Contacts of the helix formed by residues 351 - 359 (chain A) 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 PRO 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A LEU* 3.7 24.9 - - + -
326A VAL* 4.9 8.5 - - + -
327A VAL* 6.0 0.2 - - + -
349A ALA 3.6 8.1 - - - +
350A ILE* 1.3 91.1 - - + +
352A ASP* 1.3 68.1 + - - +
353A HIS* 3.2 27.8 - - + +
354A TYR* 3.1 22.2 + - - +
355A PHE* 3.7 3.2 - - - -
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLN 4.9 1.6 - - - +
208A ASN* 3.1 35.9 + - - +
209A LYS* 3.9 25.2 + - + +
210A TYR* 3.6 16.5 - - + -
350A ILE 4.4 3.9 - - - +
351A PRO* 1.3 72.4 - - - +
353A HIS* 1.3 64.2 + - + +
355A PHE* 3.1 13.4 + - - -
356A ALA 3.4 5.4 + - - -
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Residues in contact with HIS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.7 17.6 - - - +
320A LEU* 5.8 6.3 - - + +
322A GLU* 5.6 7.9 - - - -
323A LEU* 4.3 23.3 - - + +
351A PRO* 3.3 30.8 - - + +
352A ASP* 1.3 78.5 - - - +
354A TYR* 1.3 64.9 + - - +
356A ALA* 2.8 16.3 + - - +
357A LEU* 3.0 12.6 + - - +
364A TYR* 5.9 1.6 - - - -
371A MET* 3.6 34.4 - - + +
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Residues in contact with TYR 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE 2.8 28.2 + - - -
188A ASN* 5.7 0.7 - - - -
233A PHE* 5.3 2.0 - + - -
311A MET* 3.6 25.4 - - - +
315A LEU* 4.6 10.8 - - + -
323A LEU* 3.9 24.0 - - + -
327A VAL* 3.6 38.3 - - + +
350A ILE* 3.8 25.8 - - + -
351A PRO 3.1 15.2 + - - +
353A HIS* 1.3 82.3 - - - +
355A PHE* 1.3 82.0 + + - +
357A LEU* 3.3 8.6 + - + +
358A VAL* 3.2 44.4 + - + +
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ASN* 4.1 12.3 - - - +
211A LEU* 4.1 13.9 - - + +
214A ILE* 4.7 9.6 - - + -
231A TYR* 3.5 59.9 - + + -
233A PHE* 4.0 26.8 - + + -
350A ILE* 3.5 38.8 - - + -
351A PRO 3.7 8.5 - - - -
352A ASP* 3.1 12.7 + - - +
353A HIS 3.1 0.6 - - - -
354A TYR* 1.3 86.4 - + - +
356A ALA* 1.3 58.4 + - - +
358A VAL* 4.6 3.4 - - - +
359A SER* 2.9 33.5 + - - +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.6 41.9 - - + +
211A LEU* 5.0 0.9 - - - -
352A ASP 3.4 2.6 + - - -
353A HIS 2.8 11.1 + - - +
355A PHE* 1.3 78.2 - - - +
357A LEU* 1.3 60.6 + - - +
359A SER* 2.8 20.1 + - - -
362A TYR* 3.5 28.6 + - + +
371A MET* 4.0 14.1 - - + -
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A TRP* 5.6 1.0 + - - -
314A PHE* 4.0 32.5 - - + -
315A LEU* 4.7 7.9 - - + -
318A LYS* 4.9 11.7 - - + +
320A LEU* 3.6 30.7 - - + -
323A LEU* 5.9 1.1 - - + -
353A HIS 3.0 9.4 + - - +
354A TYR* 3.5 13.0 - - + +
355A PHE 3.2 0.2 - - - -
356A ALA* 1.3 75.2 - - - +
358A VAL* 1.3 68.5 + - + +
360A ARG* 3.1 17.0 + - - +
362A TYR 4.2 9.7 - - - +
363A ALA* 5.2 0.7 - - - -
364A TYR* 4.2 27.6 - - + +
371A MET* 4.5 11.6 - - + -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A TRP* 3.4 21.0 - - + +
187A ILE* 3.9 22.0 - - + -
233A PHE* 3.9 26.2 - - + -
235A ALA* 4.8 1.6 - - - +
311A MET* 4.2 15.9 - - + -
314A PHE* 5.1 6.3 - - + -
354A TYR* 3.2 47.2 + - + +
355A PHE 4.5 0.4 - - - +
357A LEU* 1.3 76.9 - - + +
359A SER* 1.3 62.8 + - - +
360A ARG* 3.0 19.2 + - - +
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Residues in contact with SER 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU* 3.7 15.3 - - - +
233A PHE* 3.8 7.1 - - - -
234A SER 3.5 21.1 - - - -
235A ALA* 3.1 5.1 - - - +
236A ARG 3.0 22.7 + - - -
355A PHE 2.9 18.4 + - - -
356A ALA* 2.8 19.8 + - - -
358A VAL* 1.3 75.6 - - - +
360A ARG* 1.3 63.6 + - - +
361A TYR* 3.1 22.6 + - - +
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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