Contacts of the strand formed by residues 222 - 236 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C LYS* 3.3 10.0 - - - +
219C TYR* 3.0 16.9 + - + +
220C ASP 3.4 0.4 - - - -
221C CYS* 1.3 125.4 - - - +
223C ALA* 1.3 65.2 + - - +
224C GLU* 3.1 11.4 + - - +
226C TYR* 4.1 21.1 - - + +
300C EPJ 4.0 22.7 - - + -
148D VAL* 4.6 13.2 - - - -
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C LYS* 3.3 24.0 - - - +
222C CYS* 1.3 69.9 - - - +
224C GLU* 1.3 77.5 + - + +
225C ILE* 5.2 1.0 - - - +
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Residues in contact with GLU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP* 3.6 32.1 - - + +
218C LYS* 3.4 13.0 - - - +
219C TYR 4.3 0.2 + - - -
222C CYS* 3.1 16.4 + - - +
223C ALA* 1.3 107.5 + - + +
225C ILE* 1.3 63.9 + - - +
226C TYR* 2.3 41.2 + - - +
300C EPJ 5.0 0.9 - - - -
108D ARG* 4.7 1.8 - - - +
138D HIS* 4.4 18.7 - - - +
140D PHE* 4.9 10.0 - - - -
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ASP* 3.1 4.5 + - - +
182C LYS* 2.9 35.6 + - + +
216C SER* 2.9 28.9 - - - +
217C LYS 3.3 15.9 - - - +
218C LYS* 4.3 14.6 - - + -
223C ALA 5.2 0.9 - - - +
224C GLU* 1.3 79.9 - - - +
226C TYR* 1.3 61.2 + - - +
227C PRO* 3.6 0.2 - - - +
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 4.2 6.6 + - - +
177C SER 4.7 3.1 - - - +
178C TRP 4.6 1.1 - - - -
179C THR 3.6 10.5 - - - -
180C TYR 3.2 23.1 - - - +
181C ASP* 3.2 25.1 - - + -
216C SER* 4.0 3.4 - - - -
217C LYS 3.2 22.3 + - - -
219C TYR* 3.9 29.0 + + + -
222C CYS* 4.1 9.4 - - + -
224C GLU* 2.3 53.9 + - + +
225C ILE* 1.3 72.6 - - - +
227C PRO* 1.3 67.7 - - + +
228C ASP* 3.8 1.7 + - - +
300C EPJ 3.2 54.4 - + + -
108D ARG* 3.8 5.4 + - - -
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Residues in contact with PRO 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 4.8 1.7 + - - -
176C GLY* 4.0 8.0 - - - -
177C SER* 4.2 7.2 + - - +
180C TYR 4.5 3.8 - - - +
181C ASP* 4.0 2.7 - - - -
182C LYS* 3.4 26.9 - - + +
185C ILE* 3.8 14.1 - - + +
186C ASP* 3.6 15.9 - - - +
187C LEU* 3.4 23.0 - - + +
214C TYR* 3.5 26.2 - - + +
215C ASN 3.5 7.4 - - - +
216C SER* 4.3 3.5 - - - +
225C ILE 3.6 1.8 - - - +
226C TYR* 1.3 90.5 - - + +
228C ASP* 1.3 60.2 + - - +
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Residues in contact with ASP 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 4.9 2.9 - - + -
174C LYS* 3.3 33.0 + - + +
175C PHE 3.4 14.8 - - - +
176C GLY* 4.7 1.3 - - - -
187C LEU* 4.2 4.0 - - - -
214C TYR* 3.5 5.9 - - - -
215C ASN* 2.8 52.3 + - - +
216C SER 4.2 1.2 + - - -
217C LYS* 4.6 6.4 - - - +
219C TYR* 3.9 7.0 + - - +
226C TYR 4.4 2.8 - - - +
227C PRO* 1.3 76.4 - - - +
229C VAL* 1.3 68.8 + - - +
230C THR* 2.9 24.9 + - - -
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 4.2 22.0 - - + -
173C MET 3.9 0.5 - - - +
175C PHE* 2.8 31.8 + - - +
187C LEU* 4.6 12.3 - - + +
189C GLN* 4.3 23.8 - - + +
213C THR 3.6 12.1 - - - +
214C TYR* 4.2 17.7 - - + -
228C ASP* 1.3 82.1 - - - +
230C THR* 1.3 64.5 + - - +
231C TYR* 3.1 37.7 + - + +
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Residues in contact with THR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ASN* 5.6 0.2 - - - +
172C LYS* 4.4 17.0 - - + -
173C MET 3.4 19.5 - - - +
174C LYS* 3.5 18.0 - - + +
212C GLY* 3.5 0.9 - - - -
213C THR* 2.7 52.1 + - - +
215C ASN* 4.8 6.5 + - - -
228C ASP* 2.9 17.5 + - - -
229C VAL* 1.3 74.4 - - - +
231C TYR* 1.3 69.3 + - - +
232C ALA* 4.2 0.8 + - + -
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Residues in contact with TYR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 4.2 9.8 + + - -
63C GLY* 3.3 10.6 - - - -
64C LEU* 2.8 58.4 + - + -
172C LYS* 3.1 2.9 - - - +
173C MET* 2.6 45.9 + - + +
175C PHE* 4.5 3.4 - + - -
189C GLN* 4.2 9.1 - - - +
192C GLN* 3.9 14.1 + - - -
196C LEU* 3.9 24.5 - - + -
211C THR 3.8 2.9 - - - -
212C GLY* 3.6 20.9 - - - -
229C VAL* 3.1 33.2 - - + +
230C THR* 1.3 74.3 - - - +
232C ALA* 1.3 60.1 + - - +
233C PHE* 3.8 19.2 - + + -
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ASN* 4.2 10.3 - - - +
171C CYS 3.9 2.2 - - - -
172C LYS* 3.8 24.9 - - + -
209C ASN* 3.7 5.9 - - - +
210C ALA* 4.3 0.2 - - - -
211C THR* 3.2 37.9 + - - +
213C THR* 6.2 3.4 - - + -
230C THR* 4.1 2.1 + - + -
231C TYR* 1.3 74.2 - - - +
233C PHE* 1.3 62.3 + - - +
234C VAL* 5.0 1.5 - - - +
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 3.9 22.0 - - + -
66C ILE* 3.7 34.1 - - + -
79C MET* 4.9 8.7 - - + -
81C THR* 5.7 0.2 - - + -
170C ASN* 2.3 27.4 + - - -
171C CYS* 2.8 48.4 + - + +
173C MET* 3.8 29.4 - - + -
196C LEU* 4.8 11.7 - - + -
207C ILE* 4.3 21.5 - - + -
209C ASN 3.6 7.0 - - - -
210C ALA* 5.4 4.0 - - + -
231C TYR* 3.8 21.5 - + + -
232C ALA* 1.3 75.0 - - - +
234C VAL* 1.3 63.1 + - - +
235C ILE* 4.8 7.4 - - + -
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Residues in contact with VAL 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLN* 3.7 31.4 - - - +
169C GLN 3.2 9.2 - - - +
170C ASN* 3.7 11.4 - - + +
207C ILE* 3.5 2.3 - - - +
208C VAL* 2.9 33.1 + - + -
209C ASN* 3.3 42.3 + - + +
232C ALA 5.0 1.1 - - - +
233C PHE* 1.3 81.3 - - - +
235C ILE* 1.3 69.7 + - - +
236C ARG* 5.1 3.6 - - + +
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 4.1 13.2 - - + -
72C VAL* 5.0 5.6 - - + -
79C MET* 5.0 9.0 - - + -
167C ASP 4.3 0.2 - - - +
168C GLN* 3.3 3.5 - - - -
169C GLN* 2.7 55.6 + - + +
171C CYS* 3.8 23.6 - - + -
206C ALA 3.3 20.4 - - - +
207C ILE* 3.7 17.9 - - + -
233C PHE* 4.8 7.0 - - + -
234C VAL* 1.3 84.5 - - - +
236C ARG* 1.3 60.9 + - - +
237C ARG* 3.4 30.8 + - - +
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Residues in contact with ARG 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C PRO* 5.2 8.4 - - - +
167C ASP* 5.9 0.9 - - - +
168C GLN* 2.7 45.1 + - + +
206C ALA* 3.1 37.7 + - + +
208C VAL* 4.3 31.9 - - + +
234C VAL* 4.2 4.0 - - + +
235C ILE* 1.3 72.6 - - - +
237C ARG* 1.3 62.7 + - - +
238C LEU* 3.6 8.4 + - + +
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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