Contacts of the strand formed by residues 134 - 140 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D LEU* 3.7 10.8 - - - +
133D SER* 1.3 76.7 - - - +
135D TRP* 1.3 62.4 + - - -
152D VAL 3.1 12.3 - - - -
154D ASN 3.6 13.0 - - - -
171D GLU* 2.7 34.9 + - - -
172D PHE* 3.4 10.2 + - - -
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Residues in contact with TRP 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LEU* 3.6 50.0 - - + +
84D HIS* 3.5 45.1 - + - -
87D TYR* 3.9 12.6 - + + -
130D LEU* 3.9 2.7 - - - +
134D GLY* 1.3 78.8 - - - -
136D THR* 1.3 60.6 + - - +
137D VAL* 4.1 7.6 - - + -
151D THR* 3.5 3.3 - - - -
152D VAL* 2.6 45.1 + - + +
154D ASN 3.4 13.7 - - - -
155D HIS* 3.0 27.0 + + - -
168D ILE* 3.5 24.2 - - + -
169D VAL 3.3 9.9 - - - +
170D ASP* 3.3 43.1 - - + -
171D GLU* 4.2 4.0 - - - +
172D PHE* 4.0 2.0 - - - -
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PHE* 3.4 32.4 - - + +
126D SER* 4.8 1.3 - - - -
127D ALA* 3.1 28.1 - - + +
130D LEU* 4.9 0.2 - - - +
135D TRP* 1.3 74.7 + - - +
137D VAL* 1.3 63.4 + - - +
149D ILE* 4.3 12.1 - - + -
150D MET 3.4 10.1 - - - +
151D THR* 3.9 8.1 - - + +
168D ILE* 3.5 2.9 - - - -
169D VAL* 3.1 33.7 + - - +
171D GLU* 2.6 25.2 + - - -
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LEU* 6.0 0.2 - - + -
123D PHE* 4.2 3.6 - - - -
135D TRP* 4.3 5.4 - - + -
136D THR* 1.3 80.8 - - - +
138D LEU* 1.3 78.6 + - - +
139D TYR* 4.0 19.7 - - + +
148D GLN 3.8 0.4 - - - +
149D ILE* 3.4 7.6 - - - +
150D MET 2.8 33.1 + - - +
152D VAL* 4.2 20.9 - - + -
159D HIS* 5.2 4.3 - - + -
165D VAL* 3.6 31.9 - - + -
167D LEU 3.4 12.3 - - - +
168D ILE* 3.8 20.9 - - + -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 4.9 6.5 - - + -
109D ILE* 5.4 0.9 - - + -
113D TYR* 4.3 0.2 - - - +
119D PHE* 3.9 30.3 - - + -
123D PHE* 4.2 6.5 - - + -
137D VAL* 1.3 78.6 - - - +
139D TYR* 1.3 63.1 + - - +
147D LEU* 3.8 42.4 - - + +
148D GLN 3.5 4.0 - - - +
149D ILE* 3.7 26.2 - - + -
165D VAL 3.8 0.5 - - - -
166D ILE* 2.8 40.1 + - + +
167D LEU* 2.9 26.8 + - + +
197D TRP* 6.1 1.6 - - + -
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Residues in contact with TYR 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 4.1 15.6 - - + +
138D LEU* 1.3 76.8 - - - +
140D TYR* 1.3 62.0 + - - +
147D LEU* 3.2 9.9 - - - +
148D GLN* 2.8 40.1 + - + +
150D MET* 3.6 27.8 - - + -
152D VAL* 3.8 8.5 - - - +
159D HIS* 2.8 39.8 + - + -
160D ILE* 3.9 31.6 - - + -
163D LEU* 3.7 45.1 - - + -
164D PRO 3.3 12.3 - - - +
165D VAL* 4.0 15.9 - - + -
166D ILE* 4.2 2.5 - - - -
161F ALA* 5.8 2.0 - - + -
162F GLU 5.9 0.7 - - - -
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Residues in contact with TYR 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D LEU* 4.2 12.6 - - + -
139D TYR* 1.3 74.9 - - - +
141D ASP* 1.3 66.8 + - - +
142D ASN* 3.5 25.2 + - + +
145D GLY* 3.8 26.9 - - - -
146D ASN 3.7 5.8 - - - -
147D LEU* 4.1 10.5 - - + -
163D LEU* 4.0 5.4 - - - +
164D PRO* 3.3 30.9 + - + +
166D ILE* 3.8 24.0 - - + +
204D LEU* 3.8 17.7 - - + -
207D TYR* 3.9 38.9 + + + -
208D LEU* 3.8 18.5 - - + +
209D 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