Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 4Z30
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 ARG 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LEU 3.6 1.4 + - - -
215A SER* 1.3 71.8 - - - +
217A LYS* 1.3 64.7 + - - +
219A LEU* 3.0 3.6 + - - +
220A VAL* 2.9 34.4 + - + +
240A GLY* 4.9 5.0 + - - -
243A VAL* 4.3 14.2 - - + +
244A GLN* 2.7 44.0 + - - +
247A TYR* 3.5 33.5 - - - +
262A SER 4.2 5.0 + - - +
264A MET* 3.7 36.2 - - + +
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Residues in contact with LYS 217 (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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215A SER* 3.2 8.0 + - - +
216A ARG* 1.3 79.3 - - - +
218A VAL* 1.3 66.1 + - + +
220A VAL* 3.4 8.1 + - - +
221A LEU* 3.1 27.8 + - + +
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Residues in contact with VAL 218 (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 LEU* 4.0 25.1 - - + -
215A SER* 3.0 34.6 + - - +
217A LYS* 1.3 78.1 - - + +
219A LEU* 1.3 63.5 + - - +
221A LEU* 3.4 6.5 + - - +
222A PHE* 3.1 23.2 + - + +
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Residues in contact with LEU 219 (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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204A VAL* 4.6 10.3 - - + -
207A ALA* 3.9 28.0 - - + -
208A LEU* 4.0 24.2 - - + -
214A LEU* 4.0 17.7 - - + +
215A SER 2.8 12.9 + - - +
216A ARG* 3.5 8.3 - - - +
218A VAL* 1.3 73.6 - - - +
220A VAL* 1.3 65.6 + - + +
222A PHE* 3.3 5.7 + - + +
223A VAL* 3.2 30.6 + - + +
243A VAL* 4.4 19.1 - - + -
252A PHE* 4.5 7.4 - - + -
264A MET* 3.5 25.1 - - + -
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Residues in contact with VAL 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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216A ARG* 2.9 25.7 + - + +
217A LYS* 3.7 9.6 - - - +
219A LEU* 1.3 75.6 - - - +
221A LEU* 1.3 66.4 + - - +
223A VAL* 3.2 3.6 + - - +
224A VAL* 3.0 22.7 + - + +
236A LYS* 3.6 41.3 - - + +
239A ILE* 4.0 15.0 - - + -
240A GLY* 4.1 22.2 - - - +
243A VAL* 4.3 14.6 - - + -
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Residues in contact with LEU 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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217A LYS* 3.1 19.7 + - + +
218A VAL* 3.8 6.7 - - - +
219A LEU 3.3 0.2 - - - -
220A VAL* 1.3 79.7 - - - +
222A PHE* 1.3 64.7 + - - +
224A VAL* 3.1 7.7 + - + +
225A GLN* 2.8 61.9 + - + +
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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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203A LEU* 3.7 22.7 - - + -
206A LEU* 4.3 15.5 - - + -
207A ALA* 3.7 33.9 - - + -
214A LEU* 5.3 5.6 - - + -
218A VAL* 3.1 12.8 + - + +
219A LEU* 3.4 12.6 - - + +
220A VAL 3.2 0.2 - - - -
221A LEU* 1.3 80.3 - - - +
223A VAL* 1.3 69.9 + - + +
225A GLN* 4.3 2.7 + - - -
226A ARG* 2.9 79.4 + - - +
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Residues in contact with VAL 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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200A ALA* 4.5 9.6 - - + +
203A LEU* 3.6 29.6 - - + +
204A VAL* 4.0 28.0 - - + +
219A LEU* 3.5 15.3 - - + +
220A VAL 3.2 6.9 + - - +
221A LEU 3.2 0.4 - - - -
222A PHE* 1.3 81.2 - - + +
224A VAL* 1.3 59.1 + - - +
226A ARG* 3.0 4.5 + - - -
227A LEU* 2.9 45.2 + - + +
239A ILE* 3.9 23.6 - - + -
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Residues in contact with VAL 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 VAL* 3.0 27.8 + - + +
221A LEU* 3.8 7.2 - - + +
223A VAL* 1.3 76.3 - - - +
225A GLN* 1.3 65.4 + - + +
227A LEU* 3.8 7.1 - - - +
228A GLU* 3.1 22.7 + - + +
234A ALA* 4.1 20.7 - - + +
235A SER 4.0 11.9 - - - +
236A LYS* 4.2 6.1 - - + +
239A ILE* 3.4 31.0 - - + -
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Residues in contact with GLN 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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221A LEU* 2.8 50.2 + - + +
222A PHE* 3.8 5.2 - - - +
224A VAL* 1.3 81.4 - - + +
226A ARG* 1.3 81.5 + - + +
228A GLU* 3.5 17.1 - - - +
229A PRO* 3.7 4.5 - - - +
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Residues in contact with ARG 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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203A LEU* 3.8 25.5 - - + +
206A LEU* 5.0 5.3 - - - +
222A PHE* 2.9 76.4 + - - +
223A VAL 3.0 5.6 + - - +
225A GLN* 1.3 100.1 + - + +
227A LEU* 1.3 60.9 + - - +
228A GLU 3.4 0.4 - - - -
229A PRO* 3.9 11.1 - - - +
230A ARG* 5.3 1.9 + - - +
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Residues in contact with LEU 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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196A MET* 4.1 12.8 - - + +
199A GLU* 3.6 33.2 - - + -
200A ALA* 4.3 8.1 - - + +
203A LEU* 3.8 12.3 - - + -
223A VAL* 2.9 21.6 + - + +
224A VAL* 3.3 6.0 + - - +
226A ARG* 1.3 77.3 - - - +
228A GLU* 1.3 64.0 + - - +
229A PRO 3.4 1.7 - - - -
230A ARG* 3.5 4.0 + - + +
231A PHE* 2.9 47.7 + - + +
234A ALA* 4.0 13.9 - - + -
239A ILE* 3.8 29.8 - - + -
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Residues in contact with GLU 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 VAL* 3.1 11.8 + - + +
225A GLN* 3.5 12.6 - - - +
227A LEU* 1.3 76.9 - - - +
229A PRO* 1.3 74.3 - - + +
231A PHE 3.2 12.5 + - - -
232A PRO* 3.4 22.2 - - + +
234A ALA* 6.0 0.7 - - - -
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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