Contacts of the strand formed by residues 189 - 195 (chain B) in PDB entry 5INQ
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 PHE 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B GLU 3.4 5.6 + - - -
163B VAL* 2.8 55.4 + - + +
164B ILE 3.9 17.0 - - - -
165B PRO* 3.9 22.4 - - + -
168B CYS* 4.1 11.0 - - + -
182B THR* 4.2 16.2 - - + -
183B GLY 4.1 1.1 - - - -
184B ASN* 3.6 47.6 - - + +
185B GLU* 3.9 13.5 - - - -
186B GLU 3.5 13.2 - - - -
188B TYR* 1.3 84.3 - - - +
190B THR* 1.3 75.9 + - - +
215B MET 6.0 0.7 - - - -
217B ASN* 6.2 0.2 - - - +
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Residues in contact with THR 190 (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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160B LEU 3.2 14.8 - - - +
161B GLN* 3.9 20.6 - - + -
163B VAL* 4.6 0.4 - - - -
182B THR* 3.6 0.2 - - - -
183B GLY* 2.9 27.3 + - - +
189B PHE* 1.3 85.5 - - - +
191B ALA* 1.3 64.8 + - - +
217B ASN* 4.2 10.4 + - - +
219B LEU* 3.7 22.0 - - - +
234B THR* 3.8 10.7 + - + -
235B SER* 4.2 8.3 - - - -
236B HIS* 4.1 21.5 - - + +
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Residues in contact with ALA 191 (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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158B VAL 3.8 0.2 - - - +
159B PHE* 3.6 0.3 - - - -
160B LEU* 2.9 34.3 + - + +
163B VAL* 4.3 18.8 - - + -
168B CYS* 6.0 0.7 - - - -
171B LEU* 5.6 2.0 - - + -
180B ILE* 4.7 5.2 - - + -
181B ILE 3.1 13.2 - - - +
182B THR* 4.3 11.4 - - + -
190B THR* 1.3 77.7 - - - +
192B ILE* 1.3 69.4 + - - +
193B LEU* 4.2 15.0 - - + -
219B LEU* 4.1 1.8 - - - -
234B THR* 4.3 1.6 - - - +
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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
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157B VAL* 4.0 14.8 - - + -
158B VAL 3.3 3.1 - - - +
159B PHE* 3.9 15.5 - - + -
179B THR 3.5 2.6 - - - +
181B ILE* 2.8 43.2 + - + +
191B ALA* 1.3 80.3 - - - +
193B LEU* 1.3 63.5 + - - +
194B LEU* 3.6 26.4 - - + +
219B LEU* 3.8 35.4 - - + +
221B VAL* 4.0 16.6 - - + -
232B LEU 3.9 16.2 - - - +
234B THR* 3.8 17.0 - - + +
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Residues in contact with LEU 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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150B LEU* 5.2 6.1 - - + -
157B VAL* 3.2 11.1 - - - +
158B VAL* 2.8 54.2 + - + +
160B LEU* 3.8 31.0 - - + -
171B LEU* 4.9 10.1 - - + -
175B ALA* 3.9 28.0 - - + -
178B TYR* 3.7 18.6 - - + -
179B THR 3.3 3.4 - - - -
180B ILE* 3.9 22.4 - - + -
191B ALA* 4.3 7.2 - - + -
192B ILE* 1.3 83.0 - - - +
194B LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 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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156B ASP 3.8 2.5 - - - -
157B VAL* 4.1 17.9 - - + -
178B TYR* 3.3 3.7 - - - -
179B THR* 2.7 48.2 + - - +
181B ILE* 4.3 12.1 - - + -
192B ILE* 3.6 28.9 - - + +
193B LEU* 1.3 75.8 - - - +
195B LYS* 1.3 64.1 + - - +
196B LYS* 3.2 0.9 + - - -
199B VAL* 4.0 21.0 - - + +
201B PHE* 3.6 38.8 - - + -
221B VAL* 4.2 10.5 - - + -
223B VAL* 3.8 14.6 - - + -
232B LEU* 4.3 1.3 - - + -
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Residues in contact with LYS 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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154B SER* 2.6 39.3 + - - -
155B PRO 3.4 10.4 - - - -
156B ASP* 2.9 29.8 + - - +
177B SER* 4.5 4.9 - - - +
178B TYR* 3.4 25.7 - - + -
194B LEU* 1.3 69.7 - - - +
196B LYS* 1.3 75.7 + - - +
198B ARG* 3.2 25.6 + - + +
199B VAL* 2.9 29.1 + - - +
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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