Contacts of the strand formed by residues 131 - 136 (chain A) in PDB entry 1DZF
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 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 5.4 0.3 - - - +
106A GLN 3.1 7.6 + - - +
107A THR* 3.5 18.7 + - - +
108A GLY 3.0 22.5 + - - -
124A VAL 5.3 0.9 - - - -
129A PRO 4.0 8.7 - - - +
130A ALA* 1.3 79.8 - - - +
132A ILE* 1.3 64.6 + - - +
133A GLU* 4.3 8.6 + - - +
191A LYS* 3.8 34.5 - - + +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET* 4.8 2.9 - - + -
96A PHE* 3.5 30.7 - - + -
97A VAL* 3.9 28.5 - - + -
100A ILE* 4.8 7.9 - - + -
108A GLY* 3.4 7.2 - - - +
110A PHE* 4.3 4.9 - - + -
123A LEU 4.2 0.4 - - - +
124A VAL* 3.4 60.1 + - + +
127A ILE* 4.2 24.7 - - + -
130A ALA 5.8 0.2 - - - +
131A THR* 1.3 80.2 - - - +
133A GLU* 1.3 73.6 + - - +
134A THR* 4.7 0.7 - - + -
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Residues in contact with GLU 133 (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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26A ARG* 2.5 48.2 + - - -
107A THR* 3.5 13.3 - - + +
108A GLY 3.0 5.4 + - - +
109A ILE* 3.7 9.3 - - + -
110A PHE* 2.7 35.7 + - - +
131A THR* 4.3 10.1 + - - +
132A ILE* 1.3 80.2 - - - +
134A THR* 1.3 57.9 + - - +
135A PHE* 3.7 20.1 - - + -
186A LEU 3.8 4.5 - - - +
189A GLY* 3.9 12.6 - - - +
191A LYS* 6.1 0.9 - - - -
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Residues in contact with THR 134 (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 MET* 4.3 1.6 - - + -
110A PHE* 3.2 17.7 - - + -
112A TYR* 3.9 18.3 + - - -
116A ILE* 3.8 20.1 - - + +
121A MET* 4.4 13.6 - - + +
124A VAL* 4.1 24.5 - - + -
132A ILE* 4.7 0.9 - - + -
133A GLU* 1.3 77.3 - - - +
135A PHE* 1.3 72.8 + - - +
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Residues in contact with PHE 135 (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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22A MET* 3.8 24.9 - - + -
109A ILE* 3.7 29.2 - - + -
110A PHE 2.9 7.9 + - - +
111A VAL* 3.2 7.1 - - + +
112A TYR* 3.0 29.4 + - - -
133A GLU* 3.7 37.5 - - + -
134A THR* 1.3 81.4 - - - +
136A ASN* 1.3 61.3 - - - +
139A ALA* 6.3 1.8 - - + -
140A LEU* 3.9 32.8 - - + -
186A LEU* 3.8 24.2 - - + -
187A TYR* 4.9 2.2 - - - -
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Residues in contact with ASN 136 (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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112A TYR* 3.5 35.0 + - - +
113A GLN 3.2 17.7 + - - +
114A ASN 3.8 11.7 + - - -
135A PHE* 1.3 71.8 - - - +
137A GLU* 1.3 82.0 + - - +
138A ALA* 3.1 20.5 + - - +
139A ALA* 3.0 26.7 + - + +
140A LEU* 3.5 12.2 + - - +
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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