Contacts of the helix formed by residues 231 - 238 (chain A) in PDB entry 2FY2
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 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASN* 3.8 24.5 - - + +
228A ARG* 5.7 3.8 - - - +
229A LEU 3.6 2.0 - - - +
230A PRO* 1.3 81.8 - - + +
232A ILE* 1.3 64.0 + - - +
233A GLY 3.1 3.8 - - - -
234A LEU* 2.9 22.2 + - + +
295A TYR* 3.8 29.4 - - + +
300A ALA* 3.7 22.9 - - + -
377A LEU* 3.5 20.0 - - + +
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Residues in contact with ILE 232 (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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194A PHE* 4.8 2.7 - - + -
230A PRO* 2.9 32.8 + - + +
231A PRO* 1.3 70.1 - - - +
233A GLY* 1.3 62.4 + - - +
235A LEU* 3.0 27.9 + - + +
236A THR 4.2 0.5 + - - -
250A LEU* 3.9 28.3 - - + -
303A TRP* 3.9 22.8 - - + -
367A TRP* 3.6 48.0 - - + +
369A CYS* 5.8 2.5 - - + -
373A ILE* 4.1 23.3 - - + -
377A LEU* 4.4 6.1 - - + -
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Residues in contact with GLY 233 (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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194A PHE* 3.7 18.9 - - - -
231A PRO 3.0 2.2 + - - -
232A ILE* 1.3 77.8 - - - +
234A LEU* 1.3 59.9 + - - +
236A THR* 2.8 25.9 + - - -
237A SER* 4.0 1.9 + - - -
300A ALA* 3.9 6.8 + - - -
302A ARG* 3.2 24.7 - - - +
303A TRP* 3.7 10.1 - - - -
304A TYR* 4.8 2.1 - - - -
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Residues in contact with LEU 234 (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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231A PRO* 2.9 17.9 + - + +
233A GLY* 1.3 76.6 - - - +
235A LEU* 1.3 59.6 + - - +
237A SER* 2.7 35.4 + - - +
238A ASP 4.1 0.2 + - - -
295A TYR* 3.9 26.2 - - + -
299A GLY 4.8 2.9 - - - +
300A ALA* 4.0 25.1 + - + +
377A LEU* 3.8 30.3 - - + +
380A SER* 3.5 31.4 - - - +
381A ALA* 3.6 16.8 - - + +
384A LEU* 4.5 8.5 - - + -
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Residues in contact with LEU 235 (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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232A ILE* 3.0 33.7 + - + +
234A LEU* 1.3 79.3 - - - +
236A THR* 1.3 60.3 + - - +
237A SER 3.1 1.3 + - - -
238A ASP* 3.4 13.0 + - - +
243A TRP* 3.5 46.3 - - + +
246A ALA* 4.3 11.9 - - + -
250A LEU* 4.2 10.8 - - + -
373A ILE* 4.7 8.3 - - + -
376A HIS* 3.7 32.1 - - + +
377A LEU* 3.8 19.7 - - + -
380A SER* 3.5 18.6 - - - +
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Residues in contact with THR 236 (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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93A PRO* 4.7 2.3 - - - +
232A ILE 4.6 0.4 - - - +
233A GLY 2.8 19.2 + - - +
235A LEU* 1.3 76.1 - - - +
237A SER* 1.3 58.3 + - - +
238A ASP 3.4 2.4 + - - +
240A ARG* 3.9 13.7 + - - -
243A TRP* 3.7 31.6 - - + +
303A TRP* 3.5 45.1 - - + +
304A TYR* 3.1 44.6 + - - +
305A ASP* 4.4 2.7 - - - +
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Residues in contact with SER 237 (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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91A ALA* 3.1 19.7 - - - +
93A PRO* 3.6 19.3 - - - +
233A GLY 4.9 0.7 - - - -
234A LEU* 2.7 34.1 + - - +
235A LEU 3.1 0.4 - - - -
236A THR* 1.3 77.4 + - - +
238A ASP* 1.3 62.1 + - - +
299A GLY 4.9 4.0 - - - -
304A TYR* 3.8 20.0 - - - -
380A SER 4.6 0.5 + - - -
383A LYS* 5.9 0.2 - - - +
384A LEU* 3.7 24.8 - - - +
387A ILE* 4.5 5.2 - - - +
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Residues in contact with ASP 238 (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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91A ALA* 3.3 13.3 - - - +
92A LEU 4.4 0.7 + - - -
235A LEU 3.4 14.1 + - - +
236A THR 3.4 7.0 - - - +
237A SER* 1.3 84.7 + - - +
239A GLY* 1.3 84.1 + - - +
240A ARG* 3.6 4.2 + - - -
242A GLU* 3.7 25.4 - - + +
243A TRP* 4.6 3.8 - - - +
379A SER* 4.1 3.6 - - - -
380A SER* 2.9 37.8 + - - +
383A LYS* 3.5 31.6 - - - +
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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