Contacts of the helix formed by residues 228 - 246 (chain A) in PDB entry 5J3V
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 GLU 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 3.9 31.5 - - + +
226A ASP* 3.3 4.1 + - - +
227A GLU* 1.3 78.4 - - - +
229A PRO* 1.3 76.0 - - - +
230A GLU* 3.4 36.1 + - + +
231A VAL* 3.0 35.5 + - + +
232A ARG* 3.5 7.7 + - - +
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Residues in contact with PRO 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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227A GLU 3.2 7.6 - - - +
228A GLU* 1.3 99.7 - - - +
230A GLU* 1.3 59.0 + - + +
232A ARG* 3.5 28.2 + - - +
233A LYS* 2.9 30.6 + - - +
269A ASP* 3.5 31.4 - - + +
272A VAL* 3.3 5.6 - - + +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 4.4 13.1 - - - +
228A GLU* 3.1 24.0 - - + +
229A PRO* 1.3 81.3 - - + +
231A VAL* 1.3 60.2 + - - +
233A LYS* 3.5 36.0 + - - +
234A ASN* 2.9 37.8 + - - +
269A ASP* 5.8 0.3 - - - +
271A ASN* 4.8 4.2 + - - -
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 3.9 22.0 - - + +
191A ARG* 4.6 5.2 - - + -
192A SER* 4.3 11.2 - - - +
195A VAL* 5.3 4.7 - - + +
223A LEU* 3.8 28.7 - - + +
226A ASP* 3.6 35.7 - - + +
228A GLU* 3.0 22.3 + - + +
230A GLU* 1.3 77.1 - - - +
232A ARG* 1.3 62.2 + - - +
233A LYS 3.1 1.3 - - - -
234A ASN* 3.1 7.1 + - - +
235A VAL* 2.9 33.6 + - + +
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Residues in contact with ARG 232 (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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223A LEU 4.7 0.7 - - - +
224A ALA 3.9 14.8 - - - +
225A GLY* 5.0 1.1 - - - -
226A ASP* 3.2 28.1 + - + +
227A GLU* 2.6 30.7 + - - +
228A GLU 3.5 2.2 + - - +
229A PRO* 3.5 26.9 + - - +
231A VAL* 1.3 75.7 - - - +
233A LYS* 1.3 57.1 + - - +
235A VAL* 3.8 8.0 - - - +
236A CYS* 2.9 37.2 + - - -
260A TYR* 4.5 6.3 - - - +
264A ARG* 3.9 20.8 - - - +
267A ASP* 2.8 41.5 + - - -
268A GLN* 5.0 4.8 - - - +
269A ASP* 4.6 2.6 - - - +
272A VAL* 4.2 10.5 - - + +
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO 2.9 18.6 + - - +
230A GLU* 3.5 38.5 + - - +
232A ARG* 1.3 78.0 - - - +
234A ASN* 1.3 63.0 + - - +
236A CYS* 3.8 3.1 - - - +
237A ARG* 3.2 51.4 + - - +
271A ASN* 3.7 35.1 - - + +
272A VAL* 4.1 17.9 - - + +
275A GLU* 4.2 11.2 - - + +
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Residues in contact with ASN 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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153A GLN* 5.9 0.2 - - - +
192A SER* 3.2 30.5 + - - +
195A VAL* 3.6 20.0 - - + -
196A ALA* 4.2 15.1 - - - +
199A ASN* 3.0 14.5 + - - +
230A GLU* 2.9 24.7 + - - +
231A VAL 3.1 6.7 + - - +
233A LYS* 1.3 81.0 - - - +
235A VAL* 1.3 60.6 + - - +
237A ARG* 2.9 24.4 + - - +
238A ALA* 2.9 25.1 + - - +
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Residues in contact with VAL 235 (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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195A VAL* 4.7 5.6 - - + -
220A LEU* 3.7 39.0 - - + +
223A LEU* 3.8 34.8 - - + +
224A ALA* 4.1 12.8 - - + -
231A VAL* 2.9 22.2 + - + +
232A ARG* 3.8 7.2 - - - +
234A ASN* 1.3 76.7 - - - +
236A CYS* 1.3 63.6 + - - +
238A ALA* 3.3 2.9 + - - +
239A LEU* 3.1 36.5 + - + +
260A TYR* 4.1 6.7 - - - +
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Residues in contact with CYS 236 (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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232A ARG 2.9 25.3 + - - +
233A LYS* 3.8 4.9 - - - +
235A VAL* 1.3 77.7 - - - +
237A ARG* 1.3 62.3 + - - +
239A LEU* 3.3 1.6 + - - -
240A VAL* 3.1 29.1 + - - +
260A TYR* 4.2 9.9 - - - -
261A MET* 3.6 18.8 - - + +
264A ARG* 4.0 33.7 - - - -
272A VAL* 4.3 7.0 - - - +
275A GLU* 4.4 3.6 - - + -
276A ALA* 4.1 23.1 - - - +
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Residues in contact with ARG 237 (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 ASN* 4.1 10.8 - - - +
233A LYS* 3.2 40.0 + - - +
234A ASN* 2.9 33.3 + - - +
235A VAL 3.3 0.2 - - - -
236A CYS* 1.3 78.6 - - - +
238A ALA* 1.3 62.9 + - - +
240A VAL* 3.4 6.5 + - + +
241A MET* 3.1 50.9 + - + +
275A GLU* 3.1 46.6 + - - +
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Residues in contact with ALA 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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195A VAL* 4.9 0.2 - - + -
199A ASN* 3.3 26.9 - - - +
202A ILE* 4.1 6.9 - - + +
216A PHE* 4.0 6.5 - - + -
220A LEU* 3.7 24.2 - - + -
234A ASN 2.9 14.3 + - - +
235A VAL 3.5 5.6 - - - +
237A ARG* 1.3 77.9 - - - +
239A LEU* 1.3 56.6 + - - +
241A MET* 3.3 3.5 + - - +
242A LEU* 2.9 34.8 + - - +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 5.4 1.3 - - + -
220A LEU* 3.9 21.5 - - + -
221A PHE* 4.3 23.6 - - + -
224A ALA* 6.1 1.1 - - + -
235A VAL* 3.1 21.0 + - + +
236A CYS 3.3 0.2 + - - -
238A ALA* 1.3 73.2 - - - +
240A VAL* 1.3 65.8 + - - +
242A LEU* 3.4 10.6 + - + +
243A LEU* 3.1 21.7 + - - +
250A LEU* 4.2 10.8 - - + +
257A ILE* 4.5 23.1 - - + -
260A TYR* 4.3 20.0 - - + -
261A MET* 3.6 30.5 - - + -
279A PHE* 4.1 9.0 - - + -
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Residues in contact with VAL 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 CYS 3.1 16.2 + - - +
237A ARG* 3.6 9.9 - - + +
239A LEU* 1.3 77.5 - - - +
241A MET* 1.3 64.1 + - + +
243A LEU* 3.2 17.5 - - - +
244A GLU* 4.0 2.6 + - - +
261A MET* 4.5 0.7 - - + -
275A GLU* 3.7 22.0 - - - +
278A GLU* 3.9 17.7 - - + +
279A PHE* 3.7 30.5 - - + -
282A THR* 3.3 32.0 - - - +
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Residues in contact with MET 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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199A ASN* 3.5 29.4 - - + +
202A ILE* 3.6 19.3 - - + -
203A ILE* 3.6 37.7 - - + +
237A ARG* 3.1 44.6 + - + +
238A ALA 3.7 2.9 - - - +
240A VAL* 1.3 73.2 - - + +
242A LEU* 1.3 61.3 + - - +
243A LEU 3.1 6.3 + - - -
244A GLU* 3.3 10.4 + - - +
245A VAL* 3.3 17.2 + - - +
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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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202A ILE* 3.6 21.5 - - + -
209A LEU* 5.4 0.7 - - + -
210A MET* 5.8 0.4 - - + -
213A ILE* 3.7 25.1 - - + -
216A PHE* 3.6 27.4 - - + -
217A ILE* 3.8 26.5 - - + -
220A LEU* 3.8 10.8 - - + -
238A ALA 2.9 19.8 + - - +
239A LEU* 3.9 11.2 - - + +
240A VAL 3.3 0.2 - - - -
241A MET* 1.3 73.4 - - - +
243A LEU* 1.3 64.1 + - - +
244A GLU 3.1 1.3 - - - -
245A VAL* 3.9 9.4 - - + -
246A ARG* 3.2 34.3 + - + +
250A LEU* 3.5 13.3 - - + +
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Residues in contact with LEU 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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239A LEU 3.1 8.8 + - - +
240A VAL 3.2 13.5 - - - +
241A MET 3.1 0.8 - - - -
242A LEU* 1.3 77.8 - - - +
244A GLU* 1.3 58.2 + - - +
247A MET* 3.2 52.1 - - + +
250A LEU* 3.9 15.5 - - + -
254A MET* 4.5 12.1 - - + -
257A ILE* 6.4 0.2 - - + -
279A PHE* 3.7 38.6 - - + +
282A THR* 3.7 10.3 - - + -
283A LEU* 3.7 40.4 - - + +
286A GLN* 3.5 7.1 + - + -
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Residues in contact with GLU 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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203A ILE* 4.4 16.9 - - + +
205A ARG* 4.1 7.8 + - - +
240A VAL* 4.4 3.7 - - - +
241A MET* 3.3 6.2 + - - +
242A LEU 3.1 0.2 - - - -
243A LEU* 1.3 80.2 - - - +
245A VAL* 1.3 69.7 + - + +
246A ARG 3.4 0.6 + - - -
247A MET* 4.2 7.0 + - - +
282A THR* 3.6 34.4 + - + +
285A GLU* 5.7 1.0 - - - +
286A GLN* 3.9 16.7 + - - +
85B ASN* 5.2 9.4 + - - +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.6 37.7 - - + +
203A ILE* 3.7 25.1 - - + +
205A ARG* 2.8 53.0 + - - +
210A MET* 4.2 4.0 - - + -
241A MET 3.3 15.0 - - - +
242A LEU* 3.9 6.7 - - + -
244A GLU* 1.3 82.3 - - + +
246A ARG* 1.3 70.9 + - + +
247A MET 4.1 0.2 + - - -
81B GLN 3.2 13.0 - - - +
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Residues in contact with ARG 246 (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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210A MET* 3.1 64.3 + - + +
211A LEU* 6.1 0.2 - - - +
213A ILE* 3.7 37.7 - - + +
217A ILE* 5.4 1.0 - - + +
242A LEU* 3.2 18.8 + - + +
245A VAL* 1.3 95.0 - - + +
247A MET* 1.3 64.2 + - - +
248A ASP* 3.2 11.3 + - - +
249A ARG* 3.3 36.3 + - + +
250A LEU* 4.0 6.4 - - - +
81B GLN* 3.4 48.8 - - - +
82B ASN* 4.3 4.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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