Contacts of the strand formed by residues 147 - 153 (chain F) in PDB entry 5IJ7
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 PRO 147 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.3 8.7 - - + -
66B GLN 3.2 27.8 - - - +
68B VAL* 3.8 24.2 - - + -
88F ASN* 4.1 20.9 - - - +
90F HIS* 5.8 0.2 - - + -
138F TRP* 4.2 9.6 - - + -
139F THR 3.4 10.5 - - - +
140F TYR* 4.3 2.9 - - + -
145F SER 4.3 1.1 - - - +
146F HIS* 1.4 89.0 - - - +
148F LEU* 1.3 64.3 + - - +
162F ASN* 4.2 0.5 - - - +
163F PRO* 3.1 24.2 - - + +
164F ILE* 3.6 13.0 - - + -
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Residues in contact with LEU 148 (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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137F ALA 4.0 0.2 - - - +
138F TRP* 3.3 8.6 - - - -
139F THR* 2.8 52.5 + - + +
140F TYR 4.3 0.9 - - - -
141F ASP* 4.1 26.9 - - + +
146F HIS* 4.1 8.3 - - + +
147F PRO* 1.3 81.3 - - - +
149F LEU* 1.3 62.0 + - - +
150F ALA 4.1 0.4 - - - -
160F ILE* 4.0 22.7 - - + -
161F ILE 3.4 15.3 - - - +
162F ASN* 3.8 27.1 - - + +
163F PRO* 4.2 1.1 - - - -
169F ILE* 4.4 10.8 - - + -
170F LYS* 6.3 2.0 - - - -
206F ILE* 5.2 9.0 - - + -
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Residues in contact with LEU 149 (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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100F ALA* 3.6 20.6 - - + -
107F VAL* 3.6 30.7 - - + -
109F LEU* 4.1 11.0 - - + -
136F CYS* 4.0 10.8 - - + -
137F ALA 3.5 18.8 - - - +
138F TRP* 3.6 41.5 - - + +
148F LEU* 1.3 74.1 - - - +
150F ALA* 1.3 62.8 + - - +
151F VAL* 4.0 6.6 + - + -
159F ARG 3.6 0.7 - - - +
160F ILE* 4.5 2.5 - - - -
161F ILE* 2.7 50.4 + - + +
163F PRO* 4.6 4.6 - - + +
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Residues in contact with ALA 150 (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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136F CYS* 3.0 7.6 - - - +
137F ALA 2.8 31.8 + - - +
148F LEU 4.1 0.4 - - - -
149F LEU* 1.3 72.7 - - - +
151F VAL* 1.3 59.3 + - - +
158F ILE* 4.6 0.4 - - + -
159F ARG 3.1 7.0 - - - +
160F ILE* 3.6 21.7 - - + +
182F LEU* 3.6 16.2 - - + -
184F PHE* 3.6 27.7 - - + -
192F LEU* 4.4 4.5 - - + -
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Residues in contact with VAL 151 (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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102F VAL* 3.8 5.4 - - + -
107F VAL* 3.6 38.8 - - + -
133F PHE* 3.8 25.4 - - + -
135F THR 3.4 8.1 - - - +
136F CYS* 3.6 17.0 - - + -
149F LEU* 4.1 7.2 - - + -
150F ALA* 1.3 78.2 - - - +
152F ALA* 1.3 62.7 + - - +
157F ILE 3.8 0.3 - - - +
158F ILE* 3.5 1.2 - - - -
159F ARG* 2.9 47.5 + - + +
161F ILE* 4.0 11.2 - - + -
182F LEU* 3.6 4.0 - - - +
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Residues in contact with ALA 152 (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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133F PHE* 3.7 10.8 - - - -
134F TYR 3.0 17.0 + - - -
135F THR* 3.1 19.8 + - + +
151F VAL* 1.3 77.8 - - - +
153F GLY* 1.3 60.1 + - - +
157F ILE 3.4 18.4 - - - +
158F ILE* 4.1 2.5 - - - -
179F ILE* 3.8 30.3 - - + -
182F LEU* 3.9 15.8 - - + +
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Residues in contact with GLY 153 (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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131F GLU* 3.9 3.3 + - - -
132F ASN 3.0 14.8 - - - -
133F PHE* 3.9 4.0 - - - -
134F TYR* 3.6 14.1 - - - -
152F ALA* 1.3 78.0 - - - +
154F SER* 1.3 62.3 + - - -
155F ARG 3.4 2.5 - - - -
156F GLY* 3.3 7.0 + - - -
157F ILE 4.3 4.0 + - - -
179F ILE 2.9 30.6 + - - -
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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