Contacts of the helix formed by residues 240 - 257 (chain B) in PDB entry 1ECX
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 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B TYR* 5.1 6.3 + - - -
67B THR 6.1 0.4 - - - +
208B LYS 5.0 1.7 - - - +
209B GLY* 3.9 11.2 - - - +
210B VAL* 3.8 19.7 - - + +
238B THR 3.6 1.6 + - - +
239B GLN* 1.3 69.4 - - - +
241B VAL* 1.3 51.1 + - - +
242B PRO* 3.6 11.5 - - - +
243B GLY* 3.0 19.7 + - - +
244B ILE* 2.7 45.1 + - + +
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Residues in contact with VAL 241 (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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24B PHE* 3.7 29.6 - - + -
28B LYS 5.1 1.3 - - - +
30B GLY 4.8 3.1 - - - +
32B PRO* 3.8 37.7 - - + -
42B ALA* 4.5 18.2 - - + +
46B MET* 4.8 12.3 - - + +
239B GLN* 3.1 12.1 + - + +
240B ASN* 1.3 68.2 - - - +
242B PRO* 1.3 77.8 - - + +
244B ILE* 3.9 6.5 - - - +
245B VAL* 3.0 29.7 + - + +
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Residues in contact with PRO 242 (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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21B MET* 3.1 38.5 - - + +
24B PHE* 3.8 29.6 - - + +
25B TYR* 3.4 47.8 - - + +
240B ASN* 3.6 7.9 - - - +
241B VAL* 1.3 95.1 - - + +
243B GLY* 1.3 62.3 + - - +
245B VAL* 4.0 1.5 - - + +
246B GLY 3.2 6.8 + - - -
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Residues in contact with GLY 243 (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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21B MET* 4.3 4.0 - - - +
25B TYR* 5.6 0.2 - - - -
207B PRO* 3.9 13.2 - - - +
210B VAL* 3.6 24.0 - - - +
240B ASN* 3.0 18.2 + - - +
242B PRO* 1.3 82.4 - - - +
244B ILE* 1.3 55.7 + - - +
246B GLY 3.5 0.5 + - - -
247B ALA* 2.9 29.8 + - - +
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Residues in contact with ILE 244 (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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46B MET* 4.3 17.3 - - + +
49B ALA* 3.7 13.2 - - + -
66B PHE* 3.4 63.2 - - + -
210B VAL* 4.6 6.5 - - + -
239B GLN* 4.0 15.3 - - + -
240B ASN* 2.7 41.3 + - + +
241B VAL* 3.9 5.6 - - - +
243B GLY* 1.3 70.2 - - - +
245B VAL* 1.3 66.9 + - + +
247B ALA* 3.3 5.9 + - - +
248B ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 245 (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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20B GLU* 3.8 28.9 - - + +
24B PHE* 3.8 45.5 - - + -
45B HIS* 4.1 19.3 - - + +
46B MET* 5.2 0.9 - - - -
49B ALA* 4.3 7.6 - - + -
241B VAL* 3.0 24.9 + - + +
242B PRO 4.0 3.1 - - - +
244B ILE* 1.3 75.7 - - - +
246B GLY* 1.3 64.6 + - - +
248B ALA* 3.4 2.6 + - - +
249B ARG* 3.0 21.4 + - + +
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Residues in contact with GLY 246 (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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17B VAL* 3.1 31.4 - - - +
20B GLU* 5.7 0.2 - - - -
21B MET* 3.8 17.0 - - - +
207B PRO* 4.2 2.0 - - - -
242B PRO 3.2 8.1 + - - -
243B GLY 3.9 1.3 - - - -
245B VAL* 1.3 82.3 - - - +
247B ALA* 1.3 50.4 + - - +
249B ARG* 3.2 3.5 + - - +
250B ALA* 2.8 32.4 + - - +
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Residues in contact with ALA 247 (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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66B PHE* 5.3 1.6 - - + -
201B ALA* 3.7 28.7 - - + -
204B PHE* 3.8 4.3 - - - -
207B PRO* 4.0 5.8 - - + +
210B VAL* 3.7 15.0 - - + -
212B ILE* 4.4 13.4 - - + +
243B GLY 2.9 19.6 + - - +
244B ILE* 3.3 4.9 + - - +
246B GLY* 1.3 72.6 - - - +
248B ALA* 1.3 57.4 + - - +
250B ALA* 3.3 5.2 + - - +
251B MET* 3.0 28.4 + - - +
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Residues in contact with ALA 248 (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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49B ALA* 3.6 38.1 - - + +
52B LYS* 3.4 18.8 - - + +
53B VAL* 3.8 18.5 + - + +
66B PHE* 5.5 0.4 - - + -
244B ILE 3.0 16.1 + - - +
245B VAL 3.7 2.5 - - - +
247B ALA* 1.3 75.1 - - - +
249B ARG* 1.3 64.4 + - - +
251B MET* 3.2 3.3 + - - +
252B GLU* 3.0 19.4 + - - +
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Residues in contact with ARG 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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16B ARG* 4.4 17.4 - - - +
17B VAL* 4.4 13.7 - - + -
20B GLU* 2.9 37.0 + - - +
52B LYS* 3.9 13.8 - - + +
245B VAL 3.0 18.1 + - - +
246B GLY* 3.5 7.0 - - - +
248B ALA* 1.3 76.5 - - - +
250B ALA* 1.3 57.9 + - - +
252B GLU* 3.0 27.2 + - - +
253B ILE* 3.0 68.2 + - + +
256B GLU* 5.4 2.8 + - - -
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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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17B VAL* 3.8 19.7 - - + +
204B PHE* 3.9 17.4 - - + +
205B HIS* 4.1 1.6 - - + +
206B GLY* 3.8 24.0 - - - +
246B GLY 2.8 19.0 + - - +
247B ALA 3.5 5.2 - - - +
248B ALA 3.2 0.2 - - - -
249B ARG* 1.3 72.4 - - - +
251B MET* 1.3 59.4 + - - +
253B ILE* 3.8 3.1 - - - +
254B ALA* 2.8 32.2 + - - +
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Residues in contact with MET 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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53B VAL* 3.9 27.1 - - + -
56B VAL* 3.7 28.0 - - + -
57B LEU* 4.1 18.4 - - + -
182B ILE* 4.3 23.6 - - + -
199B PHE* 4.5 7.4 - - + -
204B PHE* 3.6 22.4 - - + -
212B ILE* 3.6 27.1 - - + -
247B ALA 3.0 13.8 + - - +
248B ALA* 3.2 8.7 + - - +
250B ALA* 1.3 76.0 - - - +
252B GLU* 1.3 64.6 + - - +
254B ALA* 3.2 2.7 + - - +
255B VAL* 2.9 28.9 + - + +
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Residues in contact with GLU 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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52B LYS* 2.8 46.7 + - + +
56B VAL* 3.8 20.5 - - + +
248B ALA 3.0 13.6 + - - +
249B ARG* 3.0 28.0 + - - +
251B MET* 1.3 79.6 - - - +
253B ILE* 1.3 57.1 + - - +
255B VAL* 3.9 1.7 - - - +
256B GLU* 2.9 40.5 + - + +
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Residues in contact with ILE 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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14B ASP* 4.6 4.0 - - - +
16B ARG* 3.5 57.2 - - + +
17B VAL* 4.5 8.7 - - + -
249B ARG* 3.0 60.2 + - + +
250B ALA* 3.9 3.6 - - - +
252B GLU* 1.3 76.4 - - - +
254B ALA* 1.3 65.5 + - - +
256B GLU* 3.0 9.0 + - - +
257B GLU* 3.0 38.9 + - + +
355B LYS* 3.9 5.4 - - - +
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Residues in contact with ALA 254 (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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182B ILE* 3.9 20.9 - - + -
183B GLY* 3.9 17.6 - - - -
204B PHE* 4.3 13.0 - - + +
205B HIS* 5.9 2.2 - - - +
250B ALA 2.8 23.7 + - - +
251B MET 3.5 4.3 - - - +
253B ILE* 1.3 76.5 - - - +
255B VAL* 1.3 61.5 + - - +
257B GLU* 3.6 1.9 + - - +
258B LEU* 3.1 21.7 + - - +
261B ALA* 5.7 0.3 - - - +
355B LYS* 4.4 10.1 + - - +
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Residues in contact with VAL 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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56B VAL* 3.5 32.1 - - + +
182B ILE* 4.4 22.4 - - + -
183B GLY 5.0 3.8 - - - +
187B PHE 6.0 1.3 - - - +
251B MET* 2.9 19.8 + - + +
252B GLU 4.0 2.5 - - - +
254B ALA* 1.3 73.8 - - - +
256B GLU* 1.3 67.1 + - - +
258B LEU* 3.1 29.5 + - + +
259B SER 4.8 0.2 + - - -
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Residues in contact with GLU 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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249B ARG* 5.4 3.5 + - - -
252B GLU* 2.9 32.6 + - - +
253B ILE* 3.0 8.8 + - - +
255B VAL* 1.3 79.7 - - - +
257B GLU* 1.3 63.3 + - + +
258B LEU 3.8 0.3 + - - -
259B SER* 5.1 2.6 + - - -
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Residues in contact with GLU 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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16B ARG* 3.4 25.7 + - - -
253B ILE* 3.0 24.8 + - + +
254B ALA 3.8 1.8 - - - +
256B GLU* 1.3 84.1 - - + +
258B LEU* 1.3 64.5 + - - +
259B SER* 3.3 2.8 + - - -
260B GLU* 3.4 9.1 + - + +
261B ALA* 2.9 23.7 + - + +
355B LYS* 2.5 42.7 + - - +
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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
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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