Contacts of the helix formed by residues 226 - 240 (chain B) 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 ASN 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B GLY 5.9 0.4 - - - -
77B GLY* 5.1 0.4 - - - -
78B ALA* 3.7 4.3 - - - +
197B LEU* 4.3 12.1 - - + +
200B GLY 6.0 0.6 - - - -
201B ILE 4.1 6.5 + - - +
202B ASP* 2.9 43.4 + - - +
225B CYS* 1.3 77.8 - - - +
227B ALA* 1.3 63.1 + - - +
228B ARG* 3.5 12.9 - - - +
229B CYS* 2.9 28.1 + - - +
230B TRP* 3.1 17.2 + - - +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 3.3 22.2 - - + +
226B ASN* 1.3 72.2 - - - +
228B ARG* 1.3 66.5 + - - +
229B CYS 3.4 0.5 + - - -
230B TRP* 3.8 9.4 + - - +
231B GLU* 4.9 2.4 + - - +
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ARG* 3.9 7.4 - - - +
178B PRO 4.8 1.1 - - - -
179B ASP* 2.7 43.8 + - - +
180B ALA 3.0 17.8 + - - -
181B ILE* 3.4 18.0 - - - +
202B ASP* 2.9 30.7 + - - -
226B ASN* 3.3 13.4 + - - +
227B ALA* 1.3 79.0 - - - +
229B CYS* 1.3 63.5 + - - +
231B GLU* 5.1 2.1 + - - +
232B GLN* 5.7 1.6 + - - +
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.3 22.8 - - + -
181B ILE* 3.8 29.2 - - - -
202B ASP* 3.6 26.0 - - - +
203B VAL* 4.1 14.6 - - + -
225B CYS* 4.2 2.0 - - + -
226B ASN* 2.9 20.1 + - - +
228B ARG* 1.3 87.5 - - - +
230B TRP* 1.3 65.0 + - - +
231B GLU 3.5 1.8 - - - -
232B GLN* 3.6 3.3 + - - -
233B LEU* 3.2 19.6 + - - +
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Residues in contact with TRP 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 4.0 16.2 - - - -
51B ASN* 5.3 8.5 - - - -
78B ALA* 3.8 22.9 - - + -
79B GLY* 3.6 35.5 - - - +
80B CYS 4.1 5.2 + - - +
81B VAL* 4.1 12.0 - - + +
225B CYS* 3.5 13.7 - - + -
226B ASN 3.1 17.4 + - - +
227B ALA* 3.8 6.0 + - - +
228B ARG 3.6 1.6 - - - -
229B CYS* 1.3 79.0 - - - +
231B GLU* 1.3 66.6 + - + +
233B LEU* 3.3 1.0 + - - +
234B ARG* 2.9 65.5 + - + +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ALA 4.9 2.4 + - - -
228B ARG 5.1 1.7 + - - +
229B CYS 3.5 0.6 - - - -
230B TRP* 1.3 79.3 - - + +
232B GLN* 1.3 58.5 + - - +
234B ARG* 3.2 29.8 + - - +
235B GLU* 2.8 39.8 + - + +
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Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA 2.8 21.9 + - - +
97B PHE* 3.4 44.7 + - + +
149B LYS* 5.8 1.6 - - - +
228B ARG 5.7 1.1 + - - +
229B CYS* 3.6 3.6 + - - +
230B TRP 3.3 0.6 - - - -
231B GLU* 1.3 75.4 - - - +
233B LEU* 1.3 68.4 + - - +
235B GLU* 5.0 2.2 - - - -
236B ASN* 3.0 45.7 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL* 4.2 8.3 - - + -
83B PHE* 4.2 14.8 - - + -
92B ASN 4.4 0.2 - - - +
93B SER* 3.7 35.0 - - - +
96B ALA* 3.9 14.8 - - + +
97B PHE* 3.7 17.2 - - + -
203B VAL* 3.6 22.4 - - + -
223B ALA* 4.1 2.7 - - + -
225B CYS* 3.3 28.3 - - - -
229B CYS 3.2 15.7 + - - +
230B TRP 3.8 2.7 - - - +
232B GLN* 1.3 80.0 - - - +
234B ARG* 1.3 56.6 + - - +
237B ALA* 2.9 36.0 + - + +
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 3.4 28.8 + - - +
59B ARG* 4.6 6.1 - - - +
81B VAL* 3.8 19.4 - - + +
230B TRP* 2.9 77.3 + - - +
231B GLU* 3.6 32.3 + - - +
233B LEU* 1.3 78.9 - - - +
235B GLU* 1.3 85.9 + - - +
237B ALA* 3.8 1.2 - - - +
238B TYR* 2.9 28.4 + - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 5.4 0.7 + - - -
50B ALA* 3.6 3.8 - - - +
59B ARG* 2.9 35.7 + - - -
231B GLU* 2.8 32.0 + - + +
232B GLN* 4.5 2.2 - - - +
234B ARG* 1.3 110.7 + - - +
236B ASN* 1.3 63.9 + - - +
238B TYR* 3.3 7.3 + - - +
239B LEU* 3.1 34.8 + - + +
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Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA* 2.9 39.8 + - + -
232B GLN* 3.0 35.1 + - - +
235B GLU* 1.3 76.7 - - - +
237B ALA* 1.3 66.0 + - - +
239B LEU* 3.3 25.6 + - - +
240B MET* 3.4 17.6 + - - +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL* 3.9 13.2 - - + -
83B PHE* 3.8 29.8 - - + -
92B ASN* 5.0 4.9 - - + +
96B ALA* 4.7 2.1 - - - +
233B LEU* 2.9 24.3 + - + +
234B ARG 3.9 2.2 - - - +
236B ASN* 1.3 73.9 - - - +
238B TYR* 1.3 65.3 + - - +
240B MET* 3.1 17.0 + - - +
242B GLN* 3.1 25.4 + - + +
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE* 5.4 3.1 - - - -
56B TYR* 4.2 7.3 - - - +
58B ARG* 3.3 71.6 + - + +
59B ARG* 3.6 61.3 + - + +
234B ARG* 2.9 18.4 + - + +
235B GLU* 3.4 10.5 - - - +
236B ASN 3.3 0.2 - - - -
237B ALA* 1.3 76.8 - - - +
239B LEU* 1.3 62.2 + - + +
241B GLY* 2.7 25.9 + - - +
242B GLN 4.6 8.5 - - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLU* 3.1 27.5 + - + +
236B ASN* 3.6 23.8 - - - +
237B ALA 3.3 0.2 - - - -
238B TYR* 1.3 82.4 - - + +
240B MET* 1.3 65.4 + - + +
241B GLY 3.2 0.7 + - - -
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Residues in contact with MET 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASN* 3.4 26.9 - - - +
95B LEU* 4.0 28.3 - - + -
236B ASN 3.4 13.2 + - - +
237B ALA* 3.1 9.8 + - - +
239B LEU* 1.3 80.5 - - - +
241B GLY* 1.3 57.5 + - - +
242B GLN* 2.9 23.1 - - + +
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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