Contacts of the strand formed by residues 27 - 31 (chain A) 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 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 3.3 3.8 - - - +
19A ILE* 2.5 54.0 + - + -
20A GLY 2.5 22.8 + - - +
24A TYR* 4.5 5.6 - - + +
26A LYS* 1.3 79.0 - - - +
28A PHE* 1.3 60.0 + - - +
41A ALA* 4.5 2.5 - - + -
42A LEU 3.4 3.8 - - - +
43A LYS* 3.8 25.8 - - + -
164A PHE* 3.9 46.4 - - + +
166A LEU* 4.2 11.0 - - + -
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A CYS* 4.5 11.2 - - - -
17A ALA 3.0 22.2 - - - +
18A GLU* 3.3 23.8 - - + -
19A ILE* 3.6 7.6 - - - +
26A LYS* 4.0 29.6 - - + -
27A VAL* 1.3 72.9 - - - +
29A LYS* 1.3 65.2 + - - +
40A VAL 3.4 0.2 - - - +
41A ALA* 3.0 10.4 - - - +
42A LEU* 2.8 57.3 + - + +
44A ARG* 3.8 38.4 - - + -
40B ARG* 4.2 7.2 - - - -
41B PHE* 4.1 22.0 - + - -
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A CYS* 3.7 1.9 - - - -
16A VAL* 2.8 36.0 + - + +
17A ALA* 2.8 14.3 + - + +
19A ILE* 3.7 14.1 - - + +
28A PHE* 1.3 74.6 - - - +
30A ALA* 1.3 62.4 + - - +
39A PHE* 3.9 29.2 - - + -
40A VAL 3.2 7.0 - - - +
100A HIS* 4.2 15.3 - - + +
102A ASP* 2.8 29.8 + - - -
17B ALA* 4.7 11.1 + - + +
48B VAL* 2.5 41.8 + - + +
49B MET 2.7 21.0 + - - -
50B MET* 4.0 1.8 - - - +
51B PHE* 4.3 2.6 - - - -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 4.7 2.0 - - + -
14A GLU 3.3 23.8 - - - +
15A CYS* 3.9 0.7 - - - -
16A VAL* 4.0 2.2 - - - -
29A LYS* 1.3 74.7 - - - +
31A ARG* 1.3 63.3 + - - +
39A PHE* 3.1 12.3 - - - -
40A VAL* 2.7 47.1 + - + -
42A LEU* 3.7 25.1 - - + -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.2 26.0 - - - -
14A GLU* 3.1 30.2 + - + +
16A VAL* 4.3 7.8 - - + +
30A ALA* 1.3 74.6 - - - +
32A ASP* 1.3 57.5 + - - +
33A LEU* 3.0 14.9 + - + +
37A GLY* 2.8 34.3 + - - +
38A ARG 3.6 1.8 - - - -
39A PHE* 3.4 21.3 - - + -
40A VAL* 4.5 0.7 - - - -
47B GLN 5.3 0.4 + - - -
71B ASP* 2.7 38.0 + - - -
73B SER* 4.9 6.3 - - - +
75B THR* 4.0 14.0 + - - +
80B ASP* 2.5 41.6 + - - -
83B ARG* 4.2 3.0 - - - +
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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