Contacts of the helix formed by residues 247 - 270 (chain A) in PDB entry 4JVA
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 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY* 2.9 26.3 + - - -
187A ASP* 3.1 18.0 + - - +
223A ALA 3.8 4.9 + - - -
224A LEU* 3.8 38.0 + - + +
227A ASN* 2.9 26.3 + - - +
246A ASP* 1.3 74.3 - - - +
248A VAL* 1.3 71.1 + - + +
249A THR 3.3 0.2 - - - -
250A PHE* 4.0 0.4 - - - -
251A ARG* 2.8 56.3 + - + +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 5.8 4.5 - - + -
246A ASP* 3.1 9.3 + - + +
247A ARG* 1.3 85.8 - - + +
249A THR* 1.3 59.8 + - - +
251A ARG* 3.9 3.7 - - - +
252A ARG* 2.9 40.3 + - + +
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Residues in contact with THR 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 4.1 10.4 + - - +
163A GLN 4.6 4.9 - - - +
164A VAL* 4.6 4.3 - - + -
167A ALA* 3.7 15.1 - - + +
245A LEU* 3.5 22.9 - - + -
246A ASP* 2.6 40.7 + - - -
248A VAL* 1.3 72.6 - - - +
250A PHE* 1.3 59.4 + - - -
252A ARG* 3.5 25.6 + - - +
253A ILE* 2.9 40.9 + - + +
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.9 10.1 - - + -
189A PHE* 3.8 36.1 - + + -
221A GLU* 3.9 14.4 - - + -
224A LEU* 3.6 26.7 - - + -
225A MET* 3.5 32.1 - - + -
245A LEU* 4.0 10.9 - - + +
246A ASP 3.2 17.3 + - - +
247A ARG* 3.7 7.2 - - - +
248A VAL 3.3 0.2 - - - -
249A THR* 1.3 80.1 - - - +
251A ARG* 1.3 62.2 + - - +
254A ILE* 2.8 76.7 + - + +
255A VAL* 3.2 7.6 + - + -
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 2.7 41.2 + - + +
225A MET 3.6 14.5 + - - -
227A ASN* 4.0 20.9 + - - +
247A ARG* 2.8 48.9 + - - +
248A VAL* 4.2 3.8 - - - +
250A PHE* 1.3 71.9 - - + +
252A ARG* 1.3 65.8 + - - +
253A ILE 3.5 0.2 + - - -
255A VAL* 3.3 45.8 - - + +
256A LYS* 3.7 3.8 + - - +
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 2.6 52.5 - - - +
131A ILE 5.3 1.0 - - - +
163A GLN* 2.6 30.3 + - - +
248A VAL* 2.9 28.2 + - + +
249A THR* 3.2 21.1 + - - +
251A ARG* 1.3 78.3 - - - +
253A ILE* 1.3 74.6 + - + +
256A LYS* 3.3 22.0 - - - +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.5 26.2 - - + -
160A GLN* 3.7 26.9 - - + +
163A GLN* 3.5 42.4 - - + +
164A VAL* 4.1 18.2 - - + +
249A THR* 2.9 18.2 + - + +
252A ARG* 1.3 100.4 - - - +
254A ILE* 1.3 61.0 + - + +
255A VAL 3.4 0.9 - - - -
256A LYS* 3.5 5.4 + - + +
257A ASN* 2.8 26.3 + - - +
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Residues in contact with ILE 254 (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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152A LEU* 3.9 31.2 - - + +
153A PHE* 3.7 33.0 - - + -
156A LEU* 4.2 15.5 - - + -
164A VAL* 4.5 5.8 - - + -
245A LEU* 4.6 2.7 - - + -
250A PHE* 2.8 64.1 + - + +
253A ILE* 1.3 76.0 - - + +
255A VAL* 1.3 59.8 + - - +
257A ASN* 3.1 8.4 - - + +
258A ASN* 2.9 31.6 + - - +
261A LYS* 5.9 0.2 - - - +
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Residues in contact with VAL 255 (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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225A MET* 4.5 10.3 - - + +
250A PHE* 3.2 17.8 + - + +
251A ARG* 3.3 59.9 + - + +
254A ILE* 1.3 73.4 - - - +
256A LYS* 1.3 67.3 + - - +
258A ASN* 3.2 24.1 + - + +
259A ALA* 3.3 8.7 + - - +
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Residues in contact with LYS 256 (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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157A ASP* 5.5 1.6 + - - -
160A GLN* 4.2 24.5 + - - +
251A ARG 3.7 4.6 + - - +
252A ARG 3.3 23.1 - - - +
253A ILE* 3.5 5.1 + - + +
255A VAL* 1.3 76.1 - - - +
257A ASN* 1.3 58.5 + - - +
259A ALA* 2.8 36.9 + - + +
260A LYS* 3.5 7.4 + - - +
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Residues in contact with ASN 257 (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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152A LEU 3.9 13.7 - - - +
155A ASN* 3.6 19.1 + - - +
156A LEU* 3.8 22.9 - - + +
160A GLN* 4.5 5.1 + - - +
253A ILE 2.8 15.7 + - - +
254A ILE* 3.1 17.6 - - - +
256A LYS* 1.3 79.0 - - - +
258A ASN* 1.3 59.7 + - - +
260A LYS* 3.0 45.4 + - - +
261A LYS* 3.0 27.1 + - - +
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Residues in contact with ASN 258 (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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152A LEU* 4.4 2.9 - - - +
225A MET* 4.0 24.7 - - - +
254A ILE* 2.9 27.0 + - - +
255A VAL* 3.5 20.2 - - + +
256A LYS 3.1 0.4 - - - -
257A ASN* 1.3 75.6 - - - +
259A ALA* 1.3 57.8 + - - +
261A LYS* 3.0 33.1 + - - +
262A ARG* 2.8 38.0 + - + +
287A VAL 6.0 0.2 - - - -
288A ASP* 3.4 29.6 + - - +
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Residues in contact with ALA 259 (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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255A VAL 3.3 5.5 + - - +
256A LYS* 2.8 20.2 + - + +
258A ASN* 1.3 79.4 - - - +
260A LYS* 1.3 59.5 + - - +
262A ARG* 3.6 10.3 + - - +
263A LYS* 3.3 38.5 + - - +
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Residues in contact with LYS 260 (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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155A ASN* 2.9 28.3 + - + +
157A ASP* 4.8 3.2 + - - +
160A GLN* 3.8 15.9 - - - +
256A LYS* 3.5 7.3 + - - +
257A ASN* 3.0 24.7 + - - +
259A ALA* 1.3 78.1 - - - +
261A LYS* 1.3 64.5 + - - +
263A LYS* 3.3 15.4 + - + +
264A MET* 3.2 48.5 + - + +
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Residues in contact with LYS 261 (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 LEU 5.1 0.4 + - - -
152A LEU* 4.1 14.8 + - - +
155A ASN* 3.8 33.8 + - + +
257A ASN* 3.0 36.7 + - - +
258A ASN* 3.0 28.1 + - - +
260A LYS* 1.3 73.9 - - - +
262A ARG* 1.3 67.1 + - - +
264A MET* 3.3 9.3 + - + -
265A TYR* 2.8 34.4 + - + +
287A VAL* 3.4 25.3 - - + +
288A ASP 3.6 10.9 + - - -
290A ILE* 3.3 26.2 + - - -
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Residues in contact with ARG 262 (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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258A ASN* 2.8 28.6 + - - +
259A ALA* 3.7 8.5 - - - +
260A LYS 3.2 0.2 - - - -
261A LYS* 1.3 74.0 - - - +
263A LYS* 1.3 61.0 + - - +
266A GLU* 2.7 54.2 + - + +
284A LEU* 2.9 63.1 + - - +
287A VAL* 3.4 22.3 - - + +
288A ASP* 2.9 29.2 + - - +
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Residues in contact with LYS 263 (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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259A ALA* 3.3 28.9 + - - +
260A LYS* 3.3 14.4 + - + +
261A LYS 3.2 0.6 - - - -
262A ARG* 1.3 82.7 - - - +
264A MET* 1.3 65.5 + - + +
266A GLU* 3.5 6.2 + - - +
267A SER* 4.8 5.0 + - - -
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Residues in contact with MET 264 (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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155A ASN* 4.2 20.4 - - + +
260A LYS* 3.2 47.6 + - + +
261A LYS* 3.6 9.0 - - - +
263A LYS* 1.3 81.8 - - + +
265A TYR* 1.3 89.0 + - + +
267A SER* 5.5 0.9 + - - -
268A PHE* 5.0 4.3 + - - +
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Residues in contact with TYR 265 (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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155A ASN* 4.2 12.1 + - - -
261A LYS* 2.8 26.1 + - + +
264A MET* 1.3 106.2 - - + +
266A GLU* 1.3 58.7 + - - +
267A SER 3.4 2.2 - - - -
268A PHE* 4.0 10.1 - + + -
269A ILE* 2.9 48.1 + - + +
287A VAL* 4.4 1.1 - - + -
290A ILE* 4.4 13.5 - - + -
292A THR* 2.9 34.6 + - - +
315A GLU* 3.9 27.3 + - + -
370A LYS* 5.9 1.2 - - - +
372A LEU* 3.5 33.4 - - + +
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Residues in contact with GLU 266 (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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262A ARG* 2.7 41.9 + - + +
263A LYS* 3.5 4.3 + - - +
265A TYR* 1.3 70.1 - - - +
267A SER* 1.3 69.6 + - - +
269A ILE* 4.0 4.9 - - - +
270A GLU* 2.4 64.7 + - - +
283A ARG 4.8 2.9 - - - +
284A LEU* 3.7 21.1 - - - +
287A VAL* 3.9 24.3 - - - +
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Residues in contact with SER 267 (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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263A LYS 4.8 5.4 + - - -
264A MET 5.5 1.1 + - - -
266A GLU* 1.3 76.1 - - - +
268A PHE* 1.3 66.3 + - - +
270A GLU* 2.9 23.6 + - - +
271A SER* 3.2 13.4 + - - -
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Residues in contact with PHE 268 (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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264A MET 5.0 3.3 + - - +
265A TYR* 3.7 16.3 - + + +
267A SER* 1.3 79.8 - - - +
269A ILE* 1.3 61.1 + - + +
271A SER* 2.6 35.0 + - - -
272A LEU* 3.4 28.7 - - + +
313A ILE* 4.3 10.1 - - + -
314A VAL 3.5 24.0 - - - -
315A GLU* 3.9 15.3 - - + -
344A ARG* 3.3 50.3 - - + +
345A GLY* 3.8 8.1 - - - -
372A LEU* 3.7 31.9 - - + -
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Residues in contact with ILE 269 (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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265A TYR* 2.9 34.1 + - + +
266A GLU* 4.1 5.8 - - - +
268A PHE* 1.3 81.2 - - + +
270A GLU* 1.3 60.9 + - + +
271A SER 3.1 4.9 + - - -
272A LEU* 3.3 28.7 + - + +
275A LEU* 3.8 26.9 - - + +
283A ARG* 4.5 16.7 - - - +
286A VAL* 4.4 14.8 - - + -
287A VAL* 3.5 41.7 - - + +
290A ILE* 4.8 4.5 - - + -
313A ILE* 6.3 1.8 - - + -
372A LEU* 4.5 8.7 - - + -
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Residues in contact with GLU 270 (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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266A GLU* 2.4 59.9 + - - +
267A SER* 2.9 11.3 + - - +
269A ILE* 1.3 77.3 - - + +
271A SER* 1.3 55.7 + - - +
272A LEU 3.6 1.1 - - - -
283A ARG* 4.9 22.2 + - + +
284A LEU* 4.3 8.7 - - + +
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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
------------------------------------------------------------
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