Contacts of the strand formed by residues 158 - 164 (chain B) in PDB entry 1JW9
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 GLU 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ALA* 3.4 1.9 - - - -
155B ILE* 2.8 38.1 + - + +
156B ARG* 5.7 1.1 - - + -
157B MET* 1.3 80.0 - - - +
159B GLY* 1.3 62.2 + - - +
160B GLN* 3.1 14.2 + - - -
196B LEU* 3.4 6.7 - - - +
225B MET* 3.7 19.4 - - + +
226B TYR 3.4 9.6 - - - +
8D ALA* 3.6 19.9 - - + +
9D GLN* 4.9 0.5 + - - +
75D PHE* 4.0 3.8 - - - -
76D PRO* 2.6 48.8 - - - +
78D VAL* 3.3 20.1 - - + +
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Residues in contact with GLY 159 (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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153B ALA 3.3 10.8 - - - -
154B ALA* 4.3 0.4 - - - -
158B GLU* 1.3 75.6 - - - +
160B GLN* 1.3 69.2 + - - +
196B LEU* 3.9 5.5 - - - +
200B ILE* 3.8 22.4 - - - -
225B MET* 3.3 2.8 - - - +
226B TYR* 2.9 32.6 + - - -
78D VAL* 5.1 1.1 - - - -
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Residues in contact with GLN 160 (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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151B SER 4.6 0.2 - - - -
152B GLY* 3.3 4.5 - - - -
153B ALA* 2.9 39.1 + - + +
158B GLU* 3.1 23.1 + - - +
159B GLY* 1.3 80.7 - - - +
161B ILE* 1.3 62.2 + - - +
176B LEU* 4.7 7.1 - - - +
200B ILE* 3.8 6.6 - - - +
223B ILE* 3.9 33.4 - - + +
224B VAL 3.2 6.5 - - - +
225B MET* 3.9 6.9 - - + +
52D LEU* 4.3 3.1 - - - +
75D PHE* 3.8 16.0 - - - -
76D PRO 3.3 12.1 + - - -
77D PRO* 4.1 2.5 - - - +
78D VAL* 3.9 23.9 + - + +
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Residues in contact with ILE 161 (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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150B VAL* 4.2 5.2 - - + -
151B SER 3.3 10.5 - - - +
152B GLY* 4.9 1.1 - - - -
160B GLN* 1.3 76.3 - - - +
162B THR* 1.3 74.7 + - - +
163B VAL* 5.0 0.7 - - + -
200B ILE* 5.1 4.7 - - + -
203B LEU* 3.6 33.7 - - + +
204B GLN* 3.6 42.4 - - + +
207B GLU* 4.0 16.2 - - + -
219B ALA* 5.0 4.1 - - + +
222B LYS 4.0 0.9 - - - +
223B ILE* 3.7 0.9 - - - -
224B VAL* 2.9 57.6 + - + +
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Residues in contact with THR 162 (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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150B VAL* 3.9 0.3 - - - -
151B SER* 2.9 36.0 + - - +
161B ILE* 1.3 79.3 + - - +
163B VAL* 1.3 77.4 + - - +
164B PHE* 3.7 32.1 - - + -
176B LEU* 5.2 2.2 - - - +
219B ALA 3.8 6.1 - - - +
221B GLY 4.7 2.2 - - - +
222B LYS 3.0 28.9 + - - +
223B ILE* 3.5 18.4 - - - +
238B LEU* 4.6 5.2 - - + +
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Residues in contact with VAL 163 (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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148B PRO* 5.2 2.0 - - + -
149B LEU 3.5 8.3 - - - +
150B VAL* 4.3 15.9 - - + -
161B ILE* 5.0 1.1 - - + -
162B THR* 1.3 81.6 - - - +
164B PHE* 1.3 66.2 + - - +
165B THR* 4.1 21.3 - - + -
170B GLU* 3.5 1.6 - - - +
207B GLU* 3.6 44.2 - - + +
211B MET* 4.3 15.7 - - + -
218B PRO* 4.4 2.0 - - + -
219B ALA* 2.9 21.9 + - + +
220B SER* 3.2 23.3 - - - +
221B GLY 4.2 0.3 + - - -
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Residues in contact with PHE 164 (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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148B PRO* 3.3 5.5 - - - +
149B LEU* 2.9 52.2 + - + +
151B SER* 3.9 25.1 - - - -
162B THR* 3.7 26.5 - - + -
163B VAL* 1.3 72.8 - - - +
165B THR* 1.3 60.9 + - - +
166B TYR* 3.4 29.2 - - + +
170B GLU* 3.5 3.4 - - - -
171B PRO* 3.4 20.2 - - + +
172B CYS* 3.5 21.5 - - - -
173B TYR* 3.7 33.7 - + + -
176B LEU* 5.4 3.6 - - + -
221B GLY 6.3 0.2 - - - -
238B LEU* 4.0 15.5 - - + -
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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