Contacts of the helix formed by residues 221 - 241 (chain A) in PDB entry 6F0X
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 TRP 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A SER 4.0 2.6 - - - +
220A LYS* 1.3 115.5 - - + +
222A PHE* 1.3 63.2 + - - +
223A SER* 3.2 25.3 + - - -
224A GLU* 3.1 67.0 + - + +
225A SER* 3.2 10.6 + - - -
272A ASP* 5.6 2.2 - - - -
7Z ARG* 5.4 2.7 - - - +
8Z GLU 4.1 13.5 - - - +
9Z GLN* 3.7 29.4 - - - +
115Z ALA* 5.5 4.9 - - + -
116Z PRO* 3.8 33.6 - - + +
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TRP* 1.3 73.1 - - - +
223A SER* 1.3 63.5 + - - +
224A GLU 3.1 1.8 - - - -
225A SER* 2.3 39.9 + - - -
226A GLY* 2.9 12.0 + - - -
272A ASP* 3.7 29.2 + - + +
275A ARG* 3.3 45.8 - - - -
276A VAL* 5.2 4.3 - - + -
9Z GLN* 5.9 0.8 - - + +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TRP* 3.2 18.9 + - - -
222A PHE* 1.3 80.1 - - - +
224A GLU* 1.3 59.1 + - - +
226A GLY* 3.1 3.9 + - - +
227A LYS* 2.9 28.1 + - - +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 2.9 30.4 + - - +
220A LYS* 4.2 13.0 + - + -
221A TRP* 3.1 57.8 + - + +
222A PHE 3.1 0.2 - - - -
223A SER* 1.3 74.8 - - - +
225A SER* 1.3 58.4 + - - +
227A LYS* 3.0 38.2 + - - +
228A LEU* 2.9 28.4 + - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 4.0 3.2 + - - -
221A TRP 3.2 8.7 + - - -
222A PHE* 2.3 47.3 + - - -
224A GLU* 1.3 75.9 - - - +
226A GLY* 1.3 56.4 + - - +
228A LEU* 3.1 16.4 - - - +
229A VAL* 2.9 34.8 + - - +
272A ASP 5.3 2.9 - - - -
276A VAL* 4.1 23.5 - - - +
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Residues in contact with GLY 226 (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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222A PHE* 2.9 14.5 + - - -
223A SER* 3.1 6.8 + - - -
225A SER* 1.3 75.1 + - - +
227A LYS* 1.3 57.1 + - - +
229A VAL* 4.0 2.9 - - - +
230A THR* 2.7 42.3 + - - +
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A SER 2.9 10.1 + - - +
224A GLU* 3.0 56.8 + - - +
226A GLY* 1.3 72.9 - - - +
228A LEU* 1.3 61.9 + - - +
230A THR* 2.9 17.9 + - - -
231A LYS* 2.9 42.7 + - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.0 63.7 - - + +
218A PHE* 3.9 8.7 - - + -
219A SER* 4.3 4.3 - - - +
224A GLU 2.9 12.8 + - - +
225A SER* 3.1 22.4 - - - +
227A LYS* 1.3 80.8 - - - +
229A VAL* 1.3 90.4 + - + +
231A LYS* 4.4 0.3 - - - +
232A MET* 3.0 39.7 + - + +
233A PHE* 4.4 1.3 - - + -
276A VAL* 4.4 7.4 - - + -
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Residues in contact with VAL 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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225A SER 2.9 18.9 + - - +
226A GLY* 4.1 2.2 - - - +
228A LEU* 1.3 91.4 - - + +
230A THR* 1.3 69.6 + - + +
233A PHE* 2.9 52.0 + - + +
234A GLN 3.7 0.2 + - - -
276A VAL* 3.9 21.1 - - + -
279A ALA* 5.8 4.7 - - + -
283A GLN* 3.8 18.6 - - - +
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Residues in contact with THR 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 GLY* 2.7 27.6 + - - +
227A LYS* 2.9 12.6 + - - -
229A VAL* 1.3 77.2 - - + +
231A LYS* 1.3 65.7 + - - +
234A GLN* 2.6 42.9 + - - +
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Residues in contact with LYS 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 LYS* 2.9 38.2 + - - +
230A THR* 1.3 81.6 + - - +
232A MET* 1.3 64.9 + - - +
234A GLN* 3.5 3.6 - - - +
235A LYS* 2.9 44.4 + - - +
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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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122A ALA* 4.9 18.4 - - + -
210A ILE* 5.8 2.5 - - + -
212A ILE* 4.9 15.7 - - + -
217A LEU* 3.6 29.2 - - + -
228A LEU* 3.0 25.1 + - + +
231A LYS* 1.3 80.3 - - - +
233A PHE* 1.3 97.6 + - + +
235A LYS* 3.2 7.7 + - - +
236A ILE* 2.9 57.6 + - + +
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Residues in contact with PHE 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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212A ILE* 5.5 4.5 - - + -
228A LEU* 4.4 0.4 - - + -
229A VAL* 2.9 55.6 + - + +
232A MET* 1.3 103.3 - - + +
234A GLN* 1.3 60.6 + - - +
236A ILE* 3.5 18.8 - - + +
237A GLN* 2.8 33.4 + - - +
280A VAL* 3.6 33.7 - - + -
283A GLN* 3.1 51.4 - - + +
284A ILE* 5.3 1.3 - - + -
287A ILE* 5.5 4.9 - - + -
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Residues in contact with GLN 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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229A VAL 3.7 0.2 + - - -
230A THR* 2.6 28.2 + - - +
231A LYS* 3.5 4.3 - - - +
233A PHE* 1.3 75.8 - - - +
235A LYS* 1.3 64.7 + - + +
237A GLN* 4.7 2.5 - - - -
238A ASP* 2.2 64.8 + - - +
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Residues in contact with LYS 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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124A HIS* 5.9 6.7 - - + -
210A ILE* 6.5 0.9 - - + -
231A LYS* 2.9 34.1 + - - +
232A MET* 3.4 9.4 - - - +
234A GLN* 1.3 75.4 - - + +
236A ILE* 1.3 65.1 + - + +
238A ASP* 3.8 2.3 - - - +
239A LEU* 2.9 40.8 + - + +
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Residues in contact with ILE 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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210A ILE* 4.9 19.3 - - + -
212A ILE* 4.1 18.2 - - + -
232A MET* 2.9 49.8 + - + +
233A PHE* 3.5 22.9 - - + +
235A LYS* 1.3 78.0 - - + +
237A GLN* 1.3 65.6 + - - +
239A LEU* 3.0 8.0 + - - +
240A ILE* 2.9 40.5 + - + +
247A VAL* 5.7 0.9 - - + -
249A VAL* 4.9 11.2 - - + -
287A ILE* 4.1 20.6 - - + -
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Residues in contact with GLN 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 PHE 2.8 20.8 + - - +
234A GLN* 3.9 3.6 - - - +
236A ILE* 1.3 74.0 - - - +
238A ASP* 1.3 66.8 + - - +
240A ILE* 2.7 32.5 + - - +
241A ASP* 3.1 24.0 + - - +
286A GLN* 4.7 9.5 - - - +
287A ILE* 4.3 10.3 - - + +
290A HIS* 2.8 40.3 + - - -
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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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234A GLN* 2.2 57.1 + - - +
235A LYS* 4.3 2.7 - - - +
237A GLN* 1.3 80.6 - - - +
239A LEU* 1.3 63.1 + - + +
241A ASP* 3.5 29.9 - - - +
242A ASP* 4.1 2.4 + - - +
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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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124A HIS* 4.3 19.5 - - + +
208A GLN* 3.7 37.0 - - + +
210A ILE* 4.5 10.5 - - + -
235A LYS* 2.9 35.4 + - + +
236A ILE* 3.3 5.6 - - - +
238A ASP* 1.3 76.8 - - - +
240A ILE* 1.3 64.5 + - + +
241A ASP 3.1 0.4 - - - -
242A ASP* 2.9 28.0 + - + +
245A ALA* 4.8 2.9 - - - +
247A VAL* 4.5 6.1 - - + +
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Residues in contact with ILE 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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236A ILE* 3.0 32.1 - - + +
237A GLN* 2.7 26.8 + - - +
239A LEU* 1.3 72.8 - - + +
241A ASP* 1.3 60.6 + - - -
242A ASP 3.1 1.2 + - - +
243A LYS* 4.4 5.4 + - - -
247A VAL* 3.6 25.6 - - + -
287A ILE* 3.6 25.4 - - + -
290A HIS* 3.3 35.4 - - + +
292A ASN* 3.3 31.4 + - - +
293A VAL* 3.6 10.1 - - + -
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Residues in contact with ASP 241 (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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237A GLN* 3.1 24.4 + - - +
238A ASP* 3.5 31.9 - - - +
239A LEU 3.1 0.8 - - - -
240A ILE* 1.3 76.8 - - - +
242A ASP* 1.3 56.0 + - - +
243A LYS* 2.8 30.4 + - - +
290A HIS* 4.2 5.2 + - - -
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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
------------------------------------------------------------
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