Contacts of the helix formed by residues 245 - 259 (chain C) in PDB entry 1FBA
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 PRO 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243C ASN 3.9 2.7 - - - +
244C THR* 1.3 89.3 - - - +
246C GLU* 1.3 63.0 + - - +
248C ILE* 3.5 3.6 + - + +
249C ALA* 2.8 35.3 + - - +
281C VAL* 3.8 27.8 - - + -
282C ASN* 3.3 25.2 - - - +
285C ALA* 3.7 16.2 - - + +
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Residues in contact with GLU 246 (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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244C THR* 3.0 12.0 + - - +
245C PRO* 1.3 96.4 - - - +
247C GLU* 1.3 60.5 + - + +
249C ALA* 3.7 5.5 - - - +
250C LEU* 2.9 30.3 + - - +
285C ALA* 4.5 9.1 - - + +
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Residues in contact with GLU 247 (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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198C LEU* 4.2 13.9 - - + +
243C ASN* 3.2 24.4 + - + +
244C THR* 3.0 40.8 + - - +
246C GLU* 1.3 75.1 - - + +
248C ILE* 1.3 68.6 + - - +
249C ALA 3.2 0.2 + - - -
250C LEU* 3.2 5.1 + - - +
251C ALA* 3.0 26.0 + - - +
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Residues in contact with ILE 248 (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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198C LEU* 4.8 1.1 - - + -
232C MET* 4.3 11.9 - - + -
233C VAL 3.4 24.3 - - - +
234C THR* 3.8 27.1 - - + -
243C ASN* 4.0 28.5 - - + +
244C THR 2.9 17.7 + - - +
245C PRO* 3.7 4.7 - - + +
247C GLU* 1.3 77.4 - - - +
249C ALA* 1.3 58.1 + - - +
251C ALA* 3.8 0.8 - - - +
252C THR* 2.8 43.1 + - - +
282C ASN* 3.8 34.8 - - + +
286C ILE* 5.3 2.0 - - + -
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Residues in contact with ALA 249 (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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245C PRO 2.8 20.1 + - - +
246C GLU* 3.7 6.5 - - - +
247C GLU 3.1 0.4 - - - -
248C ILE* 1.3 76.2 - - - +
250C LEU* 1.3 65.6 + - - +
252C THR* 3.4 1.2 + - - -
253C VAL* 3.0 29.1 + - - +
282C ASN 4.8 0.2 - - - +
285C ALA* 3.6 35.7 - - + +
286C ILE* 3.6 14.6 - - + +
289C VAL* 3.8 8.1 - - + -
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Residues in contact with LEU 250 (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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246C GLU 2.9 16.9 + - - +
247C GLU* 3.2 5.4 + - - +
249C ALA* 1.3 73.1 - - - +
251C ALA* 1.3 69.2 + - - +
253C VAL* 3.2 1.6 + - - -
254C GLN* 2.9 53.7 + - - +
289C VAL* 4.1 14.9 - - + +
290C PRO* 5.9 1.3 - - + -
291C LEU* 3.9 23.3 - - + -
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Residues in contact with ALA 251 (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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198C LEU* 4.0 17.5 - - + -
202C GLN* 3.5 28.1 + - - +
233C VAL* 3.9 21.1 - - + -
247C GLU 3.0 16.6 + - - +
248C ILE 3.8 3.4 - - - +
250C LEU* 1.3 78.2 - - - +
252C THR* 1.3 55.5 + - - +
254C GLN* 3.5 2.4 + - - +
255C ALA* 3.0 31.4 + - - +
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Residues in contact with THR 252 (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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231C ASN 4.8 1.3 - - - +
232C MET* 3.8 11.8 - - - +
233C VAL* 2.9 32.6 + - + +
248C ILE* 2.8 22.8 + - - +
249C ALA 3.9 3.1 - - - -
251C ALA* 1.3 75.9 - - - +
253C VAL* 1.3 62.4 + - - +
255C ALA* 3.3 2.9 + - - +
256C LEU* 3.0 34.5 + - + +
269C PHE* 3.5 38.1 - - + -
286C ILE* 3.9 14.8 - - + -
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Residues in contact with VAL 253 (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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249C ALA 3.0 20.7 + - - +
250C LEU 4.1 1.6 - - - +
252C THR* 1.3 73.7 - - + +
254C GLN* 1.3 61.4 + - - +
256C LEU* 3.4 7.6 + - + +
257C ARG* 2.9 49.8 + - + +
286C ILE* 3.7 37.9 - - + +
289C VAL* 3.8 22.9 - - + -
291C LEU* 4.2 3.6 - - + -
293C ARG* 3.9 22.4 - - + -
295C TRP* 5.6 2.0 - - + -
297C LEU* 4.7 3.6 - - + -
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Residues in contact with GLN 254 (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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224B GLU* 5.2 3.1 - - - +
202C GLN* 3.1 28.6 + - - +
250C LEU* 2.9 49.9 + - + +
251C ALA* 4.6 1.0 - - - +
253C VAL* 1.3 75.7 - - - +
255C ALA* 1.3 65.4 + - - +
257C ARG* 3.3 9.6 + - - +
258C ARG* 3.0 55.4 + - - +
291C LEU* 4.3 10.7 - - + +
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Residues in contact with ALA 255 (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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202C GLN* 4.4 4.3 - - + -
205C THR* 4.4 13.5 - - + -
206C GLU* 3.6 27.0 + - + +
209C LEU* 4.7 1.0 - - - +
233C VAL* 4.0 17.3 - - + -
251C ALA 3.0 18.6 + - - +
252C THR 3.6 4.5 - - - +
254C GLN* 1.3 78.9 - - - +
256C LEU* 1.3 59.7 + - + +
258C ARG* 3.5 5.5 + - - +
259C THR* 2.8 26.8 + - - +
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Residues in contact with LEU 256 (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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205C THR* 5.7 1.8 - - + -
209C LEU* 3.8 24.2 - - + -
228C LEU* 4.4 8.7 - - + -
230C PRO* 4.5 8.5 - - + -
231C ASN 5.9 0.9 - - - +
252C THR* 3.0 26.4 + - + +
253C VAL* 3.8 4.5 - - + +
255C ALA* 1.3 74.2 - - + +
257C ARG* 1.3 62.9 + - - +
258C ARG 3.1 1.8 - - - -
259C THR* 4.0 2.0 - - - -
260C VAL* 2.9 42.4 + - + +
267C VAL* 4.1 9.6 - - + -
269C PHE* 3.7 30.1 - - + -
295C TRP* 3.6 18.8 - - + -
297C LEU* 3.8 19.5 - - + -
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Residues in contact with ARG 257 (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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224B GLU* 4.9 10.9 + - - +
261B PRO* 3.3 6.1 - - - +
262B ALA* 3.2 36.0 + - + +
263B ALA* 3.1 43.8 + - + +
294B PRO 5.6 0.6 + - - -
253C VAL* 2.9 37.9 + - + +
254C GLN* 3.6 7.4 - - - +
256C LEU* 1.3 75.9 - - - +
258C ARG* 1.3 58.9 + - - +
259C THR 3.5 0.3 + - - -
260C VAL 4.8 1.4 + - - +
291C LEU* 3.9 30.3 - - - +
292C ILE* 3.0 45.6 + - - +
295C TRP* 3.7 15.4 - - + -
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Residues in contact with ARG 258 (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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6B TYR* 4.1 15.6 + - - -
12B GLN* 5.0 4.2 + - - -
222B TYR* 3.9 17.0 + - - -
223B LEU* 3.3 26.8 - - + +
224B GLU* 2.8 39.5 + - - +
261B PRO* 3.5 9.5 - - - +
263B ALA* 3.7 13.5 - - + -
202C GLN* 3.4 11.3 - - - +
206C GLU* 3.0 37.8 + - + +
254C GLN* 3.0 43.3 + - - +
255C ALA 3.9 4.5 - - - +
256C LEU 3.1 0.4 - - - -
257C ARG* 1.3 78.1 - - - +
259C THR* 1.3 65.5 + - + +
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Residues in contact with THR 259 (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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261B PRO* 4.9 7.2 - - - +
206C GLU* 3.4 36.6 - - + +
209C LEU* 3.3 30.5 - - + +
210C ALA* 4.0 15.6 - - + +
213C TYR* 3.6 14.8 - - - +
255C ALA 2.8 21.3 + - - +
256C LEU 3.1 0.8 + - - -
257C ARG 3.3 0.8 + - - -
258C ARG* 1.3 88.0 - - + +
260C VAL* 1.3 62.7 + - - +
261C PRO* 3.4 11.3 - - - +
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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