Contacts of the strand formed by residues 146 - 153 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107N GLN* 4.1 3.8 - - - +
111N GLN* 3.5 17.7 - - - +
138N VAL 3.7 0.5 - - - +
139N LYS* 3.7 0.9 - - - -
140N ASN* 2.9 31.1 + - - +
143N ASN* 3.2 31.4 + - - +
144N GLY 3.3 1.4 - - - -
145N GLY* 1.3 76.1 - - - +
147N LEU* 1.3 62.3 + - - +
148N ASP* 5.2 1.0 - - - +
111P GLN* 4.0 10.8 - - + +
143P ASN* 5.3 0.4 - - - +
146P ALA* 4.7 6.1 - - + -
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Residues in contact with LEU 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LEU* 4.0 13.5 - - + -
107N GLN* 3.8 28.3 - - + -
108N ILE* 3.7 34.3 - - + +
111N GLN* 2.7 16.5 + - - +
112N TYR* 3.4 19.5 + - + +
118N LEU* 5.0 2.7 - - + -
137N ILE* 4.0 16.6 - - + -
138N VAL 3.2 21.3 - - - +
139N LYS* 4.4 0.4 - - - -
146N ALA* 1.3 75.0 - - - +
148N ASP* 1.3 55.2 + - - +
166N ILE* 4.2 2.7 - - + -
204N TYR* 3.9 20.6 - - + -
143P ASN* 2.8 31.0 + - - -
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Residues in contact with ASP 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N TYR* 3.6 6.5 + - - -
137N ILE* 3.4 5.9 - - - +
138N VAL* 2.8 44.9 + - + +
140N ASN* 6.5 0.9 - - + -
146N ALA 5.2 0.9 - - - +
147N LEU* 1.3 75.5 - - - +
149N VAL* 1.3 79.1 + - - +
150N VAL* 4.6 8.9 - - + +
140P ASN* 3.1 30.0 + - - +
142P GLN* 4.4 4.3 + - - -
143P ASN* 4.1 5.7 + - - +
148P ASP* 4.4 16.5 - - - +
162P HIS* 5.3 0.7 - - - -
163P LEU* 5.8 1.7 - - - +
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Residues in contact with VAL 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N TYR* 4.3 3.6 - - - +
118N LEU* 3.7 20.9 - - + -
121N ILE* 4.2 17.9 - - + -
122N THR* 3.5 36.3 - - + +
125N LYS* 3.6 43.6 + - + -
135N ALA* 5.0 2.0 - - + -
136N PHE 3.4 9.6 - - - +
137N ILE* 4.3 5.4 - - + -
148N ASP* 1.3 89.8 + - - +
150N VAL* 1.3 69.8 + - - +
302N SO4 4.3 1.6 + - - -
142P GLN* 5.2 3.6 + - - +
162P HIS* 5.8 1.2 - - - -
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Residues in contact with VAL 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N LYS* 4.6 0.2 - - - +
135N ALA* 3.4 3.8 - - - +
136N PHE* 2.8 40.0 + - + +
138N VAL* 4.0 19.7 - - + -
148N ASP* 4.6 11.4 - - + +
149N VAL* 1.3 79.5 - - - +
151N THR* 1.3 65.5 + - - +
152N THR* 5.3 0.7 - - + -
158N ILE* 3.6 31.6 - - + -
163N LEU* 6.0 4.9 - - + -
302N SO4 3.3 17.5 - - - +
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Residues in contact with THR 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N LYS* 3.8 38.1 - - + +
129N ILE* 3.8 21.7 - - + +
134N TRP 3.1 9.2 - - - +
135N ALA* 4.1 4.5 - - + -
150N VAL* 1.3 79.6 - - - +
152N THR* 1.3 68.4 + - - +
302N SO4 2.7 38.2 + - - +
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Residues in contact with THR 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N ILE* 4.8 4.2 - - - +
133N GLY* 3.2 4.3 - - - -
134N TRP* 2.8 36.9 + - - +
136N PHE* 3.4 28.6 - - + -
150N VAL* 5.3 1.1 - - + -
151N THR* 1.3 82.3 - - - +
153N ALA* 1.3 59.4 + - - +
156N ASP* 2.6 39.7 + - + +
157N THR 4.2 10.1 - - - +
158N ILE* 4.3 8.1 - - + -
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Residues in contact with ALA 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N ILE* 6.2 0.4 - - - -
132N SER 3.7 5.8 - - - +
152N THR* 1.3 72.6 - - - +
154N ASN* 1.4 68.3 + - - +
155N GLN 3.1 0.3 + - - -
156N ASP* 2.8 48.6 + - - +
154O ASN* 6.1 2.7 - - - +
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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