Contacts of the helix formed by residues 219 - 228 (chain A) in PDB entry 1ZSV
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 GLY 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASP* 2.9 21.2 + - - -
217A ASN 3.9 0.2 - - - -
218A VAL* 1.3 87.1 - - - +
220A GLY* 1.3 66.6 + - - +
221A GLU 3.7 0.3 + - - -
222A PHE* 3.6 3.8 - - - +
223A SER* 3.2 22.9 + - - -
240A GLY 4.7 0.4 - - - -
241A ALA* 3.9 12.7 - - - +
243A SER* 3.6 2.8 + - - -
257B PRO* 6.3 0.4 - - - -
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Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL 3.9 0.2 + - - -
219A GLY* 1.3 72.3 - - - -
221A GLU* 1.3 58.9 + - - -
223A SER* 3.2 5.4 + - - -
224A ASN* 3.2 30.8 + - - +
241A ALA* 5.5 0.2 - - - +
243A SER* 3.9 9.0 + - - -
244A THR* 4.4 9.4 - - - +
252A PRO* 3.9 21.3 - - - -
253A PRO 5.2 1.1 - - - -
257B PRO* 6.2 0.4 - - - +
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 5.4 0.2 - - - -
219A GLY 3.7 0.2 + - - -
220A GLY* 1.3 70.5 - - - -
222A PHE* 1.3 65.1 + - - +
224A ASN* 3.3 24.4 + - + +
225A THR* 3.0 27.0 + - - -
252A PRO* 3.9 25.3 - - + +
253A PRO* 3.7 22.1 - - - +
250D PRO* 5.8 3.8 - - - +
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MET* 3.7 9.6 - - + -
148A ASN* 3.6 23.3 - - + -
172A ALA* 3.6 25.4 - - + -
193A TYR* 3.9 31.4 - + + -
199A LEU* 3.6 38.3 - - + +
214A TYR* 3.6 10.5 - - - -
218A VAL* 3.8 13.2 - - + -
219A GLY 3.6 10.1 - - - +
221A GLU* 1.3 76.4 - - - +
223A SER* 1.3 59.8 + - - +
225A THR* 3.2 4.9 + - - -
226A VAL* 3.1 38.3 + - + +
407A CL 4.3 3.8 - - + -
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TYR* 2.7 25.5 + - - -
216A ASP* 2.7 32.5 + - - -
219A GLY* 3.2 12.6 + - - -
220A GLY 3.2 10.5 + - - -
222A PHE* 1.3 73.6 - - - +
224A ASN* 1.3 62.8 + - - +
225A THR 3.1 1.8 - - - -
226A VAL* 3.9 0.9 - - - +
227A ILE* 3.0 40.5 + - - +
255A PRO* 6.3 0.7 - - - -
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Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLY 3.2 11.6 + - - +
221A GLU* 3.3 30.8 + - + +
223A SER* 1.3 77.2 - - - +
225A THR* 1.3 63.0 + - - +
227A ILE* 3.7 5.2 + - - +
228A GLY* 3.5 13.2 + - - -
253A PRO* 3.0 27.4 + - - +
254A GLY 3.3 12.4 + - - -
255A PRO* 3.0 28.2 - - - +
256A PRO* 4.2 21.6 - - + +
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Residues in contact with THR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 3.8 18.0 - - + +
200A GLU* 3.8 42.0 - - + +
203A LEU* 4.1 6.1 - - + -
221A GLU 3.0 14.5 + - - -
222A PHE 3.5 7.9 - - - -
223A SER 3.1 0.6 - - - -
224A ASN* 1.3 75.2 - - - +
226A VAL* 1.3 66.3 + - - +
228A GLY* 3.1 14.4 + - - -
229A GLN* 3.7 10.0 + - - +
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MET* 4.1 13.9 - - + -
203A LEU* 3.8 20.6 - - + -
211A TYR* 5.1 7.2 - - + -
214A TYR* 3.7 41.1 - - + -
222A PHE* 3.1 39.1 + - + +
223A SER 3.9 5.2 - - - +
225A THR* 1.3 77.1 - - - +
227A ILE* 1.3 56.6 + - - +
229A GLN* 2.8 22.9 + - - +
230A MET* 3.2 18.9 + - - +
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TYR* 5.2 2.2 - - + -
223A SER* 3.0 30.6 + - - +
224A ASN 3.9 3.8 - - - +
226A VAL* 1.3 75.9 - - - +
228A GLY* 1.3 60.3 + - - +
229A GLN 3.4 0.7 + - - -
230A MET* 3.5 21.2 + - - +
236A ILE* 3.6 26.0 - - + -
255A PRO* 3.7 21.8 - - + -
256A PRO* 4.2 15.5 - - + -
259A ILE* 3.6 15.0 - - + +
260A VAL* 3.7 23.8 - - + -
263A GLN* 5.2 0.7 - - - +
265A LEU* 4.0 6.5 - - + +
267A MET* 3.4 24.2 - - + -
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASN 3.5 6.6 + - - -
225A THR 3.1 8.6 + - - -
226A VAL 3.1 1.6 - - - -
227A ILE* 1.3 77.6 - - - +
229A GLN* 1.3 63.8 + - - +
230A MET 3.7 1.5 - - - +
259A ILE* 4.0 25.9 - - - +
263A GLN* 6.4 0.2 - - - -
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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