Contacts of the strand formed by residues 214 - 221 (chain B) in PDB entry 5ZF6
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 LEU 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B ILE* 3.7 20.6 - - + +
194B GLY* 3.4 10.4 - - - -
195B ILE* 3.7 27.4 - - + +
204B PRO* 5.7 0.9 - - - +
212B SER* 2.8 25.8 + - - -
213B THR* 1.3 81.3 + - - +
215B ASN* 1.3 65.2 + - - +
216B LEU* 3.9 16.6 - - + +
231B ALA* 4.6 0.4 - - + -
232B SER 3.6 6.1 - - - +
233B ALA* 3.9 10.3 - - + -
236B ILE* 4.1 5.2 - - + -
241B PHE* 3.6 35.2 - - + -
244B ALA* 3.5 31.4 - - + -
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Residues in contact with ASN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 6.0 1.4 - - - +
192B ARG* 2.8 36.5 + - - +
193B ILE 4.0 1.3 - - - -
209B MET* 4.0 20.5 - - + +
214B LEU* 1.3 73.6 - - - +
216B LEU* 1.3 57.8 + - - +
217B VAL* 4.5 2.8 - - - +
230B GLU 3.7 1.4 - - - +
231B ALA* 3.1 3.6 - - - -
232B SER* 2.7 49.6 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B VAL 3.9 0.3 - - - +
192B ARG* 3.2 4.7 - - - +
193B ILE* 2.7 50.4 + - + +
214B LEU* 3.9 16.2 - - + -
215B ASN* 1.3 75.2 + - - +
217B VAL* 1.3 63.9 + - - +
218B VAL* 3.7 19.5 - - + -
229B LEU* 3.7 25.1 - - + -
230B GLU 3.4 7.2 - - - +
231B ALA* 3.5 20.9 - - + +
241B PHE* 4.3 6.3 - - + +
244B ALA* 3.8 26.5 - - + +
245B ILE* 3.9 19.3 - - + +
557B LEU* 4.6 0.7 - - + -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 4.5 11.2 - - + -
167B VAL* 4.7 3.4 - - + -
170B ILE* 3.9 22.0 - - + -
190B ALA* 5.2 0.4 - - + -
191B VAL 3.4 11.4 - - - +
192B ARG* 3.5 40.2 - - + +
215B ASN* 4.5 2.9 - - - +
216B LEU* 1.3 77.5 - - - +
218B VAL* 1.3 66.2 + - - +
228B MET* 3.7 22.9 - - + +
229B LEU* 3.6 5.2 - - - -
230B GLU* 2.8 40.0 + - + +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ALA* 3.1 24.6 - - - +
191B VAL* 3.1 12.9 + - + +
193B ILE* 5.3 1.3 - - + -
216B LEU* 3.7 22.2 - - + +
217B VAL* 1.3 78.1 - - - +
219B ALA* 1.3 69.9 + - - +
220B GLY* 4.5 0.7 - - - +
226B ILE* 5.1 3.6 - - + -
228B MET* 3.5 8.3 - - - +
229B LEU* 3.6 24.5 - - + -
245B ILE* 4.7 8.7 - - - +
248B GLY* 4.6 9.9 - - - -
249B VAL* 3.7 28.0 - - + +
252B THR* 3.6 14.0 - - + +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B SER* 3.5 33.9 - - - +
188B VAL* 4.1 6.5 - - + -
189B GLY 3.2 7.0 - - - +
190B ALA* 4.3 4.3 - - + -
218B VAL* 1.3 74.9 - - - +
220B GLY* 1.3 55.6 + - - +
226B ILE* 3.7 2.4 - - - -
227B VAL* 2.7 37.9 + - + +
228B MET* 3.0 26.7 + - + +
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Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B VAL* 3.3 7.5 - - - -
189B GLY 2.6 36.4 + - - -
218B VAL* 5.0 2.5 - - - -
219B ALA* 1.3 73.6 - - - +
221B ALA* 1.3 61.8 + - - -
225B GLN 3.4 7.9 - - - -
226B ILE* 4.8 0.7 - - - -
227B VAL* 4.4 2.5 - - - -
249B VAL* 5.4 2.2 - - - -
252B THR* 3.5 23.4 - - - +
253B GLN* 4.3 0.4 - - - -
256B ILE* 3.3 5.6 - - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 5.0 7.4 - - + -
187B PRO 4.2 1.6 - - - -
188B VAL* 4.8 1.8 - - - -
220B GLY* 1.3 71.2 - - - -
222B PRO* 1.3 74.6 - - + +
224B SER 3.6 2.1 + - - -
225B GLN* 2.7 27.2 + - + +
227B VAL* 3.6 22.9 - - + +
253B GLN* 2.6 30.3 + - - -
256B ILE* 3.4 4.5 - - - -
564B PRO 4.3 9.2 - - - +
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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