Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 1BIB
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 5.5 0.4 - - - -
103A SER* 1.3 74.6 - - - +
105A ASP* 1.4 68.9 + - - +
106A ALA* 3.4 1.9 + - - +
135A MET* 3.5 19.9 - - - +
136A PHE 2.8 12.6 + - - -
137A TRP* 3.4 8.1 - - - -
247A ARG* 2.9 37.4 + - - -
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Residues in contact with ASP 105 (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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79A GLY* 4.4 2.8 - - - -
80A SER* 3.2 36.1 + - - +
94A LEU* 4.4 4.7 - - + +
100A GLU 4.3 1.7 - - - +
101A LEU* 3.1 25.9 - - + +
102A LYS* 2.5 50.0 + - - +
103A SER 4.7 0.9 - - - +
104A GLY* 1.4 78.1 - - - +
106A ALA* 1.3 60.9 + - - +
135A MET* 3.5 0.7 - - - +
136A PHE* 3.3 22.9 + - + +
247A ARG* 4.3 0.2 - - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 2.7 15.9 + - - +
81A VAL* 3.3 6.3 + - + -
82A ALA* 2.7 31.8 + - - +
93A TYR* 5.4 0.3 - - - -
94A LEU* 4.1 8.6 - - - +
104A GLY 3.7 6.7 - - - +
105A ASP* 1.3 77.9 - - - +
107A CYS* 1.3 61.5 + - - +
133A LEU* 5.5 0.2 - - + -
134A SER 3.4 13.2 - - - +
135A MET* 4.3 6.3 - - + -
243A ILE* 3.9 27.8 - - + -
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Residues in contact with CYS 107 (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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82A ALA* 3.2 6.3 - - + +
84A LEU* 3.7 29.8 - - - -
87A ILE* 4.0 9.0 - - - -
90A THR* 4.2 17.8 - - - +
93A TYR* 3.8 20.9 - - + -
94A LEU* 4.0 20.9 - - + -
106A ALA* 1.3 80.2 - - - +
108A ILE* 1.4 66.3 + - - +
132A TYR 3.8 0.5 - - - +
133A LEU* 3.6 3.1 - - - +
134A SER* 3.0 27.8 + - - +
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Residues in contact with ILE 108 (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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67A LEU* 3.7 24.7 - - + -
72A ILE* 4.5 12.1 - - + -
81A VAL* 3.0 37.5 - - + -
82A ALA 2.6 12.6 + - - +
83A VAL* 3.5 13.6 - - + +
84A LEU* 2.8 32.6 + - - +
90A THR* 4.8 0.7 - - - -
107A CYS* 1.4 78.9 - - - +
109A ALA* 1.4 61.2 + - - +
131A LEU* 3.8 17.5 - - + -
132A TYR 3.3 11.7 - - - +
133A LEU* 4.6 7.4 - - + -
239A ALA* 4.7 9.0 - - + -
243A ILE* 3.9 21.3 - - + -
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Residues in contact with ALA 109 (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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67A LEU* 3.8 8.7 - - - -
84A LEU* 3.1 22.0 - - + +
87A ILE* 3.8 24.0 - - + -
90A THR* 3.9 12.3 - - + +
108A ILE* 1.4 72.8 - - - +
110A GLU* 1.4 60.3 + - - +
111A TYR 3.5 9.4 - - - +
131A LEU* 3.9 4.5 - - - +
132A TYR* 2.9 35.3 + - + +
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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