Contacts of the strand formed by residues 50 - 56 (chain A) in PDB entry 1BIK
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 4.0 3.1 - - - -
45A ASN* 2.8 31.2 + - - +
48A SER* 3.1 19.5 - - - +
49A MET* 1.3 79.1 - - - +
51A CYS* 1.3 66.6 + - - +
52A GLU* 3.6 6.9 + - + +
73A LEU* 5.0 0.9 - - - -
117A GLY 3.7 21.5 - - - +
118A ASN* 3.9 6.5 - - + -
119A GLY 4.3 4.9 - - - +
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Residues in contact with CYS 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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42A TYR* 4.3 11.2 - - + -
43A PHE 3.3 4.7 - - - -
44A TYR* 4.1 8.3 - - - +
50A ALA* 1.3 75.8 - - - +
52A GLU* 1.3 60.6 + - - +
69A GLU* 4.0 26.7 + - + +
72A CYS* 2.0 53.2 - - + -
73A LEU* 3.4 31.2 - - + +
116A GLN* 6.0 1.4 - - - -
117A GLY 4.6 4.2 + - - +
118A ASN 5.4 0.4 - - - -
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Residues in contact with GLU 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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42A TYR* 3.0 7.6 - - - -
43A PHE* 2.7 48.7 + - + -
45A ASN* 3.2 24.6 + - - -
48A SER* 2.8 30.1 + - - -
50A ALA* 4.0 9.3 - - + +
51A CYS* 1.3 76.7 - - - +
53A THR* 1.3 65.3 + - - +
148A NAG 3.8 16.7 + - - +
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Residues in contact with THR 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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40A SER* 4.5 17.9 + - - +
41A ARG 2.9 10.1 - - - +
42A TYR* 3.6 34.8 - - + +
43A PHE* 4.0 7.6 - - - -
52A GLU* 1.3 78.6 - - - +
54A PHE* 1.3 64.8 + - - +
55A GLN* 5.8 0.2 - - - -
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Residues in contact with PHE 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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30A TYR* 3.3 41.5 - + + -
31A SER 3.6 24.2 - - - -
39A THR 3.3 1.4 - - - +
40A SER* 3.4 0.7 - - - -
41A ARG* 2.7 54.9 + - + -
42A TYR 3.6 16.6 - - - -
43A PHE* 3.7 26.7 - + + -
53A THR* 1.3 76.5 - - - +
55A GLN* 1.3 73.6 + - - +
56A TYR* 3.5 14.8 + - + -
64A ASN 4.0 8.7 - - - -
65A ASN* 3.8 22.4 - - + -
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Residues in contact with GLN 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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30A TYR* 5.3 1.4 - - - -
32A ALA* 3.4 21.5 - - - +
38A MET* 4.2 26.1 + - + +
39A THR* 3.2 24.9 - - - +
40A SER* 2.8 24.5 + - - +
53A THR* 5.8 0.2 - - - -
54A PHE* 1.3 76.8 - - - +
56A TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 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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31A SER 3.7 12.6 - - - -
32A ALA 3.4 13.5 - - - -
37A GLY 3.4 1.0 - - - +
38A MET* 3.2 4.2 - - - -
39A THR* 2.7 35.1 + - - +
41A ARG* 3.6 48.0 - - + -
54A PHE* 3.5 11.1 + - + -
55A GLN* 1.3 73.1 - - - +
57A GLY* 1.3 60.3 + - - +
58A GLY* 3.4 23.0 + - - -
59A CYS* 3.3 40.5 + - - -
60A MET 3.9 1.4 + - - -
61A GLY* 4.2 11.1 + - - -
65A ASN* 3.3 27.4 - - - -
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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