Contacts of the strand formed by residues 148 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ASN 3.2 11.9 - - - +
140A ASN* 3.5 0.7 - - - -
141A ALA* 3.3 37.2 + - + -
145A VAL* 3.3 33.1 + - + +
146A ASP 3.3 0.4 - - - -
147A GLY* 1.3 77.8 - - - +
149A SER* 1.3 60.8 + - - +
150A PHE* 5.4 7.0 - - + -
180A THR* 3.5 24.0 - - - +
181A ALA 3.5 9.2 - - - +
182A TYR* 3.7 21.3 - - + -
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASN 3.3 15.3 - - - -
139A ASN* 3.7 19.6 + - - -
147A GLY 4.6 2.8 + - - -
148A LEU* 1.3 77.6 - - - +
150A PHE* 1.3 63.1 + - - +
180A THR* 3.0 7.9 + - - -
181A ALA* 2.8 46.1 + - - +
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 3.8 23.6 - + - -
137A ARG* 3.7 1.6 - - - +
138A ASN* 3.0 68.2 + - + +
141A ALA* 4.2 20.0 - - + -
142A PHE* 3.9 14.1 - + - -
148A LEU* 5.4 7.0 - - + -
149A SER* 1.3 77.0 - - - +
151A ALA* 1.3 64.6 + - - +
152A LEU* 4.1 27.4 - - + -
178A PHE* 5.9 2.0 - - + -
179A SER* 3.2 13.2 - - - +
180A THR* 4.1 8.3 - - - +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.8 16.4 - - + -
135A THR* 4.7 0.7 - - + -
136A TYR 3.2 11.2 - - - +
137A ARG* 3.8 23.8 - - + +
150A PHE* 1.3 76.9 - - - +
152A LEU* 1.3 65.3 + - - +
178A PHE* 3.1 9.8 - - - +
179A SER* 2.8 45.2 + - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.4 3.6 - - - +
136A TYR* 2.7 56.8 + - + +
150A PHE* 4.1 19.5 - - + -
151A ALA* 1.3 80.4 - - - +
153A GLN* 1.3 62.3 + - - +
177A GLY 3.7 3.4 - - - +
178A PHE* 4.1 15.5 - - + -
405A LDA 3.8 21.8 - - + +
407A LDA 3.9 33.9 - - + -
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR 3.2 20.8 + - - -
99A GLY* 3.1 3.3 - - - -
100A VAL* 2.8 36.4 + - + +
126A MET* 3.0 31.1 - - - +
133A LEU* 4.1 12.2 - - + +
134A LEU 3.2 9.6 - - - +
135A THR* 2.7 28.1 + - - +
152A LEU* 1.3 77.5 - - - +
154A TYR* 1.3 67.6 + - - +
176A TYR* 3.2 7.2 - - - +
177A GLY 2.9 37.8 + - - +
405A LDA 4.1 9.5 - - - +
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASN 3.6 0.9 - - - +
133A LEU* 3.5 2.4 - - - -
134A LEU* 2.9 38.9 + - + +
153A GLN* 1.3 77.0 - - - +
155A GLN* 1.3 86.3 + - - +
156A GLY 4.0 0.4 + - - -
174A ASP* 3.3 23.8 - - + +
175A GLY 3.4 15.4 + - - -
176A TYR* 4.1 6.5 - + + -
405A LDA 3.7 36.7 - - + +
412A LDA 3.5 44.0 + - + -
415A CL 4.3 6.8 - - - +
401C LDA 3.6 49.9 - - + +
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 3.4 26.5 - - - +
126A MET* 4.1 16.5 - - + +
130A ASN* 3.3 26.3 - - - +
131A ARG 3.1 21.0 + - - +
132A ASN 3.2 8.3 - - - +
133A LEU* 3.5 19.4 - - + +
153A GLN 4.3 0.2 - - - -
154A TYR* 1.3 78.0 - - - +
156A GLY* 1.3 74.2 + - - +
158A ASN* 3.6 0.2 - - - +
172A ASN* 3.4 24.5 + - - +
173A GLY 4.9 0.5 - - - +
174A ASP* 3.4 2.9 - - - -
175A GLY 2.8 36.4 + - - +
197A SER* 4.8 0.3 + - - -
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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