Contacts of the strand formed by residues 134 - 140 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C LEU* 3.8 11.6 - - - +
133C SER* 1.3 76.8 - - - +
135C TRP* 1.3 62.8 + - - -
152C VAL 3.1 12.6 - - - -
154C ASN 3.6 12.1 - - - -
171C GLU* 2.6 33.8 + - - -
172C PHE* 3.4 11.1 + - - -
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Residues in contact with TRP 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 3.7 46.6 - - + +
84C HIS* 3.6 39.3 - + - -
87C TYR* 4.0 11.0 - + + -
130C LEU* 3.9 2.3 - - - +
134C GLY* 1.3 78.4 - - - -
136C THR* 1.3 61.5 + - - +
137C VAL* 4.1 14.4 - - + -
151C THR* 3.5 3.3 - - - -
152C VAL* 2.6 43.1 + - + +
154C ASN 3.3 14.3 + - - -
155C HIS* 2.9 27.9 + + - -
168C ILE* 3.3 22.9 - - + -
169C VAL 3.3 7.0 - - - +
170C ASP* 3.4 44.0 - - + -
171C GLU* 4.1 4.3 - - - +
172C PHE* 3.8 2.4 - - - -
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Residues in contact with THR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PHE* 3.6 32.2 - - + +
127C ALA* 3.1 29.0 - - + +
130C LEU* 4.8 0.2 - - - +
135C TRP* 1.3 73.3 + - - +
137C VAL* 1.3 64.8 + - - +
149C ILE* 4.3 12.3 - - + -
150C MET 3.4 9.6 - - - +
151C THR* 3.8 10.5 - - + +
168C ILE* 3.6 2.6 - - - -
169C VAL* 3.1 35.2 + - - +
171C GLU* 2.6 25.1 + - - -
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 5.6 0.2 - - + -
123C PHE* 4.3 3.8 - - - -
135C TRP* 4.2 5.4 - - + -
136C THR* 1.3 80.8 - - - +
138C LEU* 1.3 77.3 + - - +
139C TYR* 3.9 20.0 - - + +
148C GLN 3.7 0.5 - - - +
149C ILE* 3.4 5.9 - - - +
150C MET* 2.8 38.2 + - - +
152C VAL* 4.2 19.7 - - + -
159C HIS* 5.4 4.3 - - + -
165C VAL* 3.6 32.1 - - + -
167C LEU 3.5 11.4 - - - +
168C ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 4.8 7.0 - - + -
109C ILE* 5.5 1.1 - - + -
119C PHE* 3.8 31.0 - - + -
123C PHE* 4.2 6.5 - - + -
137C VAL* 1.3 78.7 - - - +
139C TYR* 1.3 62.5 + - - +
147C LEU* 3.9 41.5 - - + +
148C GLN 3.5 3.4 - - - +
149C ILE* 3.6 28.0 - - + -
165C VAL 3.8 0.3 - - - -
166C ILE* 2.8 38.0 + - + +
167C LEU* 2.9 29.4 + - + -
197C TRP* 6.1 0.9 - - + -
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Residues in contact with TYR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 3.9 15.2 - - + +
138C LEU* 1.3 77.0 - - - +
140C TYR* 1.3 60.8 + - - +
147C LEU* 3.2 9.2 - - - +
148C GLN* 2.8 42.8 + - + +
150C MET* 3.8 25.4 - - + -
152C VAL* 3.8 8.1 - - - +
159C HIS* 2.8 39.7 + - + -
160C ILE* 3.9 33.9 - - + -
163C LEU* 3.6 42.2 - - + -
164C PRO 3.3 10.1 - - - +
165C VAL* 3.9 18.4 - - + -
166C ILE* 4.4 2.5 - - - -
161E ALA* 5.7 2.9 - - + -
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Residues in contact with TYR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.2 13.0 - - + -
139C TYR* 1.3 77.3 - - - +
141C ASP* 1.3 69.2 + - - +
142C ASN* 3.5 24.4 + - + +
145C GLY* 3.7 25.9 - - - -
146C ASN 3.7 6.3 - - - -
147C LEU* 4.3 9.6 - - + +
163C LEU* 4.0 3.3 - - - +
164C PRO* 3.3 31.4 + - + +
166C ILE* 3.9 22.0 - - + -
204C LEU* 3.7 17.5 - - + -
207C TYR* 3.9 39.4 + + + -
208C LEU* 3.6 21.1 - - + +
209C ASN 5.1 1.9 + - - -
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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