Contacts of the strand formed by residues 148 - 155 (chain B) in PDB entry 5NXR
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 LEU 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B ASN 3.2 11.7 - - - +
140B ASN* 3.5 0.5 - - - -
141B ALA* 3.3 33.0 + - + +
145B VAL* 3.3 34.6 + - + +
146B ASP 3.3 1.2 + - - -
147B GLY* 1.3 77.6 - - - +
149B SER* 1.3 62.0 + - - +
150B PHE* 5.7 4.7 - - + -
180B THR* 3.5 24.0 - - - +
181B ALA 3.5 9.4 - - - +
182B TYR* 3.7 21.1 - - + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASN 3.3 15.5 - - - -
139B ASN* 3.7 19.9 + - - -
147B GLY 4.5 2.4 + - - -
148B LEU* 1.3 76.9 - - - +
150B PHE* 1.3 64.2 + - - +
180B THR* 3.0 7.4 + - - -
181B ALA* 2.8 47.1 + - - +
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Residues in contact with PHE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR* 3.8 22.9 - + - -
137B ARG* 3.6 1.8 - - - +
138B ASN* 3.0 62.4 + - + +
141B ALA* 4.4 16.8 - - + -
142B PHE* 3.9 20.2 - + - -
148B LEU* 5.7 5.6 - - + -
149B SER* 1.3 78.4 - - - +
151B ALA* 1.3 65.3 + - - +
152B LEU* 4.1 28.9 - - + -
178B PHE* 6.0 1.3 - - + -
179B SER* 3.2 13.2 - - - +
180B THR* 4.1 8.5 - - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.7 13.2 - - + -
135B THR* 4.7 0.4 - - + -
136B TYR 3.2 10.8 - - - +
137B ARG* 3.5 32.5 - - + +
150B PHE* 1.3 76.0 - - - +
152B LEU* 1.3 66.5 - - - +
178B PHE* 3.1 9.8 - - - +
179B SER* 2.9 40.5 + - - +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU 4.0 0.2 - - - +
135B THR* 3.4 4.3 - - - +
136B TYR* 2.7 61.2 + - + +
150B PHE* 4.1 20.6 - - + -
151B ALA* 1.3 79.9 - - - +
153B GLN* 1.3 59.2 + - - +
177B GLY 3.7 3.8 - - - +
178B PHE* 4.1 15.3 - - + -
401B LDA 3.8 29.5 - - + +
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Residues in contact with GLN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR 3.2 22.0 + - - -
99B GLY* 3.1 2.8 - - - -
100B VAL* 2.8 38.0 + - + +
126B MET* 3.0 31.0 - - - +
133B LEU* 4.1 11.3 - - + +
134B LEU 3.2 10.5 - - - +
135B THR* 2.7 27.1 + - - +
152B LEU* 1.3 77.7 - - - +
154B TYR* 1.3 68.3 + - - +
176B TYR* 3.2 7.7 - - - +
177B GLY 2.9 33.6 + - - +
401B LDA 3.9 8.6 - - - +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LDA 3.6 43.2 + - + +
132B ASN 3.6 1.0 - - - +
133B LEU* 3.5 3.1 - - - -
134B LEU* 2.8 48.5 + - + +
153B GLN* 1.3 76.6 - - - +
155B GLN* 1.3 93.9 + - - +
156B GLY 3.9 1.7 + - - -
174B ASP* 3.3 23.6 - - + +
175B GLY 3.5 13.7 - - - -
176B TYR* 4.4 5.8 - - + -
401B LDA 3.3 69.6 + - + +
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.4 27.5 - - - +
126B MET* 4.1 15.5 + - + +
130B ASN* 3.3 26.7 - - - +
131B ARG 3.1 20.8 + - - +
132B ASN 3.2 9.0 - - - +
133B LEU* 3.5 19.3 - - + +
153B GLN 4.3 0.2 - - - -
154B TYR* 1.3 79.3 - - - +
156B GLY* 1.3 75.8 + - - +
158B ASN* 3.6 0.4 - - - +
172B ASN* 3.4 22.9 + - - +
173B GLY 4.9 0.5 - - - +
174B ASP* 3.4 1.4 - - - -
175B GLY* 2.8 36.0 + - - +
197B SER* 4.8 0.7 + - - -
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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