Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 1B06
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.8 11.6 - - - +
133A SER* 1.3 77.4 - - - +
135A TRP* 1.3 61.2 + - - -
152A VAL 3.1 11.9 - - - -
154A ASN 3.6 11.9 - - - -
171A GLU* 2.7 35.8 + - - -
172A PHE* 3.4 10.5 + - - -
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Residues in contact with TRP 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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83A LEU* 3.7 45.6 - - + +
84A HIS* 3.5 38.4 - + - -
87A TYR* 3.9 12.3 - - + -
130A LEU* 4.0 2.0 - - - +
134A GLY* 1.3 78.2 - - - -
136A THR* 1.3 60.6 + - - +
137A VAL* 4.1 14.1 - - + -
151A THR* 3.5 3.6 - - - -
152A VAL* 2.7 43.6 + - + +
154A ASN 3.4 14.8 + - - -
155A HIS* 3.0 25.5 + + - -
168A ILE* 3.4 22.2 - - + -
169A VAL 3.3 6.5 - - - +
170A ASP* 3.3 46.9 - - + -
171A GLU* 4.2 3.8 - - - +
172A PHE* 3.8 2.4 - - - -
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Residues in contact with THR 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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123A PHE* 3.5 31.5 - - + +
127A ALA* 3.2 27.4 - - - +
130A LEU* 4.8 0.2 - - - +
135A TRP* 1.3 73.1 + - - +
137A VAL* 1.3 65.4 + - - +
149A ILE* 4.4 12.3 - - + -
150A MET 3.4 11.0 - - - +
151A THR* 3.8 9.2 - - + +
168A ILE* 3.5 2.8 - - - -
169A VAL* 3.1 34.7 + - - +
171A GLU* 2.6 24.9 + - - -
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Residues in contact with VAL 137 (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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83A LEU* 5.6 0.4 - - + -
123A PHE* 4.3 4.4 - - - -
135A TRP* 4.2 5.8 - - + -
136A THR* 1.3 79.7 - - - +
138A LEU* 1.3 76.8 + - - +
139A TYR* 4.0 20.2 - - + +
148A GLN 3.7 0.6 - - - +
149A ILE* 3.4 6.2 - - - +
150A MET 2.8 34.5 + - - +
152A VAL* 4.1 21.3 - - + -
159A HIS* 5.3 4.5 - - + -
165A VAL* 3.4 40.2 - - + -
167A LEU 3.4 4.0 - - - +
168A ILE* 3.8 20.4 - - + -
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Residues in contact with LEU 138 (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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105A LEU* 4.8 6.5 - - + -
109A ILE* 5.4 1.3 - - + -
119A PHE* 3.9 28.7 - - + -
123A PHE* 4.2 6.5 - - + -
137A VAL* 1.3 76.4 - - - +
139A TYR* 1.3 62.6 + - - +
147A LEU* 3.8 40.8 - - + +
148A GLN 3.5 8.5 - - - +
149A ILE* 3.7 27.4 - - + -
165A VAL* 3.8 1.7 - - - -
166A ILE* 2.8 39.7 + - + +
167A LEU* 2.9 30.5 + - + -
197A TRP* 6.2 0.7 - - + -
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Residues in contact with TYR 139 (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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137A VAL* 4.0 23.2 - - + +
138A LEU* 1.3 75.2 - - - +
140A TYR* 1.3 61.7 + - - +
147A LEU* 3.2 9.2 - - - +
148A GLN* 2.8 42.8 + - + +
150A MET* 3.6 27.1 - - + -
152A VAL* 3.7 9.2 - - - +
159A HIS* 2.8 40.3 + + + -
160A ILE* 3.9 34.1 - - + -
163A LEU* 3.7 44.9 - - + -
164A PRO 3.3 12.6 - - - +
165A VAL* 4.1 8.3 - - + -
166A ILE* 4.4 2.9 - - - -
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Residues in contact with TYR 140 (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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108A LEU* 4.1 13.2 - - + -
139A TYR* 1.3 76.0 - - - +
141A ASP* 1.3 65.8 + - - +
142A ASN* 3.5 23.1 + - - +
145A GLY* 3.8 30.5 - - - -
146A ASN 3.7 3.4 - - - -
147A LEU* 4.0 12.6 - - + -
163A LEU* 4.0 3.0 - - - +
164A PRO* 3.3 31.1 + - + +
166A ILE* 3.9 22.0 - - + +
204A LEU* 3.7 20.9 - - + -
207A TYR* 3.9 40.8 + + + -
208A LEU* 3.7 18.9 - - + +
209A ASN 5.2 1.7 + - - -
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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