Contacts of the strand formed by residues 222 - 232 (chain E) in PDB entry 5FJV
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 CYS 222 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A HIS* 6.5 0.7 - - - -
148A VAL* 4.5 8.1 - - - -
218E LYS* 3.5 4.8 - - - -
219E TYR* 3.1 17.3 + - + +
220E ASP 3.5 0.2 - - - -
221E CYS* 1.3 102.6 - - - +
223E ALA* 1.3 65.0 + - - +
224E GLU* 3.1 26.8 + - - +
226E TYR* 3.9 11.2 - - + -
300E EPJ 3.1 39.3 - - - -
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Residues in contact with ALA 223 (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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218E LYS* 4.1 20.8 - - - +
222E CYS* 1.3 72.0 - - - +
224E GLU* 1.3 76.3 + - + +
225E ILE* 5.2 1.6 - - - +
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Residues in contact with GLU 224 (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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108A ARG* 4.4 2.2 - - - +
138A HIS* 3.9 28.3 + - + -
140A PHE* 4.7 6.9 - - - -
181E ASP* 3.4 34.8 - - + +
218E LYS* 4.1 6.4 - - - +
219E TYR 4.7 0.2 + - - -
222E CYS* 3.1 21.9 - - - +
223E ALA* 1.3 99.0 + - + +
225E ILE* 1.3 69.1 + - - +
226E TYR* 2.6 34.3 + - + -
300E EPJ 4.9 0.3 - - - -
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Residues in contact with ILE 225 (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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181E ASP* 3.2 4.1 + - - +
182E LYS* 2.7 42.4 + - + +
216E SER* 3.3 23.8 - - - +
217E LYS* 2.9 24.9 - - - +
218E LYS* 3.1 31.2 - - + +
223E ALA 5.2 1.6 - - - +
224E GLU* 1.3 76.7 - - - +
226E TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 226 (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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108A ARG* 4.1 2.1 + - - -
122E TYR* 4.6 4.3 - - - +
177E SER* 4.2 7.2 - - - +
178E TRP 4.4 0.2 - - - -
179E THR 3.7 13.3 + - - -
180E TYR 3.2 20.2 - - - -
181E ASP* 3.2 30.3 - - + +
216E SER* 3.8 1.8 - - - -
217E LYS* 2.8 31.9 + - - +
219E TYR* 4.2 21.1 + + + -
222E CYS* 3.9 10.8 - - + -
224E GLU* 2.6 46.1 + - + +
225E ILE* 1.3 72.4 - - - +
227E PRO* 1.3 69.7 - - + +
228E ASP* 3.9 1.2 + - - +
300E EPJ 3.4 55.3 - + + -
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Residues in contact with PRO 227 (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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122E TYR* 4.4 4.2 + - - -
176E GLY* 3.9 9.0 - - - -
177E SER* 4.5 6.1 + - - +
180E TYR 5.0 1.8 - - - +
181E ASP* 4.4 2.0 - - - -
182E LYS* 3.7 17.0 - - + +
185E ILE 3.9 12.1 - - - +
186E ASP* 3.3 18.2 - - - +
187E LEU* 3.8 22.3 - - + +
214E TYR* 3.2 31.2 - - + +
215E ASN 3.3 7.2 - - - +
216E SER* 4.1 3.8 - - - +
225E ILE 3.6 8.7 - - - +
226E TYR* 1.3 88.4 - - + +
228E ASP* 1.3 60.4 + - - +
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Residues in contact with ASP 228 (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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122E TYR* 4.6 4.5 - - + +
174E LYS* 3.8 29.5 - - + -
175E PHE 3.1 16.2 - - - +
176E GLY* 4.3 2.7 - - - -
187E LEU* 4.6 3.4 - - - -
214E TYR* 3.7 2.1 - - - -
215E ASN* 2.8 56.3 + - - +
216E SER* 4.4 2.4 + - - -
217E LYS* 5.4 4.3 - - - +
219E TYR* 4.4 7.0 + - - +
226E TYR 4.8 1.6 - - - +
227E PRO* 1.3 75.4 - - - +
229E VAL* 1.3 65.5 + - - +
230E THR* 2.9 28.0 + - - +
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Residues in contact with VAL 229 (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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62E PHE* 4.2 20.6 - - + -
173E MET 3.8 1.2 - - - +
175E PHE* 2.6 35.2 + - - +
187E LEU* 4.6 11.9 - - + +
189E GLN* 3.9 35.2 - - + +
213E THR 4.1 4.7 - - - +
214E TYR* 4.1 15.0 - - + -
228E ASP* 1.3 81.2 - - - +
230E THR* 1.3 64.8 + - - +
231E TYR* 3.3 36.3 - - + +
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Residues in contact with THR 230 (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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172E LYS* 4.9 12.4 - - + +
173E MET 3.0 11.9 - - - -
174E LYS* 3.4 25.1 - - + +
211E THR 4.0 1.2 - - - +
212E GLY* 3.7 1.4 - - - -
213E THR* 3.4 29.9 + - - +
215E ASN* 4.4 12.0 + - - +
228E ASP* 2.9 22.1 + - - +
229E VAL* 1.3 74.3 - - - +
231E TYR* 1.3 66.1 + - - +
232E ALA* 4.9 1.7 + - - +
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Residues in contact with TYR 231 (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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62E PHE* 3.7 15.8 + + - -
63E GLY* 3.6 11.1 - - - -
64E LEU* 3.4 48.0 + - + -
172E LYS* 3.1 5.1 - - - -
173E MET* 2.6 42.5 + - + +
175E PHE* 4.1 25.6 - + - -
189E GLN* 4.6 1.9 + - - -
192E GLN* 4.3 13.5 + - - -
196E LEU* 4.1 21.1 - - + -
210E ALA* 5.9 1.1 - - + -
211E THR 3.6 2.7 - - - -
212E GLY* 3.9 22.0 - - - -
229E VAL* 3.3 27.8 - - + +
230E THR* 1.3 74.5 - - - +
232E ALA* 1.3 60.8 + - - +
233E PHE* 3.8 18.8 - + + -
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Residues in contact with ALA 232 (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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170E ASN* 4.0 22.4 - - - +
171E CYS 4.0 2.7 - - - -
172E LYS* 4.4 2.7 - - + +
209E ASN 5.0 0.2 - - - -
210E ALA* 2.8 13.0 - - - +
211E THR* 2.5 52.4 + - - +
230E THR* 5.6 2.2 - - - +
231E TYR* 1.3 72.8 - - - +
233E PHE* 1.3 57.7 + - - +
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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