Contacts of the helix formed by residues 246 - 259 (chain B) in PDB entry 1EFA
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 ASN 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B TRP* 2.9 42.1 + - + +
244B VAL* 3.2 4.0 + - - +
245B ALA* 1.3 79.9 - - - +
247B ASP* 1.3 63.3 + - - +
248B GLN* 3.7 16.1 + - - +
249B MET* 2.8 24.6 + - - +
250B ALA* 3.0 17.8 + - - +
273B TYR 3.0 17.3 - - - +
274B ASP* 3.7 0.9 - - - +
902B NPF 3.1 29.5 + - - +
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASN* 1.3 73.4 - - - +
248B GLN* 1.3 64.6 + - + +
250B ALA* 3.2 2.4 + - - +
251B LEU 2.9 18.5 + - - -
273B TYR 2.8 19.8 + - - +
274B ASP* 3.6 2.0 + - - +
275B ASP* 2.8 8.3 + - - -
276B THR* 2.7 50.4 + - + +
279B SER* 3.4 8.3 - - - -
282B TYR* 3.4 13.1 - - - +
286B LEU* 3.4 20.9 - - + +
288B THR* 2.6 27.8 + - - -
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Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 5.8 2.2 - - - +
278A ASP* 3.3 38.8 + - - +
74B HIS* 3.8 28.5 - - - +
220B TRP 3.5 17.8 + - - +
221B SER* 5.4 3.0 - - - +
222B ALA* 3.1 26.7 - - - +
246B ASN* 3.3 13.5 + - - +
247B ASP* 1.3 79.2 - - + +
249B MET* 1.3 61.1 + - - +
251B LEU* 3.1 10.8 + - - +
252B GLY 3.2 0.2 + - - -
274B ASP* 4.8 2.8 + - - +
276B THR* 5.1 6.2 - - + +
282B TYR* 4.0 8.3 - - - +
902B NPF 4.7 6.2 + - - -
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 4.2 8.5 - - + +
186B ALA 3.7 13.0 - - - +
187B GLY* 3.7 6.5 - - - -
218B GLY* 3.8 15.7 - - - -
220B TRP* 3.5 30.1 - - + -
221B SER 3.4 21.1 - - - +
222B ALA* 4.2 0.4 - - - +
224B SER* 3.6 9.9 - - - +
225B GLY* 3.6 12.3 - - - -
244B VAL* 3.5 12.3 - - + -
245B ALA* 3.3 37.7 - - + +
246B ASN* 2.8 26.6 + - - +
248B GLN* 1.3 69.9 - - - +
250B ALA* 1.3 66.4 + - - +
252B GLY* 2.9 3.8 + - - -
253B ALA* 2.8 21.7 + - - +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B VAL* 3.5 18.3 - - + +
246B ASN 3.0 13.2 + - - +
247B ASP 3.4 8.5 - - - +
249B MET* 1.3 76.5 - - - +
251B LEU* 1.3 57.2 + - - +
253B ALA* 3.1 3.8 + - - +
254B MET* 2.8 36.7 + - - +
270B VAL* 4.1 17.0 - - + -
272B GLY* 4.1 3.6 - - - -
286B LEU* 3.6 24.5 - - + -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LEU* 5.3 1.8 - - + -
278A ASP* 3.9 37.2 - - + +
281A CYS* 3.6 16.1 - - + +
282A TYR* 3.9 22.0 - - + -
283A ILE* 4.8 7.1 - - + +
222B ALA* 4.1 8.3 - - + -
247B ASP 2.9 12.0 + - - +
248B GLN 3.1 9.2 - - - +
249B MET 3.0 0.2 - - - -
250B ALA* 1.3 76.3 - - - +
252B GLY* 1.3 63.2 + - - +
254B MET* 3.2 10.6 + - + +
255B ARG* 3.0 20.8 + - - +
282B TYR* 3.7 47.7 - - + +
283B ILE 5.7 0.7 - - - +
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Residues in contact with GLY 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A CYS* 4.2 8.3 - - - -
222B ALA* 3.1 26.8 + - - +
226B PHE* 3.2 21.4 - - - -
248B GLN 3.2 4.9 + - - -
249B MET 2.9 5.5 + - - -
251B LEU* 1.3 79.6 - - - +
253B ALA* 1.3 62.4 + - - +
255B ARG* 3.2 3.5 + - - +
256B ALA 3.0 17.5 + - - -
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 4.4 4.3 - - + -
225B GLY 3.7 3.0 + - - +
229B THR* 3.4 27.5 - - - +
242B MET* 4.2 18.2 - - + -
244B VAL* 4.7 4.9 - - + -
249B MET 2.8 12.4 + - - +
250B ALA* 3.4 13.0 - - - +
252B GLY* 1.3 73.7 - - - +
254B MET* 1.3 58.6 + - - +
256B ALA* 3.0 3.8 + - - +
257B ILE* 2.8 36.4 + - + +
270B VAL* 5.0 3.6 - - + -
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Residues in contact with MET 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 4.0 7.2 - - + -
250B ALA 2.8 23.5 + - - +
251B LEU* 3.5 8.3 - - + +
253B ALA* 1.3 76.3 - - - +
255B ARG* 1.3 60.7 + - - +
257B ILE* 3.7 2.7 - - - +
258B THR* 2.9 31.6 + - - -
264B VAL* 3.8 23.1 - - + -
270B VAL* 4.4 11.2 - - + -
282B TYR* 4.1 26.2 - - + -
283B ILE 3.5 21.5 - - - +
284B PRO* 3.2 31.2 - - + +
286B LEU* 4.3 8.1 - - - -
328B THR* 3.4 19.7 - - + -
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A SER* 3.1 26.6 + - - -
281A CYS* 3.5 23.5 - - + +
282A TYR 3.7 6.7 - - - +
283A ILE* 3.2 26.6 - - + +
285A PRO* 3.9 11.5 - - - +
223B MET* 4.6 7.3 - - - +
226B PHE* 3.3 37.3 - - + -
251B LEU 3.0 8.6 + - - +
252B GLY* 3.4 10.8 - - - +
253B ALA 3.2 0.2 - - - -
254B MET* 1.3 76.9 - - - +
256B ALA* 1.3 53.7 + - - +
258B THR* 3.6 1.4 - - - -
259B GLU* 2.7 100.4 + - + +
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PHE* 3.5 37.6 - - + +
229B THR* 3.8 16.4 - - + +
230B MET* 3.8 14.9 - - + +
233B LEU* 4.4 1.8 - - + -
252B GLY 3.0 10.0 + - - +
253B ALA 3.4 8.1 - - - +
255B ARG* 1.3 73.5 - - - +
257B ILE* 1.3 67.0 + - - +
259B GLU* 3.4 1.8 + - - +
260B SER* 2.8 27.8 + - - -
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B THR* 4.3 11.0 - - + -
233B LEU* 4.3 7.9 - - + -
242B MET* 4.3 7.9 - - - -
253B ALA 2.8 24.3 + - - +
254B MET 3.7 4.3 - - - +
256B ALA* 1.3 71.5 - - - +
258B THR* 1.3 64.5 + - - +
260B SER* 3.1 17.0 + - - -
262B LEU* 3.3 36.2 + - + +
264B VAL* 3.8 19.3 - - + +
268B ILE* 3.5 46.4 - - + +
270B VAL* 3.6 24.0 - - + -
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ILE* 3.9 30.8 - - + +
254B MET 2.9 18.8 + - - -
255B ARG 3.6 2.7 - - - -
257B ILE* 1.3 71.4 - - - +
259B GLU* 1.3 59.8 + - + +
260B SER 2.9 10.6 + - - -
261B GLY* 3.1 13.9 + - - -
262B LEU 3.5 12.2 + - - +
264B VAL* 3.7 14.4 + - - +
283B ILE 5.0 3.3 + - - -
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ILE* 6.0 2.7 - - + -
284A PRO* 5.4 0.7 - - - +
285A PRO* 3.8 14.2 - - - +
226B PHE* 3.7 9.6 - - + -
230B MET* 5.8 5.5 - - + +
255B ARG* 2.7 72.4 + - + +
256B ALA* 3.8 4.5 - - - +
258B THR* 1.3 73.2 - - + +
260B SER* 1.3 58.6 + - - +
261B GLY 3.4 0.4 - - - -
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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