Contacts of the strand formed by residues 142 - 148 (chain B) in PDB entry 1NOZ
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 ARG 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B TYR* 3.7 1.0 - - - -
137B ASP 3.4 22.8 + - - -
140B ASP* 2.5 53.6 + - - +
141B ASP* 1.3 73.6 - - - +
143B PHE* 1.3 65.2 + - - +
144B TYR* 3.5 30.3 + - + -
182B ARG* 3.3 17.7 - - + +
184B ILE* 3.8 31.8 - - + +
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Residues in contact with PHE 143 (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 THR* 3.9 14.6 - - + -
135B HIS 3.9 4.5 - - - -
136B TYR* 3.8 26.7 - + + +
142B ARG* 1.3 76.7 - - - +
144B TYR* 1.3 56.5 + - - +
145B VAL* 4.0 0.4 - - - -
179B ILE* 4.0 10.5 - - + -
182B ARG* 2.8 67.7 + - + +
183B VAL* 3.4 13.1 - - + -
184B ILE* 2.7 33.3 + - - +
322B ILE* 4.5 9.4 - - + -
325B VAL* 4.1 18.4 - - + -
326B GLU* 3.4 38.4 - - + -
329B GLN* 5.6 2.5 - - + -
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Residues in contact with TYR 144 (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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133B ILE 3.2 3.5 - - - +
134B THR* 3.0 4.5 - - - -
135B HIS* 2.8 47.9 + - - +
137B ASP* 4.1 9.9 - - + -
140B ASP* 3.3 34.7 + - - -
142B ARG* 3.5 38.7 + - + -
143B PHE* 1.3 72.0 - - - +
145B VAL* 1.3 61.1 + - - +
146B PHE* 3.6 13.6 - - + -
184B ILE* 3.7 18.2 - - + -
186B MET* 3.2 26.9 - - + -
201B LEU* 3.7 26.7 - - + -
205B LYS* 3.7 12.5 + - + -
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Residues in contact with VAL 145 (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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133B ILE 3.6 1.1 - - - -
134B THR* 3.3 31.2 - - + +
143B PHE 4.5 1.3 - - - +
144B TYR* 1.3 73.6 - - - +
146B PHE* 1.3 68.0 + - - +
147B ASP 3.8 0.2 + - - -
159B TRP* 5.9 0.2 - - + -
183B VAL* 3.2 33.4 - - + -
184B ILE 2.7 13.3 + - - +
185B TYR* 3.9 13.5 - - + -
186B MET* 2.7 35.0 + - - +
318B ILE* 3.8 30.1 - - + -
321B ASN* 4.8 1.8 - - - +
322B ILE* 4.4 6.5 - - + -
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Residues in contact with PHE 146 (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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132B ALA* 2.8 32.9 - - - +
133B ILE* 2.8 41.3 + - + +
135B HIS* 4.8 2.5 - - + -
144B TYR* 3.6 27.4 - - + -
145B VAL* 1.3 77.5 - - - +
147B ASP* 1.3 52.3 + - - +
186B MET* 3.4 25.4 - - + -
188B PHE* 3.8 9.6 - + - -
194B MET* 3.4 37.7 - - + -
197B GLU* 4.0 11.9 - - + -
198B TYR* 3.9 33.0 - + + -
201B LEU* 3.8 27.4 - - + -
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Residues in contact with ASP 147 (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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131B ASP 3.9 1.9 - - - +
132B ALA* 4.2 0.9 - - - -
145B VAL* 5.2 0.4 - - + -
146B PHE* 1.3 73.0 - - - +
148B LEU* 1.3 70.6 + - - +
149B LEU* 3.6 6.0 + - + +
159B TRP* 3.9 0.3 - - - +
185B TYR* 2.6 41.9 + - + +
186B MET 3.0 12.9 + - - +
187B PRO* 4.1 3.6 - - + -
188B PHE* 2.7 36.1 + - - +
194B MET* 3.8 4.2 - - - -
310B ARG* 6.0 0.2 - - - -
314B HIS* 3.1 35.7 + - - -
318B ILE* 3.6 19.4 - - + +
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Residues in contact with LEU 148 (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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129B GLU* 3.6 33.2 - - + +
130B ILE 3.5 15.9 - - - +
131B ASP* 2.6 27.8 + - - +
147B ASP* 1.3 77.6 + - - +
149B LEU* 1.3 72.8 + - - +
150B ASN 4.6 2.0 - - - +
151B SER* 2.6 46.0 + - - +
156B VAL* 4.8 3.3 - - - +
188B PHE 4.3 0.9 - - - +
190B ASN* 3.4 35.0 - - - +
191B GLU* 3.4 8.1 - - + +
194B MET* 3.6 10.3 - - + -
310B ARG* 4.7 3.5 + - - -
314B HIS* 5.0 0.9 + - - -
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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