Contacts of the strand formed by residues 222 - 233 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D LYS* 3.5 7.1 - - - -
219D TYR* 2.8 21.5 + - + +
220D ASP 3.2 0.6 - - - -
221D CYS* 1.3 127.1 - - - +
223D ALA* 1.3 65.1 + - - +
224D GLU* 3.3 11.3 + - - +
226D TYR* 4.4 14.4 - - + +
300D EPJ 3.8 31.4 - - + -
86E LYS* 5.2 0.4 - - - -
146E HIS* 6.4 1.8 - - - -
148E VAL* 4.4 13.7 - - - -
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Residues in contact with ALA 223 (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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218D LYS* 4.1 18.8 - - - +
222D CYS* 1.3 71.4 - - - +
224D GLU* 1.3 74.4 + - + +
225D ILE* 5.4 1.2 - - - +
140E PHE* 6.2 1.1 - - + -
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Residues in contact with GLU 224 (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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181D ASP* 3.3 29.4 - - - +
218D LYS* 4.0 6.4 - - - +
222D CYS* 3.3 12.7 + - - +
223D ALA* 1.3 98.6 + - + +
225D ILE* 1.3 68.6 + - - +
226D TYR* 2.1 44.6 + - - +
300D EPJ 5.1 0.9 - - - -
108E ARG* 4.0 2.0 + - - +
138E HIS* 3.6 30.6 + - + -
140E PHE* 4.2 10.2 - - - -
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Residues in contact with ILE 225 (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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181D ASP* 3.2 2.9 + - - +
182D LYS* 2.8 43.9 + - + +
216D SER* 4.3 13.7 - - - -
217D LYS* 2.9 34.8 - - - +
218D LYS* 3.1 32.3 - - + +
223D ALA 5.4 1.1 - - - +
224D GLU* 1.3 76.9 - - - +
226D TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 226 (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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122D TYR* 4.2 10.7 + - - +
177D SER 4.5 5.4 - - - +
179D THR 3.7 11.1 + - - -
180D TYR 3.6 9.0 - - - -
181D ASP* 3.1 38.7 + - + +
216D SER* 3.9 0.8 - - - -
217D LYS 2.9 29.1 + - - +
219D TYR* 4.3 16.1 + + + -
222D CYS* 4.4 5.9 - - + +
224D GLU* 2.1 60.7 + - + +
225D ILE* 1.3 74.6 - - - +
227D PRO* 1.3 68.4 - - + +
228D ASP* 3.9 5.2 + - - +
300D EPJ 3.6 56.3 - + + -
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Residues in contact with PRO 227 (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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122D TYR* 4.6 3.6 + - - -
176D GLY* 4.4 6.8 - - - -
177D SER* 4.6 5.3 + - - +
180D TYR 5.1 2.0 - - - +
181D ASP* 4.2 2.2 - - - -
182D LYS* 3.5 24.5 - - + +
185D ILE 3.9 11.7 - - - +
186D ASP* 2.9 34.3 - - - +
187D LEU* 3.5 19.8 - - + +
214D TYR* 3.2 17.0 - - + +
215D ASN 3.0 10.5 - - - +
216D SER* 4.0 3.8 - - - +
225D ILE 3.5 2.5 - - - +
226D TYR* 1.3 87.9 - - + +
228D ASP* 1.3 59.1 + - - +
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Residues in contact with ASP 228 (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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122D TYR* 4.3 12.8 - - + +
174D LYS* 2.8 30.6 + - + +
175D PHE 3.1 21.5 - - - +
187D LEU* 4.3 4.9 - - - -
214D TYR* 3.6 4.0 - - - -
215D ASN* 2.8 51.4 + - - +
217D LYS* 4.2 3.8 + - - +
219D TYR* 3.9 7.1 + - - -
226D TYR 4.4 3.6 - - - +
227D PRO* 1.3 74.6 - - - +
229D VAL* 1.3 62.5 + - - +
230D THR* 3.1 24.4 + - - -
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D PHE* 4.0 21.8 - - + -
175D PHE* 3.0 27.7 + - - +
187D LEU* 4.6 16.5 - - + +
189D GLN* 3.9 38.1 - - + +
213D THR 3.7 2.2 - - - -
214D TYR* 4.3 9.0 - - + -
228D ASP* 1.3 77.7 - - - +
230D THR* 1.3 64.5 + - - +
231D TYR* 3.1 46.7 - - + +
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Residues in contact with THR 230 (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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172D LYS* 3.7 36.2 + - + +
173D MET 3.4 15.9 - - - +
174D LYS* 3.8 13.4 + - + +
211D THR 3.9 1.0 - - - +
212D GLY* 3.2 1.0 - - - -
213D THR* 2.8 42.9 + - - +
215D ASN* 3.5 8.3 + - - -
217D LYS* 5.4 0.3 + - - -
228D ASP* 3.1 17.2 + - - -
229D VAL* 1.3 73.2 - - - +
231D TYR* 1.3 64.9 + - - +
232D ALA* 4.1 2.6 - - + +
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Residues in contact with TYR 231 (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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62D PHE* 3.6 22.6 + + - -
63D GLY* 3.6 11.4 - - - -
64D LEU* 3.5 54.5 + - + -
172D LYS* 3.5 1.6 - - - -
173D MET 2.8 37.3 + - - +
175D PHE* 4.2 2.2 - + - -
189D GLN* 4.5 7.9 + - - -
190D MET 5.3 1.2 + - - -
192D GLN* 5.7 2.5 - - + -
196D LEU* 4.6 19.1 - - + -
210D ALA* 6.3 0.4 - - + -
211D THR 3.6 4.3 - - - +
212D GLY* 3.6 21.5 - - - +
229D VAL* 3.1 37.2 - - + +
230D THR* 1.3 75.0 - - - +
232D ALA* 1.3 59.1 + - - +
233D PHE* 3.5 23.3 - - + -
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Residues in contact with ALA 232 (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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170D ASN* 5.3 6.1 - - - +
172D LYS* 4.4 13.2 - - + +
209D ASN 4.0 0.7 - - - +
210D ALA* 2.9 4.9 - - - +
211D THR* 2.8 43.4 + - - +
230D THR* 4.1 2.7 - - + +
231D TYR* 1.3 74.0 - - - +
233D PHE* 1.3 63.3 + - - +
234D VAL* 5.5 1.3 - - + -
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Residues in contact with PHE 233 (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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64D LEU* 4.2 19.1 - - + -
66D ILE* 4.2 26.0 - - + -
79D MET* 5.2 9.4 - - + -
81D THR* 5.8 1.3 - - + -
169D GLN* 3.3 1.9 + - - +
170D ASN* 2.6 25.9 + - - +
171D CYS* 3.5 22.6 + - + +
173D MET* 4.2 21.1 - - + -
196D LEU* 4.6 14.4 - - + -
197D LYS* 5.5 0.7 - - + -
207D ILE* 4.0 21.1 - - + -
210D ALA* 3.4 22.2 - - + -
231D TYR* 3.5 29.8 - - + -
232D ALA* 1.3 78.1 - - - +
234D VAL* 1.3 72.0 + - - +
235D ILE* 4.8 10.5 - - + -
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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