Contacts of the helix formed by residues 230 - 244 (chain A) in PDB entry 4XZC
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 PRO 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ASN* 4.8 7.0 - - - +
223A LYS 3.3 11.4 - - - +
224A THR* 3.8 7.2 - - + -
228A GLY 3.7 6.3 - - - +
229A ILE* 1.3 95.3 - - + +
231A LEU* 1.3 64.6 + - - +
232A ALA* 4.1 2.0 - - + +
233A VAL* 3.0 34.0 + - + +
234A THR* 3.2 11.4 + - - -
284A GLN* 4.0 21.5 - - + +
287A ASP* 5.9 1.6 - - - +
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Residues in contact with LEU 231 (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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198A HIS* 3.3 13.3 + - + +
218A TRP* 3.3 50.7 - - + -
223A LYS* 2.7 29.9 + - + +
224A THR 3.4 26.2 - - - +
225A GLY* 3.6 11.9 - - - +
229A ILE 3.4 1.2 + - - +
230A PRO* 1.3 71.4 - - - +
232A ALA* 1.3 57.0 + - - +
234A THR* 3.1 13.1 + - + +
235A SER* 2.9 32.2 + - - -
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP* 3.5 29.9 - - + -
218A TRP* 3.7 9.4 - - + -
221A ILE* 3.9 9.4 - - + +
223A LYS 4.5 0.8 + - - -
230A PRO* 4.1 1.1 - - + +
231A LEU* 1.3 79.8 - - - +
233A VAL* 1.3 57.6 + - - +
236A MET* 3.2 33.0 + - + +
284A GLN* 3.3 38.6 - - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 3.7 7.2 - - + -
230A PRO* 3.0 34.5 + - + +
232A ALA* 1.3 73.4 - - - +
234A THR* 1.3 60.1 + - - +
235A SER 3.1 1.1 - - - -
236A MET* 2.9 10.1 + - - +
237A VAL* 2.8 31.8 + - - +
284A GLN* 3.8 27.1 - - + +
287A ASP* 3.9 10.3 - - + +
288A ALA* 3.8 27.1 - - - +
291A LEU* 3.8 24.0 - - + -
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Residues in contact with THR 234 (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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198A HIS* 3.2 14.9 - - - -
226A ARG* 4.4 25.1 - - + +
229A ILE* 3.6 31.9 - - + +
230A PRO 3.2 3.1 + - - +
231A LEU* 3.1 20.4 + - + +
233A VAL* 1.3 75.4 - - - +
235A SER* 1.3 63.2 + - - +
237A VAL* 3.9 8.4 - - + +
238A LYS* 3.0 38.7 + - - +
291A LEU* 6.1 0.2 - - + -
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A HIS* 2.7 37.5 + - - -
199A VAL* 4.0 2.6 - - - +
201A TRP* 3.4 11.0 - - - -
202A GLY* 3.3 20.6 + - - -
218A TRP* 4.7 0.2 - - - -
231A LEU 2.9 20.3 + - - -
232A ALA 3.6 5.8 - - - -
234A THR* 1.3 77.8 + - - +
236A MET* 1.3 58.1 + - - +
238A LYS* 3.6 4.5 + - - +
239A VAL* 3.0 29.0 + - - +
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Residues in contact with MET 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP* 4.4 17.7 - - + -
202A GLY* 5.2 2.5 - - - -
205A LEU* 4.7 5.4 - - + -
232A ALA 3.2 23.3 + - - +
233A VAL* 2.9 7.2 + - - +
235A SER* 1.3 76.7 - - - +
237A VAL* 1.3 65.8 + - - +
239A VAL* 3.2 8.0 + - - +
240A ALA* 3.0 21.5 + - - +
248A LEU* 3.7 10.3 - - + +
251A ILE* 3.6 33.7 - - + -
255A LEU* 6.2 0.4 - - - -
281A LEU* 4.9 4.0 - - + +
284A GLN* 3.9 35.7 - - + +
285A LEU* 3.6 30.1 - - - +
288A ALA* 3.7 10.5 - - + -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 4.9 7.0 - - + -
233A VAL 2.8 27.4 + - - +
234A THR* 3.9 7.9 - - + +
236A MET* 1.3 71.4 - - - +
238A LYS* 1.3 56.6 + - + +
240A ALA* 2.9 23.4 + - - +
241A GLU* 2.9 37.8 + - + +
248A LEU* 5.3 0.2 - - - -
288A ALA* 3.9 14.1 - - - +
291A LEU* 3.7 33.7 - - + +
292A ALA* 3.9 24.7 - - - +
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Residues in contact with LYS 238 (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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198A HIS* 4.9 8.0 + - - +
199A VAL* 3.6 29.6 - - + -
226A ARG* 4.6 16.0 - - - +
234A THR* 3.0 34.1 + - - +
235A SER 3.6 0.9 - - - +
237A VAL* 1.3 77.0 - - + +
239A VAL* 1.3 61.3 + - - +
241A GLU* 3.5 24.4 + - + +
242A LEU* 3.3 33.7 + - + +
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Residues in contact with VAL 239 (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 VAL* 3.6 16.8 - - + +
202A GLY* 3.6 10.8 - - - +
203A ARG* 3.6 34.1 - - + +
206A ALA* 4.9 2.9 - - + -
235A SER 3.0 17.4 + - - +
236A MET* 3.2 9.8 + - - +
238A LYS* 1.3 73.5 - - - +
240A ALA* 1.3 60.4 + - - +
242A LEU* 4.9 2.0 - - - -
243A ASP* 2.9 41.1 + - - +
244A GLY 4.1 0.3 - - - +
247A ARG* 4.2 23.1 - - + -
248A LEU* 6.1 0.4 - - + +
251A ILE* 5.4 4.5 - - + -
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Residues in contact with ALA 240 (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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236A MET 3.0 11.3 + - - +
237A VAL 2.9 11.0 + - - +
239A VAL* 1.3 78.1 - - - +
241A GLU* 1.3 57.3 + - - +
244A GLY* 3.0 42.1 + - - +
245A HIS* 3.8 6.5 + - - +
247A ARG* 5.3 1.1 - - - -
248A LEU* 3.8 19.2 - - + +
292A ALA* 3.8 25.6 - - + -
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Residues in contact with GLU 241 (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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120A PRO* 4.5 5.0 - - - +
237A VAL* 2.9 39.7 + - + +
238A LYS* 3.7 27.8 - - - +
240A ALA* 1.3 77.4 - - + +
242A LEU* 1.3 69.8 + - + +
244A GLY* 4.6 0.4 - - - -
292A ALA* 5.6 1.3 - - - -
295A SER* 3.5 25.9 + - - -
299A ARG* 5.8 1.6 + - - -
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Residues in contact with LEU 242 (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 VAL* 5.2 15.7 - - + -
238A LYS* 3.3 23.1 + - + +
239A VAL* 4.3 2.0 - - - +
240A ALA 3.1 0.6 - - - -
241A GLU* 1.3 95.0 - - + +
243A ASP* 1.3 71.3 + - - +
244A GLY 3.2 4.8 + - - -
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Residues in contact with ASP 243 (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 ARG* 4.6 11.8 - - - +
239A VAL* 2.9 23.6 + - - +
242A LEU* 1.3 89.2 - - - +
244A GLY* 1.3 62.4 + - - +
247A ARG* 3.9 35.8 + - + +
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Residues in contact with GLY 244 (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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240A ALA* 3.0 24.1 + - - +
241A GLU 5.3 0.2 - - - -
242A LEU 3.2 3.8 + - - -
243A ASP* 1.3 84.2 - - - +
245A HIS* 1.3 67.0 + - - +
246A LYS 3.4 2.6 + - - -
247A ARG* 3.5 12.0 - - - +
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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