Contacts of the helix formed by residues 54 - 62 (chain D) 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 THR 54 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LYS* 4.3 13.0 - - - +
52D GLY 3.2 4.0 + - - -
53D SER* 1.3 72.9 - - - +
55D ALA* 1.3 54.0 + - - +
57D ALA* 3.0 6.4 + - - +
58D LEU* 2.7 36.1 + - + +
88D ASP* 2.7 42.3 + - + +
89D THR* 3.2 10.2 + - - +
92D VAL* 3.4 30.7 - - + -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ASP* 5.4 6.5 - - - +
111C LYS* 6.3 0.2 - - - +
21D VAL* 4.4 19.2 - - + +
25D ARG* 3.9 19.9 + - - +
53D SER* 3.0 3.3 + - - +
54D THR* 1.3 80.2 - - - +
56D ILE* 1.3 57.6 + - - +
58D LEU* 3.8 8.2 - - - +
59D GLU* 3.0 27.9 + - - +
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Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 3.2 37.7 - - + +
19D GLY* 3.3 26.2 - - - -
20D ASP 3.9 1.6 - - - +
21D VAL* 4.2 18.6 - - + -
24D VAL* 4.1 12.6 - - + -
49D MET* 4.1 16.4 - - + -
50D MET* 5.0 0.2 - - + -
53D SER* 2.8 22.3 + - - +
55D ALA* 1.3 75.9 - - - +
57D ALA* 1.3 68.9 + - - +
59D GLU* 3.7 4.7 - - - +
60D LEU* 2.9 43.6 + - + +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.2 4.0 - - + -
49D MET* 3.5 35.4 - - + -
53D SER 3.1 3.5 + - - +
54D THR* 3.0 10.3 + - - +
56D ILE* 1.3 81.7 - - - +
58D LEU* 1.3 63.4 + - - +
60D LEU* 3.6 1.7 - - - +
61D LEU* 3.0 31.5 + - + +
89D THR* 3.9 17.7 - - + -
92D VAL* 4.5 9.2 - - + -
93D LEU* 5.6 0.4 - - + -
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ARG* 5.6 5.6 - - - +
54D THR* 2.7 20.4 + - + +
55D ALA* 3.8 8.1 - - - +
57D ALA* 1.3 72.0 - - - +
59D GLU* 1.3 66.5 + - - +
61D LEU* 2.9 4.1 + - - +
62D LYS* 2.8 56.2 + - + +
92D VAL* 3.8 17.9 - - + +
96D HIS* 3.7 28.5 - - + -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 5.6 0.4 - - + -
24D VAL* 4.6 5.4 - - + -
25D ARG* 3.2 48.4 + - + +
28D LEU* 3.7 15.5 - - + -
29D HIS* 3.1 33.4 + - - -
55D ALA 3.0 17.0 + - - +
56D ILE* 3.3 6.7 + - - +
58D LEU* 1.3 79.9 - - - +
60D LEU* 1.3 63.2 + - - +
62D LYS* 3.3 19.1 + - - +
63D GLN* 3.3 27.4 + - - +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.3 24.2 - - + -
16D ALA* 4.7 1.6 - - + -
24D VAL* 4.3 8.1 - - + -
28D LEU* 4.3 15.7 - - + -
35D PRO* 4.2 14.1 - - + +
45D ALA* 3.9 13.0 - - + +
46D LEU* 3.4 43.7 - - + +
49D MET* 4.5 0.9 - - - -
56D ILE* 2.9 38.1 + - + +
57D ALA 3.6 3.4 - - - +
59D GLU* 1.3 75.4 - - - +
61D LEU* 1.3 59.6 + - - +
63D GLN* 3.1 17.7 + - - +
64D GLY 3.3 4.3 + - - -
65D ALA* 3.2 18.4 - - + +
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.7 23.1 - - + -
57D ALA* 3.0 17.9 + - + +
58D LEU* 2.9 4.6 + - - +
60D LEU* 1.3 76.8 - - - +
62D LYS* 1.3 60.8 + - - +
64D GLY* 2.9 17.4 + - - +
65D ALA* 3.5 21.1 - - + +
67D PRO* 3.9 15.5 - - + -
92D VAL* 3.6 40.2 - - + +
93D LEU* 3.9 19.7 - - + -
96D HIS* 3.8 29.0 - - + +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ARG* 6.0 1.2 - - - +
58D LEU* 2.8 52.9 + - + +
59D GLU* 3.8 23.9 + - - +
61D LEU* 1.3 75.1 - - - +
63D GLN* 1.3 75.7 + - - +
64D GLY 3.1 5.9 + - - -
96D HIS* 4.4 8.7 - - - +
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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