Contacts of the helix formed by residues 247 - 258 (chain C) in PDB entry 1FVU
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 LYS 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C TYR* 3.5 21.0 + - + +
246C SER* 1.3 73.2 - - - +
248C GLU* 1.3 63.3 + - - +
249C LYS 3.2 1.6 - - - -
250C ASP* 3.4 14.5 + - + +
251C PHE* 3.0 23.7 + - - +
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Residues in contact with GLU 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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209C TYR* 3.2 25.2 + - + -
210C GLU* 5.2 0.4 - - - +
214C TYR* 2.5 26.9 + - - +
241C SER 3.4 11.8 - - - +
242C ILE* 3.4 6.4 - - + -
243C LYS* 2.8 48.0 + - - +
246C SER* 3.0 14.2 + - - +
247C LYS* 1.3 80.1 - - - +
249C LYS* 1.3 56.4 + - - +
251C PHE* 4.2 2.2 - - - -
252C VAL* 2.9 48.0 + - + +
329C LYS* 3.0 16.8 + - - -
683D MET* 4.1 0.7 - - - +
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Residues in contact with LYS 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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459B LEU* 4.7 9.4 - - + +
460B LYS* 3.1 38.0 + - - +
461B GLY* 5.0 0.6 - - - -
242C ILE* 3.9 20.1 - - + +
244C ILE* 3.5 47.2 + - + +
246C SER* 3.5 8.9 + - - +
248C GLU* 1.3 79.9 - - - +
250C ASP* 1.3 78.3 + - - +
252C VAL* 4.1 1.7 - - - +
253C GLY* 3.0 26.2 + - - -
312C PHE 4.6 1.2 - - - +
313C VAL* 3.7 38.3 - - + +
314C LEU* 5.5 0.9 - - - -
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Residues in contact with ASP 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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460B LYS* 5.8 3.1 - - - +
461B GLY* 6.1 0.2 - - - -
246C SER 4.6 0.4 + - - -
247C LYS* 3.4 16.0 + - + +
248C GLU 3.3 0.2 - - - -
249C LYS* 1.3 101.9 + - - +
251C PHE* 1.3 61.6 + - - +
253C GLY* 3.9 0.2 - - - -
254C ASP* 2.9 31.9 + - - +
313C VAL* 4.1 12.1 - - - +
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Residues in contact with PHE 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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207C SER* 3.8 27.4 - - - -
208C SER 3.6 24.9 - - - -
209C TYR* 3.4 39.0 - + + -
214C TYR* 3.5 26.0 - + + -
247C LYS 3.0 17.7 + - - +
248C GLU 3.7 3.8 - - - +
250C ASP* 1.3 76.7 - - - +
252C VAL* 1.3 72.9 + - + +
254C ASP* 3.4 9.3 + - + +
255C LEU* 3.1 31.5 + - + +
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Residues in contact with VAL 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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214C TYR* 4.0 20.2 - - + -
240C VAL* 4.0 20.4 - - + -
242C ILE* 4.0 17.9 - - + -
248C GLU* 2.9 28.4 + - + +
249C LYS 4.2 1.8 - - - +
251C PHE* 1.3 76.6 - - + +
253C GLY* 1.3 67.1 + - - +
255C LEU* 3.1 16.5 + - + +
256C VAL* 3.2 12.8 + - - +
306C LEU* 3.9 21.8 - - + -
327C VAL* 4.2 23.8 - - + -
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Residues in contact with GLY 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 LYS 3.0 16.7 + - - -
250C ASP 3.9 1.1 - - - -
252C VAL* 1.3 76.6 - - - +
254C ASP* 1.3 56.9 + - - +
256C VAL* 3.3 3.4 + - - +
257C THR* 2.9 34.9 + - - -
311C GLY 3.8 8.2 - - - +
312C PHE* 3.2 28.8 + - - -
313C VAL* 4.3 2.9 - - - -
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Residues in contact with ASP 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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250C ASP 2.9 19.5 + - - +
251C PHE* 3.5 9.5 - - + +
252C VAL 3.1 0.2 - - - -
253C GLY* 1.3 75.8 - - - +
255C LEU* 1.3 69.8 + - - +
257C THR* 4.3 5.5 - - - -
258C LYS* 3.0 49.6 + - - +
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Residues in contact with LEU 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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207C SER* 3.6 21.3 - - - +
214C TYR* 3.6 41.5 - - + +
215C LYS* 4.3 7.2 - - - +
216C PHE* 4.0 14.2 - - + +
251C PHE* 3.1 32.2 + - + +
252C VAL* 3.1 11.9 + - + +
254C ASP* 1.3 82.3 + - - +
256C VAL* 1.3 63.1 + - + +
258C LYS* 5.0 0.7 - - - -
259C ASN* 2.9 40.4 + - - +
327C VAL* 5.0 6.1 - - + -
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Residues in contact with VAL 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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216C PHE* 3.8 17.9 - - + -
252C VAL 3.2 12.0 + - - +
253C GLY 3.8 5.4 - - - +
255C LEU* 1.3 75.6 - - - +
257C THR* 1.3 62.0 + - - +
259C ASN 3.0 0.3 + - - -
260C ILE* 2.8 47.9 + - + +
267C ALA* 4.1 4.0 - - + -
306C LEU* 4.0 13.7 - - + -
312C PHE* 3.6 36.1 - - + -
327C VAL* 3.4 33.0 - - + -
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Residues in contact with THR 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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253C GLY 2.9 20.9 + - - -
254C ASP* 3.8 7.8 - - - -
256C VAL* 1.3 77.9 - - - +
258C LYS* 1.3 66.5 + - + +
259C ASN 3.4 0.7 + - - -
260C ILE* 4.2 9.6 + - - +
311C GLY* 3.5 20.1 + - - -
312C PHE* 3.6 16.3 - - + -
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Residues in contact with LYS 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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254C ASP* 3.0 40.9 + - - +
255C LEU* 4.8 0.7 - - - -
257C THR* 1.3 82.1 - - + +
259C ASN* 1.3 73.2 + - - +
260C ILE 5.4 0.2 - - - -
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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