Contacts of the strand formed by residues 148 - 155 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C ASN 3.2 12.4 - - - +
140C ASN* 3.4 0.9 - - - -
141C ALA* 3.3 26.4 + - + +
145C VAL* 3.3 38.7 + - + +
146C ASP 3.3 1.6 + - - -
147C GLY* 1.3 77.9 - - - +
149C SER* 1.3 62.1 + - - +
150C PHE* 5.2 7.6 - - + -
180C THR* 3.5 23.8 - - - +
181C ALA 3.5 9.6 - - - +
182C TYR* 3.7 24.8 - - + -
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ASN 3.3 14.4 - - - -
139C ASN* 3.7 20.7 + - - -
147C GLY 4.6 2.3 + - - -
148C LEU* 1.3 76.2 - - - +
150C PHE* 1.3 61.8 + - - +
180C THR* 3.0 6.9 + - - -
181C ALA* 2.8 46.3 + - - +
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Residues in contact with PHE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C TYR* 3.8 24.0 - + - -
137C ARG* 3.7 2.2 - - - +
138C ASN* 3.0 61.8 + - + +
141C ALA* 4.2 22.2 - - + -
142C PHE* 3.9 17.3 - + - -
148C LEU* 5.2 6.5 - - + -
149C SER* 1.3 78.1 - - - +
151C ALA* 1.3 67.8 + - - +
152C LEU* 4.1 24.7 - - + -
178C PHE* 6.0 1.3 - - + -
179C SER* 3.2 13.0 - - - +
180C THR* 4.1 9.0 - - - +
441C LDA 6.6 0.2 - - + -
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C VAL* 3.7 13.2 - - + -
135C THR* 4.7 0.4 - - + -
136C TYR 3.2 11.0 - - - +
137C ARG* 3.5 32.3 - - + +
150C PHE* 1.3 78.0 - - - +
152C LEU* 1.3 65.1 + - - +
178C PHE* 3.1 10.2 - - - +
179C SER* 2.8 40.9 + - - +
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C THR* 3.4 3.7 - - - +
136C TYR* 2.7 60.6 + - + +
150C PHE* 4.1 19.7 - - + -
151C ALA* 1.3 79.2 - - - +
153C GLN* 1.3 61.1 + - - +
177C GLY 3.7 3.1 - - - +
178C PHE* 4.1 5.4 - - + -
408C LDA 3.7 19.4 - - + +
410C LDA 4.6 19.5 - - + -
440C LDA 4.1 35.2 - - + -
441C LDA 5.0 13.2 - - + -
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Residues in contact with GLN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C TYR 3.2 17.5 - - - +
99C GLY* 3.2 3.6 - - - -
100C VAL* 2.7 42.7 + - + +
126C MET* 3.0 35.0 - - - +
133C LEU* 3.9 10.2 - - + +
134C LEU 3.2 11.9 - - - +
135C THR* 2.8 23.6 + - - +
152C LEU* 1.3 77.7 - - - +
154C TYR* 1.3 66.6 + - - +
176C TYR* 3.2 7.2 - - - +
177C GLY 2.9 35.1 + - - +
408C LDA 3.9 8.9 - - - +
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Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ASN 3.6 1.0 - - - +
133C LEU* 3.5 2.6 - - - -
134C LEU* 2.8 46.1 + - + +
153C GLN* 1.3 77.6 - - - +
155C GLN* 1.3 77.4 + - - +
156C GLY 4.0 0.4 + - - -
174C ASP* 3.3 23.5 - - + +
175C GLY* 3.4 17.6 + - - -
176C TYR* 4.2 3.6 - + + -
407C LDA 3.5 56.4 - - + +
408C LDA 3.7 62.9 - - + +
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Residues in contact with GLN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 3.4 28.1 - - - +
126C MET* 4.1 14.7 + - + +
130C ASN* 3.3 27.1 - - - +
131C ARG 3.1 20.4 + - - -
132C ASN 3.2 9.0 - - - +
133C LEU* 3.5 19.8 - - + +
154C TYR* 1.3 78.2 - - - +
156C GLY* 1.3 73.7 + - - +
158C ASN* 3.6 0.2 - - - +
172C ASN* 3.4 24.4 + - - +
173C GLY 4.9 0.3 - - - +
174C ASP* 3.4 2.9 - - - -
175C GLY 2.8 39.7 + - - +
197C 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