Contacts of the strand formed by residues 49 - 57 (chain A) in PDB entry 1BLJ
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 ALA 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A SER* 3.2 15.6 + - - +
46A ASN* 3.1 35.4 + - + +
47A LYS* 4.3 17.3 - - + -
48A GLY* 1.4 77.7 - - - +
50A PHE* 1.3 69.3 + - - +
69A ILE 3.5 13.9 - - - +
70A ARG* 4.5 10.3 - - + +
71A SER* 3.2 6.4 + - - -
77A TYR* 4.9 0.2 - - - -
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Residues in contact with PHE 50 (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 PHE* 3.6 28.0 - + - -
16A PHE 3.5 20.0 - - - -
17A ARG* 5.1 2.5 - - + -
40A ILE* 3.4 22.0 - - + -
41A ARG 3.4 9.6 - - - -
42A GLU* 3.5 22.7 - - + +
43A SER* 4.5 2.7 + - - -
46A ASN* 5.1 2.2 - - - -
48A GLY* 3.6 13.2 - - - -
49A ALA* 1.3 84.7 - - - +
51A SER* 1.3 68.9 + - - +
68A LYS* 4.6 1.9 - - - -
69A ILE* 3.0 42.9 + - + +
77A TYR* 3.8 23.7 - + + -
88A LEU* 4.0 10.1 - - + -
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Residues in contact with SER 51 (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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40A ILE* 3.1 26.9 - - - +
41A ARG* 2.7 42.3 + - - -
42A GLU 4.1 3.6 - - - -
43A SER* 4.2 5.0 + - - -
50A PHE* 1.3 76.3 + - - +
52A LEU* 1.4 64.5 + - - +
67A TYR 3.4 14.6 - - - -
68A LYS* 5.5 0.4 - - - -
69A ILE* 3.3 4.9 - - - +
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Residues in contact with LEU 52 (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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14A TRP* 6.4 0.2 - - - -
38A PHE* 3.3 45.3 - - + -
39A LEU 2.8 33.9 - - - +
40A ILE* 3.5 28.9 - - + -
41A ARG* 5.0 0.4 - - - +
51A SER* 1.4 78.6 - - - +
53A SER* 1.3 63.3 + - - +
66A HIS* 3.2 8.2 - - - -
67A TYR* 2.9 47.4 + - + -
69A ILE* 3.8 11.0 - - + -
79A ILE* 4.6 18.6 - - + -
91A LEU* 4.7 6.5 - - + -
95A TYR* 5.2 0.2 - - + -
102A LEU* 4.6 3.1 - - + -
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Residues in contact with SER 53 (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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24A ALA* 3.4 12.8 - - - +
25A GLU* 2.8 34.2 + - - -
28A LEU* 3.4 15.5 - - - -
38A PHE* 3.3 23.7 - - - +
39A LEU* 3.0 14.9 + - - +
41A ARG* 4.7 7.1 - - - +
52A LEU* 1.3 73.6 - - - +
54A VAL* 1.4 68.8 - - - +
64A VAL* 3.6 2.9 - - - -
65A LYS 3.3 7.0 - - - -
66A HIS* 5.5 0.2 + - - -
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Residues in contact with VAL 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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28A LEU* 4.0 0.4 - - - -
36A GLY 4.0 4.9 - - - +
37A SER 3.9 4.0 - - - -
38A PHE* 2.9 53.6 - - + -
52A LEU* 4.4 0.2 - - + -
53A SER* 1.4 78.9 - - - +
55A LYS* 1.3 63.5 + - - +
56A ASP 3.0 1.9 + - - -
64A VAL* 2.8 34.6 - - - +
65A LYS* 2.8 14.0 + - + +
67A TYR* 3.5 22.7 - - + +
104A GLN* 3.4 30.7 - - + +
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Residues in contact with LYS 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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28A LEU* 3.0 27.5 - - + +
29A LEU* 3.0 34.1 - - - +
33A ASN 5.4 0.7 - - - +
34A LYS* 4.5 3.6 - - - -
35A ALA* 3.1 43.9 - - - +
37A SER* 3.7 15.8 + - - +
54A VAL* 1.3 76.8 - - - +
56A ASP* 1.4 61.7 + - - +
57A ILE* 3.2 11.9 + - + +
62A GLU* 3.5 40.4 - - + +
63A VAL 3.0 25.5 + - - +
64A VAL* 3.3 17.6 - - - +
104A GLN* 4.1 0.5 - - - +
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Residues in contact with ASP 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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54A VAL 3.0 4.4 + - - -
55A LYS* 1.4 68.6 - - - +
57A ILE* 1.3 62.9 + - - +
58A THR* 3.3 26.4 + - - +
60A GLN* 5.0 0.9 - - - +
62A GLU* 3.5 1.7 - - - -
63A VAL* 2.6 60.8 + - - +
64A VAL 3.4 10.8 - - - +
65A LYS* 3.6 23.5 + - + -
103A CYS* 5.3 0.2 - - - -
104A GLN* 3.1 31.3 + - - +
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Residues in contact with ILE 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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33A ASN 5.3 0.9 - - - +
34A LYS* 4.0 16.6 - - + -
35A ALA* 3.6 30.8 - - + +
55A LYS* 3.2 27.8 + - + +
56A ASP* 1.3 74.3 + - - +
58A THR* 1.3 62.0 + - - +
62A GLU* 4.2 17.0 - - + +
104A GLN* 4.4 3.6 - - - +
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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