Contacts of the strand formed by residues 189 - 195 (chain B) in PDB entry 4NJ4
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 SER 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B PHE 3.6 3.8 - - - -
137B GLU* 3.4 27.7 + - - +
164B ILE* 4.5 0.2 - - - -
187B VAL* 3.6 4.6 - - - +
188B ASN* 1.3 84.8 - - - +
190B ALA* 1.3 61.2 + - - +
191B VAL* 4.2 11.1 - - - +
211B PHE* 3.9 27.4 - - - -
281B ILE 3.5 0.9 - - - +
282B LEU* 3.4 5.0 - - - -
283B ARG* 2.9 41.9 + - - +
285B THR* 4.6 0.7 - - - -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 2.8 50.5 + - + +
164B ILE* 4.2 17.8 - - + +
168B VAL* 4.1 19.3 - - + -
189B SER* 1.3 73.9 + - - +
191B VAL* 1.3 60.3 + - - +
192B ILE* 5.4 1.1 - - + -
280B ILE* 4.7 4.7 - - + -
281B ILE 3.4 3.6 - - - -
282B LEU* 3.7 21.5 - - + -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LYS* 4.6 1.1 - - + -
133B TYR 3.2 12.3 - - - +
134B PHE* 3.4 38.6 - - + -
137B GLU 4.7 1.6 - - - +
139B TYR* 5.2 0.9 - - + -
189B SER* 4.2 10.1 - - - +
190B ALA* 1.3 77.2 - - - +
192B ILE* 1.3 65.7 + - - +
193B ASN* 3.8 24.6 + - - +
279B VAL 3.6 1.4 - - - +
280B ILE* 3.4 2.8 - - - -
281B ILE* 2.8 42.1 + - + +
283B ARG* 3.4 28.3 - - - +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 4.3 28.3 - - + -
110B VAL* 4.3 13.5 - - + -
132B LYS* 3.3 4.2 - - - -
133B TYR* 2.8 54.8 + - + +
135B PHE* 3.9 27.1 - - + -
167B TRP* 4.0 31.2 - - + -
168B VAL* 5.1 4.7 - - + -
190B ALA* 5.4 1.3 - - + -
191B VAL* 1.3 76.3 - - - +
193B ASN* 1.3 71.5 + - - +
194B ASP* 4.8 0.9 - - + +
278B ALA* 4.8 1.6 - - + -
279B VAL 3.4 7.6 - - - +
280B ILE* 4.2 16.8 - - + -
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Residues in contact with ASN 193 (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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130B ARG* 5.9 0.4 - - - -
131B ASN 3.6 3.4 - - - +
132B LYS* 2.8 40.8 - - + +
191B VAL* 3.8 10.6 + - - +
192B ILE* 1.3 73.7 - - - +
194B ASP* 1.3 60.6 + - - +
195B TYR* 3.4 32.4 + - + +
277B ARG 3.9 0.5 - - - +
278B ALA* 3.1 5.7 - - - +
279B VAL* 2.8 44.8 + - + +
281B ILE* 3.0 38.2 - - - +
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Residues in contact with ASP 194 (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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107B ILE* 5.1 2.5 - - + -
111B VAL* 3.7 15.3 - - + +
130B ARG* 3.3 3.7 - - - -
131B ASN* 2.8 43.3 + - + +
133B TYR* 4.2 16.3 + - + -
192B ILE* 4.1 3.3 - - + -
193B ASN* 1.3 72.9 - - - +
195B TYR* 1.3 64.6 + - - +
196B GLN* 4.0 14.7 + - - -
276B ARG* 3.0 45.5 + - - +
277B ARG 3.7 6.9 - - - +
278B ALA* 3.8 9.4 - - + +
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Residues in contact with TYR 195 (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 LEU 3.8 4.0 - - - +
130B ARG* 3.8 17.7 - - + -
193B ASN* 3.4 27.9 + - + +
194B ASP* 1.3 73.0 + - - +
196B GLN* 1.3 67.6 + - - +
199B GLY* 5.0 2.2 - - - -
200B CYS 5.3 7.0 - - - -
201B ILE* 3.4 35.8 - - + +
268B ILE* 3.5 19.4 - - + +
273B ILE* 4.4 17.0 - - + -
276B ARG* 3.4 9.2 - - - +
277B ARG* 2.8 68.9 + - + +
279B VAL* 3.6 28.0 - - + +
281B ILE* 5.4 0.9 - - - +
302B NO3 4.2 1.7 + - - -
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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
------------------------------------------------------------
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