Contacts of the helix formed by residues 245 - 265 (chain E) in PDB entry 5AJI
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 ASP 245 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214E ARG* 3.4 36.4 + - + +
241E SER* 4.1 6.3 - - - -
242E ASN* 2.8 37.7 + - - +
244E GLY* 1.3 74.2 - - - +
246E LEU* 1.3 65.6 + - - +
247E GLN 3.3 0.4 - - - -
248E ASN* 3.0 9.7 + - - +
249E VAL* 2.9 38.2 + - + +
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Residues in contact with LEU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E ARG* 3.4 70.7 - - + +
185E ARG 3.7 6.1 - - - +
186E ASN* 3.2 51.0 + - - +
241E SER* 4.5 10.3 - - - +
242E ASN 3.1 5.8 + - - +
243E SER* 3.1 16.4 + - - +
245E ASP* 1.3 74.1 - - - +
247E GLN* 1.3 64.2 + - - +
249E VAL* 3.6 0.4 + - - -
250E TYR* 3.2 9.5 + - - +
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Residues in contact with GLN 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ARG* 4.4 8.2 + - - +
243E SER 4.6 0.8 + - - +
244E GLY 4.6 4.2 + - - +
245E ASP 3.1 0.4 + - - -
246E LEU* 1.3 81.9 - - - +
248E ASN* 1.3 70.5 + - - +
250E TYR* 3.3 8.9 + - - +
251E TRP* 3.2 65.7 + - + +
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Residues in contact with ASN 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ARG* 3.4 22.5 + - - +
214E ARG* 3.5 20.1 - - - +
244E GLY 4.3 14.6 + - - -
245E ASP* 3.0 4.9 + - - +
247E GLN* 1.3 81.0 - - - +
249E VAL* 1.3 61.8 + - - +
251E TRP* 3.9 12.9 - - - -
252E ASP* 2.8 40.0 + - - +
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Residues in contact with VAL 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E ASN* 4.0 6.3 - - - +
188E PHE* 5.3 2.2 - - + -
212E GLU* 4.3 3.4 - - + -
214E ARG* 3.7 39.9 - - + +
215E ILE* 3.8 27.8 - - + -
239E VAL* 5.4 1.1 - - + -
241E SER* 3.8 16.8 - - - +
245E ASP* 2.9 30.2 + - + +
246E LEU 3.9 4.3 - - - +
248E ASN* 1.3 77.2 - - - +
250E TYR* 1.3 56.9 + - - +
252E ASP* 4.7 0.4 - - - -
253E VAL* 2.9 46.8 + - + +
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Residues in contact with TYR 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ASN* 3.8 15.5 + - - -
227D GLU* 5.5 1.0 - - - -
186E ASN* 3.7 16.5 - - - +
187E GLU 3.8 17.0 - - - -
188E PHE* 3.3 44.6 - + - -
189E ILE 5.8 0.2 + - - -
246E LEU 3.2 11.8 + - - +
247E GLN* 3.5 14.4 - - - +
249E VAL* 1.3 78.6 - - - +
251E TRP* 1.3 76.1 + + - +
254E LEU* 2.9 56.3 + - + +
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Residues in contact with TRP 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D GLU* 5.7 0.7 - - - -
222D THR* 3.7 25.4 - - + -
224D ARG* 3.4 49.6 + - + +
225D LEU 3.4 23.5 - - - +
226D ASN* 3.0 25.2 + - - -
236D VAL* 4.1 12.8 - - + -
238D ARG* 3.7 21.8 - - - -
247E GLN* 3.2 52.9 + - + +
248E ASN* 3.9 11.7 - - - +
249E VAL 3.4 0.2 - - - -
250E TYR* 1.3 91.2 - + - +
252E ASP* 1.3 63.4 + - - +
254E LEU* 3.3 3.6 + - - +
255E GLU* 3.1 24.3 + - - +
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Residues in contact with ASP 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ARG* 2.3 28.9 + - - -
212E GLU* 4.6 8.1 - - - +
214E ARG* 2.6 34.0 + - - +
248E ASN* 2.8 22.2 + - - +
249E VAL 4.1 0.9 - - - +
251E TRP* 1.3 74.2 - - - +
253E VAL* 1.3 61.7 + - - +
255E GLU* 3.3 9.8 + - - +
256E ARG* 3.2 30.6 + - + +
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Residues in contact with VAL 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E PHE* 3.5 28.3 - - + -
208E ILE* 4.0 19.3 - - + -
209E ILE* 4.7 8.1 - - + -
212E GLU* 4.4 14.1 - - + +
215E ILE* 4.2 15.0 - - + -
237E VAL* 5.9 0.2 - - + -
249E VAL* 2.9 40.7 + - + +
252E ASP* 1.3 71.8 - - - +
254E LEU* 1.3 62.4 + - - +
256E ARG* 3.3 9.2 + - - +
257E ILE* 3.0 34.9 + - + +
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Residues in contact with LEU 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU* 4.1 15.0 - - + +
226D ASN 3.4 33.7 - - - +
227D GLU* 4.1 8.1 - - - +
228D LEU* 3.9 28.3 - - + +
188E PHE* 4.5 10.1 - - + -
190E ILE* 5.1 5.8 - - + -
250E TYR* 2.9 39.5 + - + +
251E TRP 3.7 4.7 - - - +
253E VAL* 1.3 78.5 - - - +
255E GLU* 1.3 61.1 + - - +
257E ILE* 3.3 19.2 + - + +
258E LYS* 3.1 21.0 + - - +
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Residues in contact with GLU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ILE* 3.9 17.7 - - + +
199D ASP* 4.5 0.3 - - - +
202D LYS* 2.9 34.6 + - - -
224D ARG* 5.0 5.0 + - - -
225D LEU* 4.0 21.6 + - + +
251E TRP 3.1 16.1 + - - +
252E ASP* 3.3 9.1 + - - +
254E LEU* 1.3 76.4 - - - +
256E ARG* 1.3 63.6 + - + +
258E LYS* 3.3 3.1 + - - +
259E ARG* 3.0 58.4 + - + +
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Residues in contact with ARG 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ASN* 4.4 1.6 + - - +
208E ILE* 3.3 41.0 + - + +
211E SER* 2.7 32.9 + - - -
212E GLU* 4.3 17.0 + - - +
252E ASP* 3.2 20.0 + - + +
253E VAL* 3.6 8.1 - - - +
255E GLU* 1.3 74.6 - - + +
257E ILE* 1.3 60.3 + - - +
259E ARG* 3.1 8.8 + - - +
260E GLU* 2.7 59.0 + - + +
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Residues in contact with ILE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LEU* 4.8 3.8 - - + -
188E PHE* 4.5 7.6 - - + -
190E ILE* 3.7 42.2 - - + -
205E LEU* 3.7 20.4 - - + -
208E ILE* 3.9 15.9 - - + +
237E VAL* 5.6 2.0 - - + -
253E VAL* 3.0 35.8 + - + +
254E LEU* 3.3 13.2 + - + +
256E ARG* 1.3 75.2 - - - +
258E LYS* 1.3 63.5 + - - +
260E GLU* 4.6 0.2 - - - -
261E PHE* 3.0 46.4 + - + +
268E PHE* 4.3 6.5 - - + -
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Residues in contact with LYS 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D TYR* 3.2 32.9 + - - -
196D SER 4.8 3.0 + - - -
198D ILE* 3.9 30.3 - - + +
225D LEU* 4.2 16.4 - - + -
228D LEU* 4.5 11.0 - - + -
233D ILE* 3.9 24.1 - - - +
254E LEU 3.1 12.4 + - - +
255E GLU 3.4 9.4 - - - +
256E ARG 3.1 0.6 - - - -
257E ILE* 1.3 77.3 - - - +
259E ARG* 1.3 62.5 + - - +
261E PHE* 4.0 1.0 - - - +
262E ASP* 2.7 54.8 + - - +
268E PHE* 3.6 21.8 - - + -
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Residues in contact with ARG 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ASP* 5.2 4.0 + - - -
198D ILE* 3.7 31.1 - - + +
199D ASP* 2.6 39.1 + - - -
255E GLU* 3.0 46.2 + - + +
256E ARG* 3.1 8.4 + - - +
258E LYS* 1.3 76.1 - - - +
260E GLU* 1.3 60.7 + - + +
262E ASP* 3.5 6.5 + - - +
263E ALA* 3.0 28.8 + - - +
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Residues in contact with GLU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E ILE* 3.8 21.6 - - + +
208E ILE* 3.7 18.9 - - + +
256E ARG* 2.7 54.5 + - + +
257E ILE 4.0 2.5 - - - +
259E ARG* 1.3 71.1 - - + +
261E PHE* 1.3 61.2 + - - +
263E ALA* 3.1 8.6 + - - +
264E ALA* 2.8 30.7 + - - +
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Residues in contact with PHE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ILE* 3.7 12.8 - - + -
192E VAL* 3.5 22.2 - - + -
201E VAL* 4.0 13.2 - - + -
204E ILE* 3.6 32.5 - - + -
205E LEU* 3.8 32.5 - - + -
257E ILE* 3.0 22.7 + - + +
260E GLU* 1.3 78.8 - - + +
262E ASP* 1.3 56.9 + - - +
264E ALA* 3.3 2.4 + - - +
265E GLY 2.9 8.7 + - - -
266E ILE* 2.7 64.2 + - + +
268E PHE* 3.4 30.5 - + + -
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Residues in contact with ASP 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D TYR 4.6 1.6 - - - +
198D ILE* 5.4 1.0 - - - +
258E LYS* 2.7 50.1 + - - +
259E ARG* 3.6 6.4 - - - +
261E PHE* 1.3 77.1 - - - +
263E ALA* 1.3 62.0 + - - +
265E GLY* 3.3 11.6 + - - -
266E ILE 4.5 3.9 - - - +
268E PHE* 3.7 19.4 - - - -
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Residues in contact with ALA 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E ARG 3.0 14.9 + - - +
260E GLU* 3.4 13.7 - - - +
262E ASP* 1.3 78.2 - - - +
264E ALA* 1.3 60.3 + - - +
265E GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E GLN* 3.9 21.2 + - - +
204E ILE* 3.6 28.5 - - + -
260E GLU 2.8 19.8 + - - +
261E PHE 4.0 2.7 - - - +
263E ALA* 1.3 72.4 - - - +
265E GLY* 1.3 61.5 + - - +
266E ILE* 3.5 5.1 + - + +
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Residues in contact with GLY 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E PHE 2.9 4.8 + - - -
262E ASP* 3.3 7.6 + - - -
263E ALA 3.1 6.0 + - - -
264E ALA* 1.3 79.9 - - - +
266E ILE* 1.3 62.0 + - - +
267E SER* 3.8 3.5 + - - -
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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
------------------------------------------------------------
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