Contacts of the strand formed by residues 52 - 58 (chain A) in PDB entry 1B8M
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 TYR 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TRP* 4.2 24.2 - + + -
20A VAL 3.2 18.6 - - - +
21A THR* 3.9 22.2 - - - -
50A LYS* 3.6 48.6 + - + +
51A GLN* 1.3 73.8 - - - +
53A PHE* 1.3 75.4 + - - +
98B ARG* 4.6 3.1 - - - -
112B TRP* 3.6 37.4 - + + -
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Residues in contact with PHE 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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18A GLU 3.5 0.5 - - - +
19A TRP* 3.3 8.0 - - - -
20A VAL* 2.7 46.2 + - + +
22A ALA* 4.9 6.1 - - - -
25A LYS* 3.9 31.6 - - + -
38A VAL* 3.8 22.7 - - + -
51A GLN* 4.0 17.3 - - + -
52A TYR* 1.3 83.9 - - - +
54A TYR* 1.3 60.3 + - - +
55A GLU* 3.7 2.2 + - - +
87A VAL* 4.1 25.6 - - + -
88A ARG 4.5 4.9 - - - -
89A ALA* 3.6 33.2 - - + -
103A ILE* 3.9 11.2 - - + -
105A ILE* 4.2 12.6 - - + -
112B TRP* 5.3 1.3 - - - -
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Residues in contact with TYR 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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17A SER* 3.6 23.3 + - - -
18A GLU* 3.7 5.6 - - - -
19A TRP* 3.6 47.5 - + + -
53A PHE* 1.3 73.0 - - - +
55A GLU* 1.3 59.4 + - - +
56A THR* 3.9 18.2 + - - -
105A ILE* 4.0 13.3 - - - +
106A ASP 4.2 1.4 - - - +
107A THR* 5.2 1.0 - - - +
94B GLN 4.4 5.2 - - - -
95B SER* 3.9 21.0 + - - -
96B TYR* 3.7 61.1 + + - +
112B TRP* 5.5 0.6 - - - -
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Residues in contact with GLU 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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16A ILE 4.0 0.2 - - - +
17A SER* 3.0 4.2 - - - -
18A GLU* 2.8 46.9 + - + +
20A VAL* 3.2 30.7 - - + +
25A LYS* 2.9 30.5 + - - -
53A PHE* 3.7 1.8 + - - +
54A TYR* 1.3 75.4 - - - +
56A THR* 1.3 59.4 + - - +
57A LYS* 4.0 22.6 + - + +
105A ILE* 4.3 6.0 - - + +
106A ASP* 3.1 41.8 + - + +
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Residues in contact with THR 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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15A SER* 4.0 22.2 - - - +
16A ILE 3.2 11.4 - - - +
17A SER* 3.2 20.1 + - - +
54A TYR* 3.9 14.0 + - - -
55A GLU* 1.3 74.6 - - - +
57A LYS* 1.3 63.9 + - - +
106A ASP* 3.0 24.5 + - - +
107A THR* 3.6 21.4 + - - +
108A SER* 3.4 17.3 + - - +
93B LYS* 5.0 9.6 - - + +
94B GLN 5.0 2.6 + - - -
95B SER* 4.8 2.9 + - - -
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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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15A SER* 3.3 4.9 - - - -
16A ILE* 2.9 39.2 + - + +
18A GLU* 3.9 23.9 + - - -
55A GLU* 4.0 20.2 + - - +
56A THR* 1.3 76.2 - - - +
58A CYS* 1.3 73.9 + - - +
60A PRO* 5.9 0.2 - - + -
82A THR* 3.7 22.2 - - + +
106A ASP* 4.3 14.2 + - + +
108A SER 4.5 0.9 - - - -
109A CYS* 3.9 5.2 - - - -
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Residues in contact with CYS 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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14A ASP 3.6 1.3 - - - +
16A ILE* 4.6 0.2 - - - +
57A LYS* 1.3 83.5 - - - +
59A ASN* 1.3 62.5 + - - +
60A PRO* 3.3 10.4 - - - +
80A CYS* 3.6 11.0 - - + +
81A ARG* 3.3 36.8 - - - -
82A THR* 3.3 12.3 + - - +
109A CYS* 2.0 48.6 - - - +
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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