Contacts of the helix formed by residues 229 - 240 (chain A) in PDB entry 2FQ6
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 CYS 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.4 22.2 - - + -
181A ILE* 3.8 27.8 - - - -
202A ASP* 3.6 30.1 - - - -
203A VAL* 4.4 13.2 - - + -
225A CYS* 4.2 3.1 - - + -
226A ASN* 3.1 13.8 + - - +
228A ARG* 1.3 87.8 - - - +
230A TRP* 1.3 67.4 + - - +
231A GLU 3.3 2.6 + - - -
232A GLN* 3.4 4.2 + - - +
233A LEU* 3.1 18.9 + - - +
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Residues in contact with TRP 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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50A ALA 4.0 18.2 - - - -
51A ASN* 5.5 6.7 - - + -
78A ALA* 3.9 22.9 - - + -
79A GLY* 3.4 36.7 - - - +
80A CYS 3.9 4.4 + - - +
81A VAL* 4.1 11.0 - - + +
225A CYS* 3.6 12.5 - - + +
226A ASN 3.0 17.4 + - - +
227A ALA* 3.9 6.1 + - - +
228A ARG 3.7 0.8 - - - -
229A CYS* 1.3 78.3 - - - +
231A GLU* 1.3 59.4 + - + +
233A LEU* 3.8 0.9 - - - +
234A ARG* 2.8 77.2 + - + +
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Residues in contact with GLU 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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227A ALA 4.9 3.5 + - - +
228A ARG 5.4 1.0 + - - +
229A CYS 3.4 0.4 - - - -
230A TRP* 1.3 80.9 - - + +
232A GLN* 1.3 59.1 + - - +
234A ARG* 3.7 31.7 + - - +
235A GLU* 2.8 39.9 + - + +
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Residues in contact with GLN 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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96A ALA 2.9 25.1 + - - +
97A PHE* 3.5 41.5 + - + +
149A LYS* 5.6 3.0 - - - +
228A ARG 5.7 1.1 + - - +
229A CYS* 3.4 4.3 + - - +
230A TRP 3.3 0.6 - - - -
231A GLU* 1.3 76.5 - - - +
233A LEU* 1.3 67.0 + - - +
235A GLU* 5.0 1.6 - - - -
236A ASN* 2.9 41.9 + - - +
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Residues in contact with LEU 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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81A VAL* 4.2 7.2 - - + -
83A PHE* 4.1 17.3 - - + -
93A SER* 3.7 36.6 - - - +
96A ALA* 4.0 13.2 - - + -
97A PHE* 3.6 24.1 - - + -
203A VAL* 3.7 21.5 - - + -
223A ALA* 4.3 1.6 - - + -
225A CYS* 3.5 26.9 - - - -
229A CYS 3.1 11.2 + - - +
230A TRP 3.9 2.5 - - - +
232A GLN* 1.3 77.9 - - - +
234A ARG* 1.3 57.4 + - - +
237A ALA* 2.8 37.8 + - + +
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Residues in contact with ARG 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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50A ALA* 3.4 29.2 + - - +
59A ARG* 4.4 6.5 - - - +
81A VAL* 3.8 19.8 - - + +
230A TRP* 2.8 76.8 + - - +
231A GLU* 3.7 36.1 + - - +
233A LEU* 1.3 78.2 - - - +
235A GLU* 1.3 84.4 + - - +
237A ALA* 3.8 1.7 - - - +
238A TYR* 3.0 27.7 + - - +
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Residues in contact with GLU 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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49A ARG* 5.6 1.4 + - - -
50A ALA* 3.8 2.1 - - - +
59A ARG* 2.8 39.1 + - - -
231A GLU* 2.8 33.1 + - + +
232A GLN* 4.4 2.0 - - - +
234A ARG* 1.3 109.3 + - - +
236A ASN* 1.3 66.2 + - - +
238A TYR* 3.3 6.1 + - - +
239A LEU* 3.1 28.4 + - + +
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Residues in contact with ASN 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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96A ALA* 2.8 41.8 + - + -
232A GLN* 2.9 33.0 + - - +
235A GLU* 1.3 78.4 - - - +
237A ALA* 1.3 65.1 + - - +
239A LEU* 3.2 26.8 + - - +
240A MET* 3.3 18.0 + - - +
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Residues in contact with ALA 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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81A VAL* 3.9 13.2 - - + -
83A PHE* 3.8 30.1 - - + -
92A ASN* 5.1 4.7 - - + -
96A ALA* 4.6 2.9 - - - +
233A LEU* 2.8 23.1 + - + +
234A ARG 3.8 3.1 - - - +
236A ASN* 1.3 78.4 - - - +
238A TYR* 1.3 61.4 + - - +
240A MET* 3.1 18.2 + - - +
241A GLY 3.2 0.2 + - - -
242A GLN* 3.2 24.2 + - + +
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Residues in contact with TYR 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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55A PHE* 5.5 2.8 - - - -
56A TYR* 4.1 8.1 - - - +
58A ARG* 3.3 67.1 + - + +
59A ARG* 3.5 64.4 + - + +
234A ARG* 3.0 19.1 + - + +
235A GLU* 3.5 10.1 - - - +
236A ASN 3.2 0.2 - - - -
237A ALA* 1.3 76.6 - - - +
239A LEU* 1.3 59.4 + - + +
241A GLY* 2.7 25.4 + - - +
242A GLN 4.6 9.0 - - - +
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Residues in contact with LEU 239 (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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235A GLU* 3.1 19.9 + - + +
236A ASN* 3.2 22.4 + - - +
238A TYR* 1.3 80.1 - - + +
240A MET* 1.3 64.8 + - + +
241A GLY 3.2 0.4 + - - -
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Residues in contact with MET 240 (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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92A ASN* 3.5 25.1 - - - +
95A LEU* 4.0 27.4 - - + -
236A ASN 3.3 12.3 + - - +
237A ALA* 3.1 10.0 + - - +
238A TYR 3.0 0.6 - - - -
239A LEU* 1.3 85.3 - - - +
241A GLY* 1.3 56.1 + - - +
242A GLN* 3.0 19.1 - - + +
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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