Contacts of the helix formed by residues 54 - 62 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.3 12.6 - - - +
52B GLY 3.2 4.0 + - - -
53B SER* 1.3 72.6 - - - +
55B ALA* 1.3 53.1 + - - +
57B ALA* 3.0 6.0 + - - +
58B LEU* 2.7 35.8 + - + +
88B ASP* 2.7 43.0 + - + +
89B THR* 3.2 9.9 + - - +
92B VAL* 3.4 30.3 - - + -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP* 5.4 6.7 - - - +
111A LYS* 6.3 0.4 - - - +
21B VAL* 4.4 19.0 - - + +
25B ARG* 3.9 19.5 + - - +
53B SER* 3.0 3.3 + - - +
54B THR* 1.3 78.5 - - - +
56B ILE* 1.3 58.2 + - - +
58B LEU* 3.8 8.4 - - - +
59B GLU* 3.0 27.9 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.2 37.5 - - + +
19B GLY* 3.3 26.0 - - - -
20B ASP 3.9 2.0 - - - +
21B VAL* 4.2 18.6 - - + -
24B VAL* 4.1 13.0 - - + -
49B MET* 4.1 16.8 - - + -
50B MET* 5.0 0.2 - - + -
53B SER* 2.8 22.3 + - - +
55B ALA* 1.3 76.7 - - - +
57B ALA* 1.3 68.6 + - - +
59B GLU* 3.7 5.3 - - - +
60B LEU* 2.9 43.2 + - + +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.8 4.4 - - + +
49B MET* 3.5 35.4 - - + -
53B SER 3.1 3.3 + - - +
54B THR* 3.0 10.9 + - - +
56B ILE* 1.3 80.9 - - - +
58B LEU* 1.3 63.6 + - - +
60B LEU* 3.2 1.9 + - - +
61B LEU* 3.0 32.4 + - + +
89B THR* 3.9 17.7 - - + -
92B VAL* 4.5 9.4 - - + -
93B LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 5.6 5.6 - - - +
54B THR* 2.7 20.9 + - + +
55B ALA* 3.8 8.1 - - - +
57B ALA* 1.3 72.1 - - - +
59B GLU* 1.3 65.9 + - - +
61B LEU* 2.9 4.1 + - - +
62B LYS* 2.8 55.9 + - + +
92B VAL* 3.8 17.9 - - + +
96B HIS* 3.7 28.7 - - + -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 5.6 0.4 - - + -
24B VAL* 4.6 5.4 - - + -
25B ARG* 3.2 47.6 + - + +
28B LEU* 3.7 15.7 - - + -
29B HIS* 3.1 33.6 + - - -
55B ALA 3.0 17.9 + - - +
56B ILE* 3.3 6.9 + - - +
58B LEU* 1.3 78.8 - - - +
60B LEU* 1.3 61.9 + - - +
62B LYS* 3.3 19.2 + - - +
63B GLN* 3.3 28.8 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.3 24.2 - - + -
16B ALA* 4.7 1.8 - - + -
24B VAL* 4.3 8.3 - - + -
28B LEU* 4.3 15.9 - - + -
35B PRO* 4.2 13.7 - - + +
45B ALA* 3.9 12.3 - - + -
46B LEU* 3.4 44.2 - - + +
49B MET* 4.5 1.3 - - - -
56B ILE* 2.9 35.7 + - + +
57B ALA 3.6 3.6 - - - +
59B GLU* 1.3 75.6 - - - +
61B LEU* 1.3 59.2 + - - +
63B GLN* 3.1 18.9 + - - +
64B GLY 3.3 4.0 + - - -
65B ALA* 3.2 19.1 + - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.7 22.9 - - + -
57B ALA* 3.0 18.1 + - + +
58B LEU 2.9 4.4 + - - +
60B LEU* 1.3 76.2 - - - +
62B LYS* 1.3 60.9 + - - +
63B GLN 3.3 0.2 - - - -
64B GLY* 2.9 18.1 + - - +
65B ALA* 3.5 20.4 - - + +
67B PRO* 3.9 14.8 - - + -
92B VAL* 3.6 39.9 - - + +
93B LEU* 3.9 19.5 - - + -
96B HIS* 3.8 31.6 - - + +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 6.0 1.4 - - - +
58B LEU* 2.8 53.7 + - + +
59B GLU* 3.8 22.9 + - - +
60B LEU 3.1 0.2 - - - -
61B LEU* 1.3 75.7 - - - +
63B GLN* 1.3 73.9 + - - +
64B GLY 3.1 5.9 + - - -
96B HIS* 4.4 8.5 - - - +
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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