Contacts of the strand formed by residues 146 - 153 (chain F) in PDB entry 4GUN
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 ALA 146 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107F GLN* 4.3 3.6 - - - +
111F GLN* 3.4 18.2 - - - +
138F VAL* 3.8 0.7 - - - +
139F LYS* 3.7 0.3 - - - -
140F ASN* 2.9 27.7 + - - +
143F ASN* 3.1 33.7 + - - +
144F GLY 3.4 2.0 - - - -
145F GLY* 1.4 75.0 - - - +
147F LEU* 1.3 64.0 + - - +
148F ASP* 5.3 0.9 - - - +
111H GLN* 4.2 11.9 - - + +
143H ASN* 5.2 0.4 - - - +
146H ALA* 4.4 7.2 - - + -
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Residues in contact with LEU 147 (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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104F LEU* 3.9 14.1 - - + -
107F GLN* 3.9 24.5 - - + -
108F ILE* 3.7 34.1 - - + +
111F GLN* 2.8 15.5 + - - +
112F TYR* 3.4 18.7 + - + -
118F LEU* 5.0 2.9 - - + -
137F ILE* 4.1 10.8 - - + -
138F VAL 3.2 23.3 - - - +
139F LYS* 4.2 0.9 - - - -
146F ALA* 1.3 75.4 - - - +
148F ASP* 1.3 55.8 + - - +
166F ILE* 4.1 6.1 - - + -
204F TYR* 3.7 26.0 - - + -
143H ASN* 2.8 30.7 + - - -
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Residues in contact with ASP 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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112F TYR* 3.6 7.1 + - - -
125F LYS* 5.1 0.7 + - - -
137F ILE* 3.4 6.0 - - - +
138F VAL* 2.8 44.9 + - + +
146F ALA 5.3 0.7 - - - +
147F LEU* 1.3 76.4 - - - +
149F VAL* 1.3 80.1 + - - +
150F VAL* 6.0 0.9 - - + -
140H ASN* 3.1 30.1 + - - +
142H GLN* 4.5 4.5 + - - -
143H ASN* 4.1 5.6 + - - +
148H ASP* 4.4 15.7 - - - +
162H HIS* 5.3 0.4 - - - -
163H LEU* 5.7 1.6 - - - +
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Residues in contact with VAL 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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112F TYR* 4.3 3.4 - - - +
118F LEU* 3.7 21.3 - - + -
121F ILE* 3.8 17.9 - - + -
122F THR* 3.6 39.9 - - + +
125F LYS* 2.7 56.2 + - + +
135F ALA* 5.0 2.2 - - + -
136F PHE 3.4 9.4 - - - +
137F ILE* 4.4 2.7 - - + -
148F ASP* 1.3 90.4 + - - +
150F VAL* 1.3 61.0 + - - +
302F SO4 4.4 0.9 + - - -
142H GLN* 5.2 0.9 - - - +
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Residues in contact with VAL 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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125F LYS* 4.7 0.2 - - - +
135F ALA* 3.4 2.1 - - - +
136F PHE* 2.7 41.5 + - + +
138F VAL* 3.4 41.3 - - + -
148F ASP* 6.0 0.9 - - + -
149F VAL* 1.3 74.8 - - - +
151F THR* 1.3 76.1 + - - +
152F THR* 5.0 2.0 - - + -
158F ILE* 3.6 20.0 - - + -
163F LEU* 6.1 2.0 - - + -
302F SO4 3.3 14.4 - - - +
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Residues in contact with THR 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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125F LYS* 3.8 38.6 - - + +
129F ILE* 3.9 21.3 - - + +
134F TRP 3.1 9.0 - - - +
135F ALA* 4.2 4.5 - - + -
150F VAL* 1.3 83.2 - - - +
152F THR* 1.3 68.0 + - - +
302F SO4 2.7 39.8 + - - +
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Residues in contact with THR 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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129F ILE* 4.8 3.1 - - - +
133F GLY* 3.2 3.6 - - - -
134F TRP* 2.9 37.3 + - - +
136F PHE* 3.4 28.0 - - + -
150F VAL* 5.0 2.0 - - + -
151F THR* 1.3 81.1 - - - +
153F ALA* 1.3 59.9 + - - +
156F ASP* 2.8 39.9 + - + +
157F THR 4.1 11.9 - - - +
158F ILE* 4.3 7.4 - - + -
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Residues in contact with ALA 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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129F ILE* 6.1 0.4 - - - -
130F GLN 6.0 1.3 - - - +
132F SER 3.6 6.7 - - - +
152F THR* 1.3 73.6 - - - +
154F ASN* 1.3 77.2 + - - +
156F ASP* 3.0 35.3 + - - +
154G ASN* 5.9 4.5 - - - +
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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