Contacts of the helix formed by residues 240 - 252 (chain C) in PDB entry 1FLO
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 ASP 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C PHE 4.0 0.2 - - - +
234C SER* 3.3 10.4 - - - -
235C ALA 2.8 35.8 + - - +
237C GLY 5.4 2.5 - - - +
239C ILE* 1.3 76.5 - - - +
241C PRO* 1.3 56.5 - - - +
242C LEU* 4.0 2.5 - - - -
243C VAL* 2.8 62.6 + - + +
244C TYR* 3.1 12.3 - - - -
418C TYR* 3.2 29.4 + - - -
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Residues in contact with PRO 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C TRP* 6.3 1.3 - - + -
180C PHE* 5.8 0.2 - - - -
183C LEU* 3.8 26.6 - - + +
187C ILE* 4.5 24.2 - - + -
232C PHE* 5.1 13.0 - - + -
233C PHE* 3.1 33.2 - - + +
235C ALA* 3.1 25.8 - - + -
239C ILE* 4.0 2.0 - - + +
240C ASP* 1.3 82.9 - - - +
242C LEU* 1.3 62.2 + - - +
244C TYR* 3.0 5.0 + - - +
245C LEU* 2.9 23.2 + - - +
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ILE* 3.4 34.1 - - + -
232C PHE* 4.3 4.3 - - + +
233C PHE* 3.3 21.7 + - - +
234C SER* 3.5 33.2 - - - +
240C ASP* 3.2 9.4 - - - +
241C PRO* 1.3 79.3 - - - +
243C VAL* 1.3 57.9 + - - +
245C LEU* 3.4 6.7 + - + +
246C ASP* 3.0 28.4 + - - +
414C TYR* 4.4 15.9 - - + +
415C LEU* 4.0 14.8 - - + +
418C TYR* 3.6 30.5 - - + -
419C ILE* 4.2 1.7 - - - +
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASP* 2.8 46.4 + - + +
242C LEU* 1.3 78.3 - - - +
244C TYR* 1.3 66.2 + - + +
246C ASP* 3.2 8.0 - - + +
247C GLU* 3.0 41.1 + - + +
418C TYR* 5.0 4.3 - - + -
419C ILE* 4.8 8.7 - - + -
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Residues in contact with TYR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LEU* 3.7 21.6 - - + +
163C ASN* 5.3 4.0 + - - -
176C THR* 5.0 1.2 - - - +
179C GLN* 3.5 47.4 + - + -
180C PHE* 4.0 17.0 - - + +
183C LEU* 3.6 21.1 - - + -
238C ARG 4.6 4.6 + - - -
239C ILE* 3.8 24.6 - - + +
240C ASP 3.1 21.8 - - - -
241C PRO 3.0 6.1 + - - +
243C VAL* 1.3 83.3 - - + +
245C LEU* 1.3 60.0 + - - +
247C GLU* 3.6 8.5 + - + +
248C PHE* 2.9 27.7 + - - +
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PHE* 3.8 30.7 - - + -
203C PHE* 4.9 9.9 - - + -
215C ILE* 3.6 33.9 - - + -
232C PHE* 4.2 25.6 - - + -
241C PRO 2.9 12.8 + - - +
242C LEU* 3.5 9.2 - - + +
244C TYR* 1.3 74.5 - - - +
246C ASP* 1.3 59.9 + - - +
248C PHE* 2.9 14.9 + - + +
249C LEU* 2.9 44.9 + - + +
411C VAL* 6.2 0.9 - - + -
415C LEU* 3.9 15.9 - - + -
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Residues in contact with ASP 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU 3.0 14.4 + - - +
243C VAL* 3.2 10.5 - - - +
245C LEU* 1.3 78.2 - - - +
247C GLU* 1.3 77.4 + - - +
248C PHE 3.0 1.2 + - - -
249C LEU* 3.2 1.7 + - - +
250C ARG* 3.2 30.7 + - - +
399C ARG* 2.6 26.7 + - - -
400C TYR* 2.9 34.7 + - - +
415C LEU* 4.3 5.1 - - + +
419C ILE* 3.4 20.0 - - + +
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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
----------------------------------------------------------
176C THR* 2.9 25.9 + - + +
243C VAL* 3.0 26.9 + - + +
244C TYR* 3.9 9.4 - - + +
246C ASP* 1.3 91.4 - - - +
248C PHE* 1.3 59.1 + - - +
250C ARG* 3.3 30.1 + - - -
251C ASN* 3.4 22.5 + - - +
419C ILE* 5.7 0.3 - - - +
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Residues in contact with PHE 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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176C THR* 3.1 10.7 - - + +
177C LEU* 3.6 19.5 - - + -
180C PHE* 3.6 41.7 - + + -
244C TYR 2.9 15.9 + - - +
245C LEU* 2.9 18.3 + - + +
247C GLU* 1.3 75.8 - - - +
249C LEU* 1.3 85.0 + - + +
250C ARG 3.3 0.5 + - - -
251C ASN 3.3 2.4 + - - -
252C SER* 3.0 56.4 + - - -
253C GLU 6.0 0.2 - - - -
274C LEU* 3.9 27.1 - - + -
275C LEU* 3.8 25.4 - - + -
403C TRP* 4.5 6.5 - + - -
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C PHE* 6.1 4.0 - - + -
245C LEU* 2.9 31.0 + - + +
246C ASP 3.8 3.8 - - - +
248C PHE* 1.3 87.9 - - + +
250C ARG* 1.3 59.3 + - - +
252C SER 2.7 24.8 - - - +
274C LEU* 5.7 2.2 - - + -
400C TYR* 4.1 17.7 - - + -
401C PRO 5.0 1.2 - - - +
403C TRP* 2.7 54.8 + - + +
407C ILE* 5.1 8.1 - - + -
412C LEU* 5.0 6.5 - - + -
415C LEU* 3.6 32.1 - - + -
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ASP* 3.2 28.1 + - - +
247C GLU* 3.3 26.1 + - - +
249C LEU* 1.3 77.3 - - - +
251C ASN* 1.3 68.9 + - - +
252C SER 3.7 1.4 + - - +
399C ARG* 3.2 56.3 - - - +
400C TYR* 3.7 15.0 - - + +
401C PRO* 6.1 2.7 - - - -
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Residues in contact with ASN 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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172C THR* 3.5 27.9 - - - +
173C LYS* 3.2 40.8 - - + +
176C THR* 4.0 14.6 + - + +
247C GLU* 3.4 21.6 + - - +
248C PHE 3.3 2.2 + - - -
250C ARG* 1.3 83.0 - - - +
252C SER* 1.3 59.9 + - - +
253C GLU* 5.2 0.7 - - - +
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LYS* 4.0 10.2 - - - +
176C THR* 4.6 1.7 - - - +
177C LEU* 3.0 29.1 - - - +
248C PHE* 3.0 37.8 + - - -
249C LEU 2.7 21.3 - - - +
250C ARG 4.5 1.4 - - - +
251C ASN* 1.3 82.6 + - - +
253C GLU* 1.3 66.1 + - - +
401C PRO 5.4 0.2 - - - +
402C ALA* 5.2 2.3 - - - +
403C TRP* 2.8 9.2 + - - -
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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