Contacts of the helix formed by residues 219 - 229 (chain B) in PDB entry 5VZ4
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 THR 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B PRO 3.8 0.6 + - - -
218B PRO* 1.3 75.7 - - - +
220B CYS* 1.3 63.7 + - - +
221B LEU* 3.3 3.5 + - - +
222B SER* 2.7 25.9 + - - -
223B VAL* 3.0 19.8 + - - +
291B CYS* 3.9 0.7 - - - -
292B THR* 3.2 11.6 - - - +
295B THR* 3.1 35.4 - - + -
296B ILE* 3.4 23.1 - - + -
403B EDO 3.0 17.9 + - - +
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Residues in contact with CYS 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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219B THR* 1.3 70.4 - - - +
221B LEU* 1.3 57.5 + - - +
223B VAL* 3.2 4.3 + - - +
224B ILE* 2.9 34.3 + - - +
291B CYS* 2.1 58.6 - - - -
292B THR 3.1 15.2 + - - -
293B CYS* 4.0 0.9 - - - -
304B CYS* 3.6 22.1 - - - +
307B PHE* 4.3 4.3 - - + -
308B GLN* 3.5 31.0 - - - +
311B LEU* 5.2 0.7 - - + -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 3.2 6.0 - - - +
220B CYS* 1.3 72.0 - - - +
222B SER* 1.3 66.9 + - - +
223B VAL 3.3 0.2 + - - -
224B ILE* 3.3 5.1 + - - +
225B ARG* 3.0 54.8 + - - +
296B ILE* 4.2 11.0 - - + -
300B GLU* 3.6 39.9 - - + +
303B LEU* 3.8 9.6 - - + -
304B CYS* 3.4 38.3 - - + +
307B PHE* 3.7 17.5 - - + -
403B EDO 4.0 12.6 - - - +
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Residues in contact with SER 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO* 4.5 8.7 - - - +
219B THR* 2.7 33.8 + - - -
221B LEU* 1.3 74.1 - - - +
223B VAL* 1.3 57.8 + - - +
225B ARG* 4.2 1.1 - - - +
226B SER* 2.9 34.7 + - - -
403B EDO 3.7 23.5 + - - -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO* 3.7 29.6 - - + -
219B THR 3.0 10.3 + - - +
220B CYS* 3.4 8.7 - - - +
221B LEU 3.1 0.2 - - - -
222B SER* 1.3 74.3 - - - +
224B ILE* 1.3 67.1 + - - +
227B CYS* 3.2 22.7 + - - +
286B VAL* 3.7 38.6 - - + +
287B LEU* 3.8 14.4 - - + +
289B VAL* 4.3 4.0 - - + +
291B CYS* 3.9 11.9 - - + -
311B LEU* 3.7 29.2 - - + -
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Residues in contact with ILE 224 (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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220B CYS 2.9 19.6 + - - +
221B LEU 3.9 3.1 - - - +
223B VAL* 1.3 73.7 - - - +
225B ARG* 1.3 68.2 + - + +
227B CYS* 3.2 7.6 + - + +
228B GLN* 3.1 43.6 + - + +
237B TYR* 3.9 31.4 - - + -
256B GLU* 5.1 2.7 - - - +
287B LEU* 4.0 6.7 - - + -
307B PHE* 3.5 53.2 - - + -
311B LEU* 3.8 23.1 - - + -
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Residues in contact with ARG 225 (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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221B LEU* 3.0 46.0 + - - +
222B SER 4.2 1.8 - - - +
224B ILE* 1.3 78.0 - - + +
226B SER* 1.3 64.1 + - - +
228B GLN* 2.9 23.7 + - + +
229B ASN* 3.2 19.6 + - - +
256B GLU* 2.9 41.6 + - - +
300B GLU* 3.8 14.5 + - - -
303B LEU* 4.3 2.6 - - - +
307B PHE* 6.1 0.8 - - - -
403B EDO 3.3 34.0 + - - +
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Residues in contact with SER 226 (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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222B SER* 2.9 22.3 + - - -
223B VAL 4.1 3.1 - - - -
225B ARG* 1.3 76.3 - - - +
227B CYS* 1.3 61.1 + - - +
229B ASN* 3.3 20.0 + - - +
230B ASP* 3.6 11.4 + - - +
286B VAL* 4.0 21.6 - - - +
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Residues in contact with CYS 227 (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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223B VAL 3.2 14.2 + - - +
224B ILE 3.2 10.3 - - - +
225B ARG 3.1 0.4 - - - -
226B SER* 1.3 75.3 - - - +
228B GLN* 1.3 65.7 + - - +
230B ASP 3.0 21.1 + - - +
233B CYS* 2.1 63.5 - - - +
234B ARG* 3.4 3.6 + - - -
237B TYR* 3.8 11.9 - - + -
286B VAL* 3.9 4.8 - - + +
287B LEU* 3.7 21.1 - - + -
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Residues in contact with GLN 228 (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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224B ILE* 3.3 32.3 - - + +
225B ARG* 2.9 15.9 + - + +
227B CYS* 1.3 80.0 - - - +
229B ASN* 1.3 62.4 + - - +
230B ASP 3.4 0.2 + - - -
234B ARG* 3.1 43.9 + - + +
237B TYR* 4.0 26.1 - - - +
254B GLU* 4.2 29.2 + - - +
256B GLU* 5.6 3.5 + - - +
307B PHE* 5.9 0.4 - - - -
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Residues in contact with ASN 229 (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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225B ARG* 3.2 20.9 + - - +
226B SER* 3.9 11.9 - - - +
227B CYS 3.1 1.2 - - - -
228B GLN* 1.3 81.6 - - - +
230B ASP* 1.3 56.4 + - - +
234B ARG* 4.3 6.0 + - - +
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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