Contacts of the strand formed by residues 84 - 91 (chain A) in PDB entry 1BX4
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.3 27.4 - - + +
70A ILE* 3.7 28.9 - - + +
74A GLN* 3.2 17.8 + - + +
77A ILE* 5.4 1.3 - - + -
82A LYS 4.2 2.0 - - - -
83A ALA* 1.3 79.5 - - + +
85A THR* 1.3 58.6 + - - +
108A VAL* 3.5 8.0 - - + +
109A ASP* 2.9 27.1 + - - +
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Residues in contact with THR 85 (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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7A ASN* 3.0 31.7 + - - +
9A LEU 2.8 13.8 + - - -
10A PHE* 3.9 16.8 - - + +
11A GLY* 2.9 24.8 + - - -
70A ILE* 4.1 6.6 - - - +
84A ALA* 1.3 72.9 - - - +
86A PHE* 1.3 66.0 + - - +
87A PHE* 3.7 26.9 - - + -
108A VAL* 4.5 1.1 - - - -
109A ASP* 3.4 14.4 - - + +
158A LEU* 4.4 19.1 + - + -
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Residues in contact with PHE 86 (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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11A GLY 3.2 16.2 - - - -
13A GLY 3.7 31.4 - - - -
14A ASN 4.7 0.9 - - - -
15A PRO* 4.0 11.7 - - + -
66A THR* 3.9 9.9 - - + -
67A GLN* 3.5 62.6 - - + -
70A ILE* 4.4 8.1 - - + -
85A THR* 1.3 75.8 - - - +
87A PHE* 1.3 81.2 + - - +
108A VAL* 4.0 17.7 - - + -
109A ASP 3.1 8.1 + - - -
110A ALA* 3.3 4.0 - - + -
111A HIS 3.0 26.7 + - - +
112A TYR* 3.9 19.5 - + - -
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Residues in contact with PHE 87 (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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10A PHE* 3.6 27.8 - + - -
11A GLY 3.1 7.3 + - - -
12A MET* 3.2 14.8 - - + +
13A GLY 3.1 24.6 + - - -
85A THR* 3.7 19.1 - - + -
86A PHE* 1.3 88.4 - - - +
88A GLY* 1.3 58.7 + - - +
111A HIS* 3.4 31.4 - + + +
144A TYR* 3.9 16.8 - - - +
149A HIS* 3.7 15.5 - + + -
150A LEU* 4.1 14.8 - - + -
155A ASN* 3.4 47.8 - - + -
158A LEU* 4.2 6.7 - - + -
159A VAL* 4.1 0.9 - - + -
171A PHE* 5.6 0.2 - - - -
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Residues in contact with GLY 88 (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 GLY 3.6 15.5 - - - -
15A PRO* 3.8 13.0 - - - -
86A PHE* 4.1 1.8 - - - -
87A PHE* 1.3 75.4 - - - +
89A CYS* 1.3 59.5 + - - -
111A HIS 3.8 3.4 + - - -
112A TYR* 3.3 9.3 - - - -
113A TYR* 2.8 24.4 + - - +
144A TYR* 3.8 15.2 - - - -
171A PHE* 5.8 0.4 - - - -
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Residues in contact with CYS 89 (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 GLY 4.5 0.6 + - - -
15A PRO* 3.5 18.8 - - - +
88A GLY* 1.3 72.9 - - - -
90A ILE* 1.3 69.5 + - - +
113A TYR* 3.2 31.0 - - + +
115A GLN* 3.7 26.5 - - - -
140A ALA 3.1 26.2 - - - +
141A ALA* 3.6 14.5 + - - +
143A CYS* 4.0 5.8 - - - -
144A TYR* 4.0 22.8 - - + +
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Residues in contact with ILE 90 (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 PRO* 3.9 22.2 - - + +
89A CYS* 1.3 79.1 - - - +
91A GLY* 1.3 71.5 + - - +
96A GLY* 4.0 10.3 - - - +
99A LEU* 4.1 16.2 - - + -
100A LYS* 4.0 29.4 - - + +
112A TYR* 4.0 21.3 - - + -
113A TYR 2.9 7.2 + - - +
114A GLU* 3.9 28.0 - - + +
115A GLN* 3.1 28.2 + - - -
120A THR* 3.9 10.5 - - + +
140A ALA* 3.6 10.3 - - - -
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Residues in contact with GLY 91 (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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90A ILE* 1.3 92.1 - - - +
92A ILE* 1.3 64.1 + - - +
93A ASP* 3.5 9.9 + - - +
96A GLY* 4.2 2.3 - - - -
100A LYS* 5.7 0.3 + - - -
114A GLU* 4.6 1.4 - - - +
115A GLN 3.4 10.1 - - - -
118A GLN 3.6 17.3 - - - -
120A THR* 3.0 21.8 + - - -
140A ALA* 3.6 4.0 - - - +
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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