Contacts of the strand formed by residues 184 - 191 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.2 39.0 - - + +
19D ILE* 3.6 21.3 - - + -
20D ALA* 3.9 13.2 - - + +
23D ILE* 5.2 0.2 - - + -
144D ASP 2.8 13.2 + - - +
145D PHE* 2.9 16.4 - - + +
146D ALA 2.8 25.6 + - - -
183D ILE* 1.3 70.2 - - - +
185D PRO* 1.3 67.4 - - + +
186D ILE* 5.8 0.4 - - + -
226D GLY 3.3 23.1 - - - +
227D THR* 3.9 11.9 - - - +
228D LEU* 4.6 8.7 - - + +
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Residues in contact with PRO 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ALA 3.9 1.6 - - - +
174D TYR* 3.5 24.2 - - + +
175D ALA* 3.8 35.9 - - + +
178D CYS* 3.8 9.4 - - + -
179D GLN* 3.8 9.4 - - + -
183D ILE 3.2 8.1 - - - +
184D VAL* 1.3 85.1 - - - +
186D ILE* 1.3 62.3 + - - +
187D VAL* 3.6 2.6 + - + +
226D GLY 3.2 16.8 - - - +
227D THR* 3.6 13.3 - - + -
228D LEU 3.2 21.0 + - - -
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Residues in contact with ILE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.8 20.0 - - + -
78D ILE* 4.1 13.5 - - + -
145D PHE* 3.6 36.8 - - + -
146D ALA 2.8 18.5 + - - +
147D LYS* 4.3 5.8 - - + -
148D TRP 3.7 7.4 + - - +
174D TYR* 2.9 17.4 + - - -
184D VAL 5.1 0.4 - - - +
185D PRO* 1.3 72.1 - - - +
187D VAL* 1.3 62.5 + - - +
188D GLU* 3.4 4.7 + - + +
228D LEU* 3.4 24.2 - - + +
230D LYS* 3.4 39.0 - - + +
269D THR* 4.5 4.3 - - - +
301D SER* 4.9 0.9 - - - +
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Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.5 37.5 - - + -
174D TYR* 4.4 7.2 - - + -
175D ALA* 4.5 19.5 - - + -
185D PRO 4.3 6.5 - - - +
186D ILE* 1.3 72.1 - - - +
188D GLU* 1.3 57.3 + - - +
189D PRO* 3.0 9.9 - - + +
213D VAL* 3.9 18.4 - - + -
214D TYR* 5.7 2.0 - - - +
217D LEU* 4.4 19.3 - - + -
227D THR* 4.8 7.4 - - - -
228D LEU 2.8 15.5 + - - +
229D LEU* 3.4 8.6 - - + +
230D LYS 3.0 20.6 + - - -
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Residues in contact with GLU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LYS* 2.8 36.8 + - + +
148D TRP 3.3 14.0 + - - +
149D ARG* 3.3 31.0 - - + +
150D CYS* 3.0 24.4 + - - +
171D LEU* 4.0 4.7 - - - +
186D ILE* 3.4 6.5 + - + +
187D VAL* 1.3 72.9 - - - +
189D PRO* 1.3 58.4 - - - +
190D GLU* 3.3 14.0 + - - +
230D LYS* 3.3 41.6 - - + +
271D LEU* 3.7 12.3 - - + +
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Residues in contact with PRO 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D CYS* 4.2 7.0 - - + +
152D LEU* 5.6 5.2 - - + -
171D LEU* 3.8 17.7 - - + -
187D VAL* 3.0 17.3 - - + +
188D GLU* 1.3 81.8 - - - +
190D GLU* 1.3 63.1 + - - +
191D ILE* 3.4 8.8 + - - +
209D VAL* 4.2 11.0 - - + +
210D LEU* 4.0 26.5 - - + -
213D VAL* 4.1 15.7 - - + -
229D LEU* 3.8 9.6 - - + -
230D LYS 3.8 7.0 - - - +
231D PRO* 4.5 5.7 - - + +
232D ASN* 3.6 8.5 + - - -
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ARG* 2.4 31.1 + - + +
150D CYS 3.2 17.0 + - - +
151D VAL* 3.4 3.5 - - - +
152D LEU* 2.8 27.8 + - - +
188D GLU* 3.3 17.3 + - + +
189D PRO* 1.3 71.8 - - - +
191D ILE* 1.3 68.2 + - - +
192D LEU* 3.2 23.5 + - + +
193D PRO* 4.7 4.3 - - - +
232D ASN* 4.0 3.1 - - + +
271D LEU* 3.7 39.2 - - + +
273D GLY* 5.0 6.0 - - - -
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D LEU* 3.6 22.9 - - + +
154D ILE* 3.5 38.8 - - + -
189D PRO 4.2 5.6 - - - +
190D GLU* 1.3 74.2 - - - +
192D LEU* 1.3 65.2 + - - +
193D PRO* 3.7 2.6 - - - +
202D CYS* 5.2 3.6 - - - -
205D VAL* 3.7 5.4 - - + -
206D THR* 3.4 42.6 - - + +
209D VAL* 3.6 24.9 - - + -
232D ASN* 2.7 38.4 - - - +
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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