Contacts of the strand formed by residues 184 - 191 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E LEU* 3.2 39.9 - - + +
19E ILE* 3.6 21.5 - - + -
20E ALA* 3.9 12.6 - - + +
23E ILE* 5.2 0.2 - - + -
144E ASP 2.8 14.2 + - - +
145E PHE* 2.9 15.9 - - + +
146E ALA 2.8 25.6 + - - -
183E ILE* 1.3 68.8 - - - +
185E PRO* 1.3 68.7 - - + +
186E ILE* 5.8 0.2 - - + -
226E GLY 3.3 21.8 - - - +
227E THR* 3.9 11.4 - - - +
228E LEU* 4.6 8.3 - - + +
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Residues in contact with PRO 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ALA 3.9 1.1 - - - +
174E TYR* 3.5 25.4 - - + +
175E ALA* 3.8 35.9 - - + +
178E CYS* 3.8 9.2 - - + -
179E GLN* 3.8 8.7 - - + -
183E ILE 3.2 8.1 - - - +
184E VAL* 1.3 84.9 - - - +
186E ILE* 1.3 63.0 + - - +
187E VAL* 3.6 2.8 + - + +
226E GLY 3.2 16.4 - - - +
227E THR* 3.6 12.9 - - + -
228E LEU 3.2 20.7 + - - -
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Residues in contact with ILE 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE* 3.8 20.4 - - + -
78E ILE* 4.1 14.8 - - + -
145E PHE* 3.6 35.7 - - + -
146E ALA 2.8 20.1 + - - +
147E LYS* 4.3 5.8 - - + -
148E TRP 3.7 7.3 + - - -
174E TYR* 2.9 18.1 + - - -
184E VAL* 5.1 0.7 - - + +
185E PRO* 1.3 71.8 - - - +
187E VAL* 1.3 60.7 + - - +
188E GLU* 3.4 3.9 + - + +
228E LEU* 3.4 24.7 - - + +
230E LYS* 3.4 39.0 - - + +
269E THR* 4.5 4.9 - - - +
301E SER* 4.9 0.9 - - - +
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Residues in contact with VAL 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LEU* 3.5 37.0 - - + -
174E TYR* 4.4 7.4 - - + -
175E ALA* 4.5 19.3 - - + -
185E PRO 4.3 7.0 - - - +
186E ILE* 1.3 71.8 - - - +
188E GLU* 1.3 56.6 + - - +
189E PRO* 3.1 10.3 - - + +
213E VAL* 3.9 18.4 - - + -
214E TYR* 5.7 2.0 - - + +
217E LEU* 4.4 19.1 - - + -
227E THR* 4.8 7.4 - - - -
228E LEU 2.8 16.3 + - - +
229E LEU* 3.4 8.3 - - + +
230E LYS 3.0 21.0 + - - -
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Residues in contact with GLU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LYS* 2.8 36.9 + - + +
148E TRP 3.3 15.0 + - - +
149E ARG* 3.3 30.1 - - + +
150E CYS* 3.0 24.4 + - - +
171E LEU* 4.0 4.7 - - - +
186E ILE* 3.4 6.3 + - + +
187E VAL* 1.3 72.7 - - - +
189E PRO* 1.3 57.5 - - - +
190E GLU* 3.3 13.7 + - - +
230E LYS* 3.3 40.7 - - + +
271E LEU* 3.7 12.5 - - + +
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Residues in contact with PRO 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E CYS* 4.2 7.2 - - + +
152E LEU* 5.6 5.4 - - + -
171E LEU* 3.8 17.9 - - + -
187E VAL* 3.1 17.7 - - + +
188E GLU* 1.3 81.3 - - - +
190E GLU* 1.3 62.7 + - - +
191E ILE* 3.4 8.6 + - - +
209E VAL* 4.2 11.5 - - + +
210E LEU* 4.0 26.5 - - + -
213E VAL* 4.1 15.3 - - + -
229E LEU* 3.8 9.2 - - + -
230E LYS 3.8 7.2 - - - +
231E PRO* 4.5 5.6 - - + +
232E ASN* 3.6 8.7 + - - -
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Residues in contact with GLU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ARG* 2.4 31.6 + - - +
150E CYS 3.2 16.4 + - - +
151E VAL* 3.4 3.3 - - - +
152E LEU* 2.8 27.9 + - - +
188E GLU* 3.3 18.5 + - + +
189E PRO* 1.3 71.2 - - - +
191E ILE* 1.3 69.9 + - - +
192E LEU* 3.2 24.2 + - + +
193E PRO* 4.7 4.5 - - - +
232E ASN* 4.0 3.4 - - + +
271E LEU* 3.7 39.1 - - + +
273E GLY* 5.0 6.0 - - - -
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Residues in contact with ILE 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E LEU* 3.6 22.0 - - + +
154E ILE* 3.5 38.6 - - + -
159E PRO* 5.8 0.2 - - + -
189E PRO 4.2 5.6 - - - +
190E GLU* 1.3 75.3 - - - +
192E LEU* 1.3 65.0 + - - +
193E PRO* 3.7 2.8 - - - +
202E CYS* 5.2 4.3 - - - -
205E VAL* 3.7 4.9 - - + -
206E THR* 3.4 42.0 - - + +
209E VAL* 3.6 24.9 - - + -
232E ASN* 2.7 37.6 - - - +
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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