Contacts of the strand formed by residues 134 - 140 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LEU* 3.7 12.1 - - - +
133F SER* 1.3 75.8 - - - +
135F TRP* 1.3 61.5 + - - -
152F VAL 3.1 12.6 - - - -
154F ASN 3.6 12.3 - - - -
171F GLU* 2.6 36.2 + - - -
172F PHE* 3.4 10.4 + - - -
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Residues in contact with TRP 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LEU* 3.5 48.2 - - + +
84F HIS* 3.4 42.4 - + - -
87F TYR* 4.0 11.9 - + + -
130F LEU* 3.8 2.8 - - - +
134F GLY* 1.3 78.1 - - - -
136F THR* 1.3 60.8 + - - +
137F VAL* 4.1 14.8 - - + -
151F THR* 3.5 2.9 - - - -
152F VAL* 2.6 42.8 + - + +
154F ASN 3.3 15.0 + - - -
155F HIS* 2.9 27.0 + + - -
168F ILE* 3.5 18.6 - - + -
169F VAL 3.3 6.7 - - - +
170F ASP* 3.3 47.1 - - + -
171F GLU* 4.1 3.8 - - - +
172F PHE* 3.8 1.8 - - - -
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Residues in contact with THR 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PHE* 3.6 32.8 - - + +
127F ALA* 3.1 28.5 - - + +
130F LEU* 4.8 0.3 - - - +
135F TRP* 1.3 74.0 + - - +
137F VAL* 1.3 65.1 + - - +
149F ILE* 4.4 10.3 - - + -
150F MET 3.4 9.9 - - - +
151F THR* 3.8 10.5 - - + +
168F ILE* 3.5 2.8 - - - -
169F VAL* 3.1 35.1 + - - +
171F GLU* 2.6 24.5 + - - -
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LEU* 5.6 0.4 - - + -
123F PHE* 4.2 3.9 - - - -
135F TRP* 4.3 4.9 - - + -
136F THR* 1.3 81.0 - - - +
138F LEU* 1.3 74.6 + - - +
139F TYR* 4.0 18.4 - - + +
148F GLN 3.7 0.2 - - - +
149F ILE* 3.4 6.9 - - - +
150F MET 2.8 36.0 + - - +
152F VAL* 4.0 24.2 - - + -
159F HIS* 5.4 3.8 - - + -
165F VAL* 3.5 33.7 - - + -
167F LEU 3.4 13.2 - - - +
168F ILE* 3.9 17.9 - - + -
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F LEU* 4.9 6.5 - - + -
109F ILE* 5.5 1.1 - - + -
113F TYR* 4.4 0.4 - - - +
119F PHE* 3.9 29.2 - - + -
123F PHE* 4.3 6.1 - - + -
137F VAL* 1.3 74.4 - - - +
139F TYR* 1.3 65.0 + - - +
147F LEU* 3.8 45.5 - - + +
148F GLN 3.5 1.8 - - - +
149F ILE* 3.7 27.8 - - + -
165F VAL* 3.8 1.7 - - - -
166F ILE* 2.8 39.2 + - + +
167F LEU* 2.9 30.1 + - + -
197F TRP* 6.1 0.9 - - + -
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Residues in contact with TYR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ALA* 5.7 2.0 - - + -
162D GLU 5.9 0.2 - - - -
137F VAL* 4.1 12.8 - - + +
138F LEU* 1.3 77.2 - - - +
140F TYR* 1.3 61.5 + - - +
147F LEU* 3.2 9.5 - - - +
148F GLN* 2.8 41.7 + - + +
150F MET* 3.7 27.1 - - + -
152F VAL* 3.7 9.4 - - - +
159F HIS* 2.9 38.2 + - + -
160F ILE* 4.0 31.6 - - + -
163F LEU* 3.6 46.0 - - + -
164F PRO 3.3 12.6 - - - +
165F VAL* 4.1 17.9 - - + -
166F ILE* 4.2 2.7 - - - -
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Residues in contact with TYR 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LEU* 4.1 14.1 - - + -
139F TYR* 1.3 77.1 - - - +
141F ASP* 1.3 65.1 + - - +
142F ASN* 3.5 26.1 + - + +
145F GLY* 3.8 30.5 - - - -
146F ASN 3.7 6.1 - - - -
147F LEU* 4.1 10.1 - - + -
163F LEU* 3.9 2.6 - - - +
164F PRO* 3.3 30.8 + - + +
166F ILE* 3.8 23.3 - - + -
204F LEU* 3.7 17.3 - - + -
207F TYR* 4.0 37.0 + - + -
208F LEU* 3.6 19.9 - - + +
209F ASN 5.1 1.6 + - - -
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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