C TYR* 4.4 10.3 - - + -
28C PHE 3.4 0.2 - - - +
29C LYS* 3.2 7.1 - - - +
30C ALA* 2.7 60.3 + - + +
31C ARG 4.2 2.5 - - - +
32C ASP* 4.7 8.7 - - + +
38C ARG* 4.4 3.8 - - + +
39C PHE* 1.3 77.3 - - - +
41C ALA* 1.3 59.5 + - - +
42C LEU* 4.4 3.1 - - + -
80C PHE* 4.3 13.9 - - + -
97C VAL* 3.3 33.7 - - + -
98C PHE 2.8 26.7 - - - +
99C GLU* 4.9 0.2 - - - -
100C HIS* 4.0 6.5 - - - -
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Residues in contact with ALA 41 (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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19C ILE* 4.4 9.2 - - + -
27C VAL* 4.5 8.1 - - + -
28C PHE 3.0 7.9 - - - +
40C VAL* 1.3 75.4 - - - +
42C LEU* 1.3 62.6 + - - +
43C LYS* 4.1 8.5 - - - +
96C LEU 3.4 1.4 - - - +
97C VAL* 3.4 4.5 - - - -
98C PHE* 2.7 50.4 + - + +
99C GLU 4.6 0.9 - - - +
100C HIS* 3.9 22.8 - - + +
164C PHE* 5.1 1.8 - - + -
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Residues in contact with LEU 42 (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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13C TYR* 5.1 10.3 - - + -
15C CYS* 3.7 30.1 - - - +
27C VAL* 3.4 7.0 - - - -
28C PHE* 2.8 47.2 + - + +
30C ALA* 3.7 20.9 - - + -
40C VAL* 4.4 2.9 - - + -
41C ALA* 1.3 73.0 - - - +
43C LYS* 1.3 61.4 + - - +
44C ARG* 3.9 11.9 - - - +
95C THR* 4.1 13.5 - - + -
96C LEU 3.3 4.5 - - - +
97C VAL* 3.5 43.7 - - + -
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Residues in contact with LYS 43 (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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24C TYR* 5.3 16.4 - - + -
26C LYS 4.3 4.3 - - - +
27C VAL* 3.8 22.0 - - + -
41C ALA* 4.1 7.5 + - - +
42C LEU* 1.3 74.9 - - - +
44C ARG* 1.3 64.5 + - - +
45C VAL* 3.7 6.9 + - + +
77C VAL* 5.1 6.3 - - - +
95C THR* 4.6 0.7 - - - -
96C LEU* 3.0 35.9 + - + +
98C PHE* 4.0 40.7 - - + +
99C GLU 5.9 0.2 + - - -
162C ALA* 4.8 2.8 - - - +
163C ASP* 3.5 32.8 + - - +
164C PHE* 3.8 32.5 - - - +
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Residues in contact with ARG 44 (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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15C CYS* 4.0 18.7 - - - -
25C GLY* 5.3 9.4 + - - -
26C LYS* 4.3 11.6 + - + +
28C PHE* 3.8 31.1 - - + -
42C LEU* 3.9 19.1 + - - +
43C LYS* 1.3 71.8 - - - +
45C VAL* 1.3 64.9 + - - +
85C VAL* 5.5 6.0 - - + +
93C LYS* 6.0 5.8 - - - -
94C LEU 3.9 4.9 - - - +
95C THR* 3.9 33.3 + - - +
41D PHE* 5.7 3.0 - - - -
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Residues in contact with VAL 45 (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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24C TYR* 6.4 2.5 - - + -
43C LYS* 3.7 13.6 + - + +
44C ARG* 1.3 83.0 - - - +
46C ARG* 1.3 72.9 + - - +
47C VAL* 4.3 12.3 - - + -
92C THR 3.8 1.0 - - - +
93C LYS* 3.5 1.7 - - - -
94C LEU* 2.6 56.1 + - + +
96C LEU* 4.7 16.6 - - + -
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Residues in contact with ARG 46 (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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45C VAL* 1.3 81.5 - - - +
47C VAL* 1.3 65.1 + - - +
48C GLN* 2.7 52.6 + - - +
92C THR 3.3 9.3 - - - +
93C LYS* 4.2 17.5 - - + +
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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