Contacts of the helix formed by residues 221 - 235 (chain C) 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 SER 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C ASP* 2.8 25.8 + - - -
220C TRP* 1.3 80.4 - - - +
222C ALA* 1.3 62.6 + - - +
223C MET* 3.5 8.3 + - - +
224C SER* 2.7 36.2 + - - -
225C GLY 3.2 3.6 + - - -
248C GLN* 4.8 4.0 - - - +
249C MET* 3.3 6.7 - - - +
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C TRP 3.9 1.0 + - - -
221C SER* 1.3 73.4 - - - +
223C MET* 1.3 57.6 + - - +
225C GLY 3.0 1.7 + - - -
226C PHE* 2.8 25.9 + - - +
248C GLN* 3.1 35.5 + - + +
249C MET* 4.2 0.2 - - - +
251C LEU* 4.1 17.5 - - + -
252C GLY* 3.1 17.4 - - - +
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Residues in contact with MET 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C SER* 3.2 8.0 - - - +
222C ALA* 1.3 79.8 - - - +
224C SER* 1.3 56.6 + - - +
226C PHE* 3.1 40.6 + - + +
227C GLN* 2.8 63.9 + - + +
255C ARG* 4.6 11.2 - - - +
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C GLY* 3.6 11.0 - - - -
219C ASP* 2.8 44.4 + - - -
221C SER* 2.7 25.4 + - - -
223C MET* 1.3 76.0 - - - +
225C GLY* 1.3 57.5 + - - +
227C GLN* 4.0 12.3 - - - +
228C GLN* 2.9 39.3 + - - +
249C MET* 3.7 2.8 - - - -
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Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.8 16.2 - - - +
221C SER 3.2 2.6 + - - -
222C ALA 3.0 8.0 + - - -
224C SER* 1.3 82.6 + - - +
226C PHE* 1.3 58.8 + - - +
229C THR* 3.0 31.0 + - - -
249C MET* 3.6 22.2 - - - -
252C GLY 3.7 6.7 - - - -
253C ALA 3.7 1.3 + - - -
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ALA 2.8 12.1 + - - +
223C MET* 3.1 37.0 + - + +
225C GLY* 1.3 78.7 - - - +
227C GLN* 1.3 60.1 + - + +
229C THR 3.5 0.2 + - - -
230C MET* 2.9 55.1 + - + +
252C GLY* 3.2 17.9 - - - +
255C ARG* 3.2 52.9 - - - +
256C ALA* 3.4 36.7 - - + +
259C GLU* 3.7 8.5 - - - -
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Residues in contact with GLN 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C MET* 2.8 55.4 + - + +
224C SER* 3.9 11.7 - - - +
226C PHE* 1.3 77.8 - - + +
228C GLN* 1.3 65.8 + - + +
230C MET* 3.1 6.2 + - - +
231C GLN* 2.9 37.5 + - - +
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Residues in contact with GLN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.8 23.3 - - + -
216C ARG* 3.2 37.7 + - + +
217C GLU 3.4 27.1 + - - +
218C GLY* 4.4 1.1 - - - -
224C SER* 2.9 26.2 + - - +
225C GLY 4.2 0.7 - - - +
227C GLN* 1.3 77.5 - - - +
229C THR* 1.3 62.2 + - - +
231C GLN* 3.3 24.5 + - - +
232C MET* 3.0 23.9 + - - +
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.7 3.8 - - - +
216C ARG* 6.0 0.4 - - - -
225C GLY 3.0 19.0 + - - -
228C GLN* 1.3 77.5 - - - +
230C MET* 1.3 60.4 + - - +
232C MET* 3.8 11.7 - - + +
233C LEU* 3.2 33.9 + - + +
242C MET* 3.2 40.0 - - + +
253C ALA* 3.3 16.6 - - - +
256C ALA* 3.8 20.0 - - + -
257C ILE* 4.3 3.6 - - + -
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Residues in contact with MET 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C PHE* 2.9 47.8 + - + +
227C GLN* 3.1 7.8 + - - +
229C THR* 1.3 75.8 - - - +
231C GLN* 1.3 55.9 + - + +
233C LEU* 3.2 4.8 + - - +
234C ASN* 2.8 63.4 + - - +
256C ALA* 3.8 17.9 - - + +
259C GLU* 5.8 5.6 - - + +
260C SER* 4.0 21.5 - - - +
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Residues in contact with GLN 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ARG* 3.0 27.1 - - - +
227C GLN* 2.9 26.3 + - + +
228C GLN* 3.7 26.0 + - - +
230C MET* 1.3 76.2 - - + +
232C MET* 1.3 62.4 + - - +
234C ASN* 3.1 10.9 + - - +
235C GLU* 3.0 29.2 + - - +
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Residues in contact with MET 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ALA* 3.6 24.0 - - - -
214C ALA* 3.8 14.1 - - + -
216C ARG* 3.7 27.0 - - - +
228C GLN 3.0 17.5 + - - +
229C THR* 3.8 13.5 - - + +
231C GLN* 1.3 76.9 - - - +
233C LEU* 1.3 68.3 + - + +
235C GLU* 3.2 13.9 + - - +
237C ILE* 3.2 36.7 + - + +
239C PRO* 3.5 31.4 - - + -
242C MET* 3.9 28.7 - - + -
268C ILE* 5.6 0.7 - - + -
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Residues in contact with LEU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C THR* 3.2 32.7 + - + +
230C MET* 3.8 5.4 - - - +
232C MET* 1.3 83.3 - - + +
234C ASN* 1.3 66.1 + - - +
236C GLY* 3.1 13.9 + - - -
237C ILE 3.8 16.2 - - - +
238C VAL* 4.0 26.4 - - + +
256C ALA* 4.0 11.0 - - + +
257C ILE* 4.3 9.4 - - + -
260C SER* 3.6 29.8 - - - +
262C LEU* 4.6 4.0 - - + -
268C ILE* 4.2 12.1 - - + -
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Residues in contact with ASN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C MET* 2.8 50.7 + - - +
231C GLN* 3.6 9.6 - - - +
233C LEU* 1.3 74.2 - - - +
235C GLU* 1.3 58.8 + - + +
236C GLY 3.0 7.7 + - - -
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Residues in contact with GLU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ARG* 3.3 38.0 + - - -
231C GLN* 3.0 15.7 + - - +
232C MET 3.5 7.6 - - - +
233C LEU 3.1 0.8 - - - -
234C ASN* 1.3 76.6 - - + +
236C GLY* 1.3 56.4 + - - +
237C ILE* 3.1 30.5 + - + +
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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
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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