Contacts of the helix formed by residues 220 - 230 (chain A) in PDB entry 3NX4
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ASP* 2.8 24.7 + - - -
218A THR 3.9 0.2 - - - -
219A VAL* 1.3 78.6 - - - +
221A ASP* 1.3 75.2 + - - +
223A VAL 3.4 4.7 + - - -
224A LEU* 3.2 24.6 + - - -
241A GLY 4.0 9.3 + - - -
245A GLY 3.9 4.0 - - - -
252B VAL* 4.2 4.3 - - - -
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Residues in contact with ASP 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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219A VAL* 5.4 0.7 - - + -
220A GLY* 1.3 73.8 - - - +
222A LYS* 1.3 84.9 + - - +
223A VAL* 4.6 0.4 - - + +
224A LEU* 3.7 2.5 - - - +
225A ALA* 3.0 25.5 + - - +
244A GLY* 3.6 28.0 - - - +
245A GLY* 3.4 10.4 + - - +
247A ALA* 3.1 40.7 + - - +
248A LEU* 4.0 1.8 - - - +
249A PRO* 3.8 15.8 - - - +
252B VAL* 4.7 1.0 - - - +
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Residues in contact with LYS 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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201A PHE 3.9 12.4 - - - +
202A ALA* 3.3 26.5 - - - +
203A GLU* 6.4 0.2 - - - -
204A SER* 5.3 0.5 + - - -
221A ASP* 1.3 95.6 + - - +
223A VAL* 1.3 66.9 + - + +
225A ALA* 3.2 7.6 + - + +
226A LYS* 2.9 25.1 + - - +
249A PRO* 4.4 17.3 - - + +
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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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153A THR* 3.7 33.9 - - + -
177A VAL* 5.3 4.5 - - + -
198A ARG* 4.2 20.9 - - + -
201A PHE* 3.9 36.5 - - + +
217A ASP* 4.2 2.7 - - - +
219A VAL* 3.9 20.4 - - + -
220A GLY 3.4 7.3 + - - +
221A ASP* 3.3 1.0 - - + +
222A LYS* 1.3 77.4 - - + +
224A LEU* 1.3 58.6 + - - +
226A LYS* 3.2 2.1 + - - +
227A VAL* 2.9 27.9 + - - +
330A NAP 4.9 1.6 - - + -
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Residues in contact with LEU 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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217A ASP* 3.5 37.0 + - + +
220A GLY* 3.2 14.6 + - - -
221A ASP 3.7 1.1 - - - +
223A VAL* 1.3 77.6 - - - +
225A ALA* 1.3 59.3 + - - +
227A VAL* 3.3 6.7 + - + +
228A LEU* 2.9 40.0 + - + +
237A VAL* 3.9 24.2 - - + -
239A ALA* 4.5 11.2 - - + -
248A LEU* 3.8 23.3 - - + -
262A LEU* 4.6 5.6 - - + -
252B VAL* 3.7 28.9 - - + -
255B PHE* 6.4 0.2 - - + -
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Residues in contact with ALA 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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204A SER* 4.5 7.5 + - - +
221A ASP 3.0 15.2 + - - +
222A LYS* 3.2 13.0 + - + +
224A LEU* 1.3 78.2 - - - +
226A LYS* 1.3 61.6 + - - +
228A LEU* 3.4 9.1 + - - +
229A ALA* 3.2 19.8 + - - +
248A LEU* 4.2 7.4 - - + +
249A PRO* 3.4 30.3 - - + +
250A THR* 4.4 8.5 + - - -
254A PRO* 5.8 0.2 - - - +
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Residues in contact with LYS 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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200A GLU* 2.8 30.7 + - - +
201A PHE* 3.9 17.3 - - + +
202A ALA 4.9 0.4 - - - +
203A GLU 3.2 28.6 + - - +
204A SER* 3.5 18.1 + - - -
208A GLU* 4.0 19.3 + - + -
222A LYS 2.9 16.0 + - - +
223A VAL 3.9 3.1 - - - +
225A ALA* 1.3 74.4 - - - +
227A VAL* 1.3 66.8 + - - +
229A ALA* 3.0 11.8 + - - +
230A GLN* 3.1 38.7 + - + +
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Residues in contact with VAL 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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151A VAL* 4.1 11.7 - - + -
153A THR* 3.9 24.5 - - + -
201A PHE* 3.8 21.1 - - + -
212A TRP* 4.4 0.9 - - + -
215A ALA* 3.7 30.3 - - + -
217A ASP* 5.7 1.8 - - + +
223A VAL 2.9 21.0 + - - +
224A LEU* 3.7 8.1 - - + +
226A LYS* 1.3 76.5 - - - +
228A LEU* 1.3 63.0 + - - +
230A GLN* 3.0 19.8 + - - +
231A MSE 3.2 21.0 + - - +
237A VAL* 4.3 9.4 - - + -
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Residues in contact with LEU 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 LEU* 2.9 35.9 + - + +
225A ALA* 3.5 6.7 - - - +
227A VAL* 1.3 77.4 - - - +
229A ALA* 1.3 61.3 + - - +
230A GLN 3.1 1.1 + - - -
231A MSE 3.4 16.7 + - - +
237A VAL* 3.8 25.4 - - + -
248A LEU* 4.3 6.3 - - + -
250A THR* 3.9 26.0 - - + +
254A PRO* 3.4 27.4 - - + +
255A PHE* 3.9 28.5 - - + -
258A ARG* 5.3 0.7 + - - -
260A VAL* 4.1 13.0 - - + +
262A LEU* 4.5 13.5 - - + -
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Residues in contact with ALA 229 (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 SER* 4.7 1.1 - - - +
205A ARG 3.4 25.6 - - - +
206A PRO 3.5 16.6 - - - +
207A LEU* 3.8 0.6 - - - -
208A GLU* 2.8 37.0 + - + +
225A ALA 3.2 12.7 + - - +
226A LYS* 3.0 13.2 + - - +
228A LEU* 1.3 75.4 - - - +
230A GLN* 1.3 57.5 + - - +
231A MSE 3.5 0.4 - - - -
254A PRO* 4.2 3.3 - - + +
258A ARG* 3.0 14.6 + - - -
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Residues in contact with GLN 230 (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 GLU 5.0 0.6 + - - -
201A PHE* 3.3 24.5 - - - -
208A GLU* 3.9 18.9 - - + +
209A LYS 3.5 10.8 - - - +
210A GLN* 4.2 0.4 - - - -
211A LEU* 2.7 52.0 + - + +
212A TRP* 2.9 32.6 + - - +
226A LYS* 3.1 43.3 + - - +
227A VAL* 3.0 6.5 + - - +
229A ALA* 1.3 77.6 - - - +
231A MSE 1.3 57.3 + - - +
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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