Contacts of the strand formed by residues 184 - 191 (chain J) in PDB entry 1XFB
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 VAL 184 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16J LEU* 3.2 39.2 - - + +
19J ILE* 3.6 20.9 - - + -
20J ALA* 3.9 12.6 - - + +
23J ILE* 5.2 0.4 - - + -
144J ASP 2.8 13.4 + - - +
145J PHE* 2.9 14.9 - - + +
146J ALA 2.8 25.8 + - - -
183J ILE* 1.3 70.7 - - - +
185J PRO* 1.3 68.9 - - + +
186J ILE* 5.8 0.2 - - + -
226J GLY 3.3 21.8 - - - +
227J THR* 3.9 12.3 - - - +
228J LEU* 4.6 8.5 - - + +
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Residues in contact with PRO 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J ALA 3.9 1.3 - - - +
174J TYR* 3.5 24.7 - - + +
175J ALA* 3.8 34.3 - - + +
178J CYS* 3.8 9.0 - - + -
179J GLN* 3.8 9.0 - - + -
183J ILE 3.2 7.9 - - - +
184J VAL* 1.3 84.5 - - - +
186J ILE* 1.3 63.4 + - - +
187J VAL* 3.6 2.7 + - + +
226J GLY 3.2 16.6 - - - +
227J THR* 3.6 14.0 - - + -
228J LEU 3.2 20.6 + - - -
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Residues in contact with ILE 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ILE* 3.8 19.7 - - + -
78J ILE* 4.1 14.4 - - + -
145J PHE* 3.6 36.3 - - + -
146J ALA 2.8 18.6 + - - +
147J LYS* 4.3 5.6 - - + -
148J TRP 3.7 7.4 + - - -
174J TYR* 2.9 18.3 + - - -
184J VAL* 5.1 0.7 - - + +
185J PRO* 1.3 73.6 - - - +
187J VAL* 1.3 63.0 + - - +
188J GLU* 3.4 5.7 + - + +
228J LEU* 3.4 24.2 - - + +
230J LYS* 3.4 38.6 - - + +
269J THR* 4.5 4.7 - - - +
301J SER* 4.9 0.7 - - - +
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Residues in contact with VAL 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J LEU* 3.5 37.7 - - + -
174J TYR* 4.4 7.2 - - + -
175J ALA* 4.5 20.2 - - + -
185J PRO 4.3 6.5 - - - +
186J ILE* 1.3 72.5 - - - +
188J GLU* 1.3 57.7 + - - +
189J PRO* 3.1 9.9 - - + +
213J VAL* 3.9 17.5 - - + -
214J TYR* 5.7 1.6 - - - +
217J LEU* 4.4 20.0 - - + -
227J THR* 4.8 7.6 - - - -
228J LEU 2.8 15.5 + - - +
229J LEU* 3.4 9.0 - - + +
230J LYS 3.0 20.8 + - - -
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Residues in contact with GLU 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J LYS* 2.8 36.6 + - + +
148J TRP 3.3 14.6 + - - +
149J ARG* 3.3 31.2 - - + +
150J CYS* 3.0 24.3 + - - +
171J LEU* 4.0 4.7 - - - +
186J ILE* 3.4 7.2 + - + +
187J VAL* 1.3 73.9 - - - +
189J PRO* 1.3 58.4 - - - +
190J GLU* 3.3 14.7 + - - +
230J LYS* 3.3 40.2 - - + +
271J LEU* 3.7 12.6 - - + +
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Residues in contact with PRO 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J CYS* 4.2 7.4 - - + +
152J LEU* 5.6 4.5 - - + -
171J LEU* 3.8 17.3 - - + -
187J VAL* 3.1 17.5 - - + +
188J GLU* 1.3 81.4 - - - +
190J GLU* 1.3 62.6 - - - +
191J ILE* 3.4 8.6 + - - +
209J VAL* 4.2 10.8 - - + +
210J LEU* 4.0 26.5 - - + -
213J VAL* 4.1 14.8 - - + -
229J LEU* 3.8 10.1 - - + -
230J LYS 3.8 7.2 - - - +
231J PRO* 4.5 5.3 - - + +
232J ASN* 3.6 9.0 + - - -
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Residues in contact with GLU 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J ARG* 2.4 31.9 + - - +
150J CYS 3.2 16.4 + - - +
151J VAL* 3.4 3.6 - - - +
152J LEU* 2.8 27.2 + - - +
188J GLU* 3.3 17.7 + - + +
189J PRO* 1.3 71.7 - - - +
191J ILE* 1.3 69.5 + - - +
192J LEU* 3.2 23.6 + - + +
193J PRO* 4.7 4.3 - - - +
232J ASN* 4.0 3.1 - - + +
271J LEU* 3.7 37.0 - - + +
273J GLY* 5.0 5.8 - - - -
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Residues in contact with ILE 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J LEU* 3.6 21.8 - - + +
154J ILE* 3.5 38.8 - - + -
189J PRO 4.2 5.8 - - - +
190J GLU* 1.3 74.9 - - - +
192J LEU* 1.3 65.0 + - - +
193J PRO* 3.7 2.3 - - - +
202J CYS* 5.2 4.9 - - - -
205J VAL* 3.7 5.4 - - + -
206J THR* 3.4 41.5 - - + +
209J VAL* 3.6 26.0 - - + -
232J ASN* 2.7 37.3 - - - +
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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