Contacts of the strand formed by residues 53 - 61 (chain A) in PDB entry 1BKL
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.4 19.2 - - - -
49A ASP 2.7 27.2 + - - -
50A ASN 4.1 2.3 + - - -
51A ALA 3.6 1.8 - - - -
52A LYS* 1.3 74.8 - - - +
54A LEU* 1.3 62.3 + - - -
55A ASN* 2.8 27.7 + - - -
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Residues in contact with LEU 54 (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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19A LEU 5.4 2.5 - - - +
20A LEU* 4.0 25.4 - - + +
21A ASN 4.6 5.4 - - - +
22A PRO* 4.1 35.2 - - + +
24A ASN* 5.0 11.4 - - + +
46A SER* 5.3 9.6 - - - -
47A ASP 3.6 15.5 - - - +
48A PHE* 3.3 22.1 - - + -
52A LYS 4.5 3.3 - - - +
53A GLY* 1.3 70.4 - - - -
55A ASN* 1.3 60.4 + - - +
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Residues in contact with ASN 55 (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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20A LEU* 4.1 5.9 - - - +
46A SER* 3.6 4.2 - - - -
47A ASP* 2.8 42.5 + - - +
48A PHE 4.6 0.2 - - - -
49A ASP* 3.7 10.9 + - - +
52A LYS* 3.5 28.6 - - + +
53A GLY 2.8 22.6 + - - +
54A LEU* 1.3 75.9 - - - +
56A VAL* 1.3 67.1 + - - +
57A LYS* 2.7 36.2 + - - +
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Residues in contact with VAL 56 (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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16A GLU* 4.0 29.9 - - + +
19A LEU* 3.6 26.2 - - + -
20A LEU* 4.0 24.4 - - + +
45A VAL 3.2 25.6 - - - +
46A SER* 4.0 4.0 - - - +
55A ASN* 1.3 81.0 - - - +
57A LYS* 1.3 69.5 + - - +
58A HIS* 3.9 19.9 + - + -
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Residues in contact with LYS 57 (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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43A LEU 3.6 1.0 - - - +
44A SER* 3.6 2.8 - - - -
45A VAL 2.9 36.7 + - - +
47A ASP* 2.7 24.9 + - + +
52A LYS* 5.8 3.8 - - - +
55A ASN* 2.7 25.8 + - - +
56A VAL* 1.3 75.0 - - - +
58A HIS* 1.3 65.0 + - - +
59A TYR* 3.6 32.1 - - + +
95A CYS* 3.6 26.4 - - + +
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Residues in contact with HIS 58 (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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12A ARG* 3.1 46.2 + - + +
15A SER* 3.7 9.4 - - - -
16A GLU* 3.2 29.7 + - + +
32A ARG* 3.0 23.7 + - - +
42A CYS* 5.1 8.1 - - - -
43A LEU 3.5 1.3 - - - +
44A SER* 2.9 28.0 + - - -
56A VAL* 3.9 19.6 + - + +
57A LYS* 1.3 75.2 - - - +
59A TYR* 1.3 76.7 + - - +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A CYS* 3.1 9.5 - - - +
43A LEU* 2.7 58.4 + - + +
45A VAL* 3.9 24.7 - - + -
57A LYS* 3.6 24.0 - - + +
58A HIS* 1.3 85.3 - - - +
60A LYS* 1.3 62.7 + - - +
71A ILE* 4.1 25.4 - - + -
93A GLY 5.1 1.5 + - - -
94A LEU* 4.1 19.3 - - + -
95A CYS* 2.9 38.3 + - - +
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Residues in contact with LYS 60 (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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34A SER* 3.9 19.7 - - - -
37A THR* 5.2 15.6 + - - +
40A ALA* 4.6 11.2 - - + -
41A TYR 3.6 9.2 - - - +
42A CYS* 4.6 8.2 - - - +
59A TYR* 1.3 71.9 - - - +
61A ILE* 1.3 68.3 + - - +
62A ARG* 3.4 31.9 + - + +
71A ILE* 3.2 27.0 - - + +
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Residues in contact with ILE 61 (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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31A VAL* 4.2 20.0 - - + -
40A ALA* 3.6 4.3 - - - +
41A TYR* 2.8 43.6 + - + -
42A CYS 4.3 0.2 - - - -
43A LEU* 3.7 31.0 - - + +
59A TYR 4.0 0.9 - - - +
60A LYS* 1.3 77.4 - - - +
62A ARG* 1.3 64.2 + - - +
63A LYS 3.5 2.1 + - - -
69A PHE* 4.0 21.5 - - + -
70A TYR 3.8 2.9 - - - +
71A ILE* 4.3 9.2 - - + -
80A LEU* 4.0 12.3 - - + -
83A LEU* 3.7 43.3 - - + -
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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