Contacts of the helix formed by residues 227 - 237 (chain A) in PDB entry 5W6V
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLN* 1.3 89.6 - - + +
228A VAL* 1.3 61.7 + - - +
229A ILE* 4.3 8.7 - - + +
230A GLU* 3.0 33.7 + - + +
231A PHE* 2.8 24.3 + - - +
339A LEU 5.8 0.2 - - - +
340A GLU* 5.9 3.1 - - - +
342A CYS 3.8 2.5 - - - +
343A ASN* 3.2 24.2 - - - +
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Residues in contact with VAL 228 (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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226A GLN 3.5 0.4 + - - -
227A PRO* 1.3 71.6 - - - +
229A ILE* 1.3 52.7 + - - +
231A PHE* 3.2 7.8 + - + +
232A MET* 2.7 33.1 + - - +
256A PHE* 4.1 7.0 - - + -
260A ILE* 4.0 17.5 - - + -
265A VAL* 3.8 20.4 - - + -
326A LEU* 4.3 3.6 - - + -
339A LEU* 3.4 35.7 - - + +
342A CYS* 2.9 42.4 + - + +
343A ASN 4.1 1.6 - - - -
344A ILE* 4.0 11.9 - - + -
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Residues in contact with ILE 229 (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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227A PRO* 3.1 6.2 - - + +
228A VAL* 1.3 77.4 - - - +
230A GLU* 1.3 60.6 + - + +
232A MET* 3.2 10.4 + - + +
233A CYS* 3.0 39.0 + - - -
240A ASN* 5.2 3.8 - - - +
320A TYR* 4.1 35.2 - - + +
323A LEU* 3.8 24.0 - - + -
339A LEU* 3.6 35.9 + - + +
340A GLU* 3.9 14.8 - - + +
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Residues in contact with GLU 230 (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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226A GLN* 3.6 21.7 - - - +
227A PRO* 3.0 38.5 + - + +
229A ILE* 1.3 78.8 - - + +
231A PHE* 1.3 63.1 + - - +
233A CYS* 3.3 8.5 + - - +
234A GLU* 3.1 28.9 + - - +
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Residues in contact with PHE 231 (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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192A GLY 4.1 3.8 - - - -
193A GLY* 3.9 17.3 - - - -
223A TYR* 3.9 26.5 - + - -
224A LYS 5.4 0.2 - - - -
226A GLN* 3.4 23.8 - - + +
227A PRO 2.8 12.7 + - - +
228A VAL* 3.2 6.9 + - - +
230A GLU* 1.3 76.8 - - - +
232A MET* 1.3 62.6 + - - +
234A GLU* 3.4 2.1 + - - +
235A VAL* 3.1 41.3 + - + +
256A PHE* 4.1 13.5 - + - -
259A GLU* 4.1 18.6 - - + -
260A ILE* 3.9 33.7 - - + -
263A LEU* 4.1 9.9 - - + -
344A ILE* 4.0 24.0 - - + -
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Residues in contact with MET 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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228A VAL 2.7 20.4 + - - +
229A ILE* 3.5 13.5 - - + +
231A PHE* 1.3 75.5 - - - +
233A CYS* 1.3 67.8 + - - +
235A VAL* 3.3 1.2 + - - +
236A LEU* 3.0 39.6 + - + +
238A ILE* 5.1 6.1 - - + -
240A ASN* 5.7 3.8 - - - +
248A LEU* 3.9 31.2 - - + -
256A PHE* 3.7 35.4 - - + -
323A LEU* 3.8 22.9 - - + -
339A LEU* 3.7 24.7 - - + -
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Residues in contact with CYS 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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229A ILE* 3.0 29.7 + - - +
230A GLU* 3.7 8.1 - - - +
231A PHE 3.3 0.2 - - - -
232A MET* 1.3 85.5 - - - +
234A GLU* 1.3 55.5 + - + +
237A ASP* 2.6 30.7 + - - -
238A ILE* 3.1 48.4 + - - +
240A ASN* 4.3 20.4 - - - -
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Residues in contact with GLU 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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187A TYR* 5.1 1.0 + - - -
191A GLY* 4.4 3.0 - - - -
192A GLY* 3.6 18.0 + - - +
193A GLY* 3.0 19.4 + - - +
224A LYS* 2.8 35.5 + - - +
226A GLN* 2.9 26.4 - - - +
230A GLU* 3.1 16.1 + - - +
231A PHE 3.9 2.5 - - - +
233A CYS* 1.3 75.4 - - + +
235A VAL* 1.3 65.2 + - - +
237A ASP* 3.8 7.3 + - - +
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Residues in contact with VAL 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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192A GLY* 3.8 24.7 - - - +
231A PHE* 3.1 43.9 + - + +
232A MET* 3.8 5.2 - - - +
233A CYS 3.3 0.2 - - - -
234A GLU* 1.3 77.7 - - - +
236A LEU* 1.3 72.5 + - + +
237A ASP* 3.6 0.7 + - - +
255A ARG* 3.7 29.4 + - + +
256A PHE* 4.3 6.7 - - + -
259A GLU* 3.6 33.9 - - + +
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Residues in contact with LEU 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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232A MET* 3.0 31.8 + - + +
235A VAL* 1.3 92.4 - - + +
237A ASP* 1.3 72.9 + - - +
238A ILE* 3.8 17.2 - - + +
248A LEU* 3.9 21.3 - - + -
252A GLN* 3.8 57.3 + - + +
255A ARG* 4.2 13.9 - - - +
256A PHE* 4.2 9.4 - - + +
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Residues in contact with ASP 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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233A CYS 2.6 14.9 + - - -
234A GLU* 3.8 7.1 + - - +
235A VAL 3.6 2.0 - - - -
236A LEU* 1.3 76.3 - - - +
238A ILE* 1.3 66.2 + - - +
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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