Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 1B4A
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 THR 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL* 3.6 29.8 - - + -
96A LEU 3.4 8.5 - - - +
97A ARG* 4.0 19.2 + - - -
103A ALA* 3.2 6.5 - - - +
122A ILE 4.2 0.3 - - - +
123A CYS* 3.6 0.3 - - - -
124A GLY* 2.8 28.8 + - - -
125A ASP 3.7 2.1 + - - +
126A ASP* 1.3 90.7 + - - +
128A CYS* 1.3 64.9 + - - +
129A LEU 4.3 0.2 - - - -
111B ASP* 5.2 2.3 + - - -
120B GLY* 5.7 0.2 - - - -
121B THR 3.4 24.4 + - - +
122B ILE* 4.0 8.4 - - + +
123B CYS 5.7 0.6 + - - -
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Residues in contact with CYS 128 (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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94A LEU 3.5 2.6 - - - +
95A VAL* 3.6 0.3 - - - -
96A LEU* 2.8 51.7 + - + +
98A THR* 5.5 0.7 - - + -
103A ALA* 4.3 10.3 - - + +
106A ILE* 5.0 3.8 - - + -
107A GLY* 4.2 12.8 - - - -
110A LEU* 4.4 9.4 - - - -
121A THR* 4.5 3.8 - - - -
122A ILE 3.7 2.9 - - - -
123A CYS* 3.4 28.0 - - - -
127A THR* 1.3 76.8 - - - +
129A LEU* 1.3 69.0 + - - +
130A ILE* 3.7 16.5 + - - +
122B ILE* 4.0 2.9 - - - -
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Residues in contact with LEU 129 (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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93A LEU* 4.0 25.6 - - + -
94A LEU 3.2 21.8 - - - +
95A VAL* 4.3 1.6 - - + +
121A THR* 3.1 7.8 - - - -
122A ILE* 2.8 42.7 + - + +
128A CYS* 1.3 71.7 - - - +
130A ILE* 1.3 65.2 + - - +
131A ILE* 3.6 34.4 + - + +
93B LEU* 6.5 0.2 - - + -
122B ILE* 3.4 29.0 - - + +
129B LEU* 4.5 8.3 - - + -
131B ILE* 4.1 16.8 - - + -
93C LEU* 6.2 0.4 - - + -
129C LEU* 4.1 16.8 - - + -
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Residues in contact with ILE 130 (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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87A LEU* 5.4 0.7 - - + -
92A ASN 3.9 0.3 - - - +
93A LEU* 3.7 4.2 - - - -
94A LEU* 2.8 52.0 + - + +
96A LEU* 4.8 13.7 - - + -
110A LEU* 3.9 24.2 - - + -
118A ILE* 3.9 36.1 - - + -
120A GLY 3.9 1.6 - - - -
121A THR* 4.2 5.8 - - + -
128A CYS* 4.1 15.3 - - - +
129A LEU* 1.3 76.0 - - - +
131A ILE* 1.3 61.8 + - - +
132A CYS* 3.7 12.2 + - - -
141A VAL* 4.9 1.3 - - + -
145A LEU* 4.2 23.6 - - + -
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Residues in contact with ILE 131 (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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93A LEU* 4.0 13.0 - - + -
118A ILE* 3.6 3.1 - - - +
119A VAL* 2.8 35.4 + - + -
120A GLY 2.9 34.8 + - - +
121A THR* 4.2 3.4 - - - +
122A ILE* 4.5 4.9 - - + +
129A LEU* 3.6 35.4 - - + +
130A ILE* 1.3 70.7 - - - +
132A CYS* 1.3 55.6 + - - +
90C THR* 3.6 28.0 - - + -
93C LEU* 3.9 24.2 - - + -
95C VAL* 4.4 8.7 - - + -
129C LEU* 4.3 19.7 - - + -
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Residues in contact with CYS 132 (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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92A ASN* 2.9 42.4 + - - +
94A LEU* 3.5 31.6 - - - -
117A GLU 3.0 13.9 - - - +
118A ILE* 4.6 1.6 - - - -
119A VAL* 3.8 3.1 - - - -
130A ILE* 4.1 13.5 - - - -
131A ILE* 1.3 76.8 - - - +
133A ARG* 1.3 61.5 + - - +
134A THR 3.3 3.1 + - - +
137A ASP 4.3 0.9 - - - -
138A ALA* 3.7 24.7 - - - +
141A VAL* 4.1 11.7 - - - -
90C THR* 3.6 4.7 - - - +
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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