Contacts of the helix formed by residues 21 - 28 (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 VAL 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A THR* 5.5 2.5 - - + -
110A ASP* 5.3 11.4 - - - +
19B GLY 3.0 10.9 + - - +
20B ASP* 1.3 70.7 + - - +
22B GLN* 1.3 86.4 + - - +
24B VAL* 2.8 6.7 + - + +
25B ARG* 2.8 63.1 + - + +
53B SER* 4.3 5.8 - - - +
55B ALA* 4.4 17.3 - - + +
56B ILE* 4.2 20.2 - - + -
59B GLU* 5.6 0.4 - - + -
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Residues in contact with GLN 22 (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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110A ASP* 5.9 1.4 + - - -
168A ARG* 3.0 30.9 + - - +
20B ASP* 3.1 9.1 - - - +
21B VAL* 1.3 90.3 + - - +
23B GLU* 1.3 51.6 + - - +
25B ARG* 3.0 10.8 + - - +
26B ARG* 2.7 35.3 + - - +
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Residues in contact with GLU 23 (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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11B ARG* 5.3 0.5 - - - +
15B ALA* 3.8 13.7 - - + -
18B ARG* 4.8 9.0 - - - +
20B ASP* 3.3 22.4 + - - +
22B GLN* 1.3 77.4 - - - +
24B VAL* 1.3 53.8 + - - +
26B ARG* 2.6 49.4 + - - +
27B LEU* 2.6 67.8 + - + +
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Residues in contact with VAL 24 (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* 3.9 18.9 - - + +
15B ALA* 3.4 20.6 - - + -
16B ALA* 3.4 20.4 - - + +
20B ASP 3.2 15.5 - - - +
21B VAL* 2.8 10.8 + - + +
23B GLU* 1.3 77.7 - - - +
25B ARG* 1.3 58.5 + - + +
27B LEU* 3.9 0.6 - - - -
28B LEU* 2.9 49.9 + - + +
56B ILE* 4.1 12.8 - - + -
59B GLU* 4.6 10.1 - - + -
60B LEU* 4.3 17.5 - - + -
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Residues in contact with ARG 25 (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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21B VAL* 2.8 43.5 + - + +
22B GLN* 3.5 9.2 - - - +
24B VAL* 1.3 72.5 - - + +
26B ARG* 1.3 57.6 + - - +
28B LEU* 4.3 3.8 - - - -
29B HIS* 2.9 41.6 + - + +
55B ALA* 3.9 24.5 + - - +
58B LEU* 5.6 5.7 - - - +
59B GLU* 3.2 42.5 + - + +
62B LYS* 6.0 1.4 - - - +
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Residues in contact with ARG 26 (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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11B ARG* 4.3 5.7 - - - +
22B GLN 2.7 13.8 + - - +
23B GLU* 2.6 50.8 + - - +
25B ARG* 1.3 73.4 - - - +
27B LEU* 1.3 71.2 + - - +
28B LEU 2.8 4.8 + - - -
29B HIS 2.9 12.6 + - - -
30B ARG* 3.0 62.3 + - - +
31B GLU* 3.4 32.4 + - - +
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Residues in contact with LEU 27 (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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11B ARG* 3.6 66.0 - - + +
12B LEU* 3.7 16.6 - - + +
15B ALA* 4.0 5.8 - - + -
23B GLU* 2.6 61.9 + - + +
24B VAL 4.0 0.7 - - - +
26B ARG* 1.3 77.9 - - - +
28B LEU* 1.3 56.0 + - - +
31B GLU* 3.1 22.0 - - + +
33B VAL* 2.9 38.0 + - + +
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Residues in contact with LEU 28 (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* 4.1 22.7 - - + -
24B VAL* 2.9 31.1 + - + +
25B ARG 3.7 2.0 - - - +
26B ARG 2.8 1.8 + - - -
27B LEU* 1.3 78.7 - - - +
29B HIS* 1.3 69.8 + - + +
32B LEU* 3.0 25.8 - - - +
33B VAL 3.4 22.7 + - - +
35B PRO* 4.0 17.7 - - + -
59B GLU* 3.7 31.0 - - + +
60B LEU* 4.3 5.4 - - + -
63B GLN* 3.7 24.9 - - + -
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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