Contacts of the helix formed by residues 222 - 239 (chain A) in PDB entry 5FI6
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 ASP 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 3.3 33.3 + - - +
220A ILE* 3.5 4.8 - - - +
221A PRO* 1.3 75.6 - - + +
223A PHE* 1.3 63.0 + - - +
224A MET* 3.1 7.6 + - - +
225A SER* 2.9 41.2 + - - -
226A PHE* 3.2 9.5 + - - +
541A PRO 5.0 1.7 + - - +
543A ARG 5.5 4.7 + - - +
544A GLU* 5.0 4.9 - - + -
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER 4.5 2.3 + - - +
165A THR 4.1 9.9 - - - +
166A GLY* 3.3 24.7 - - - -
220A ILE* 3.5 18.8 + - + +
221A PRO 3.0 6.3 + - - +
222A ASP* 1.3 75.8 - - - +
224A MET* 1.3 67.2 + - + +
226A PHE* 3.7 18.6 - + - -
227A THR* 3.0 49.1 + - + +
264A VAL* 4.4 3.8 - - + -
266A THR* 3.6 22.0 - - + -
270A GLN* 3.4 39.3 - - + +
271A ARG 3.1 34.8 - - - -
272A HIS* 4.0 4.5 - - + -
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Residues in contact with MET 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LYS 4.1 7.9 - - - +
164A SER* 3.5 47.5 + - - +
166A GLY* 5.3 0.2 - - - -
222A ASP* 2.9 7.7 + - - +
223A PHE* 1.3 91.3 - - + +
225A SER* 1.3 62.7 + - - +
227A THR* 3.3 15.1 + - + +
228A SER* 3.2 19.8 + - - -
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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
----------------------------------------------------------
222A ASP* 2.9 33.4 + - - -
224A MET* 1.3 78.6 - - - +
226A PHE* 1.3 62.9 + - - +
228A SER* 3.0 22.9 - - - -
229A HIS* 3.1 25.3 + - - -
539A LEU* 5.9 2.6 - - - +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ILE* 3.7 31.9 - - + -
222A ASP 3.2 4.4 + - - +
223A PHE* 3.8 22.2 - + - +
224A MET 3.2 0.6 - - - -
225A SER* 1.3 77.3 - - - +
227A THR* 1.3 65.1 + - + +
229A HIS* 2.9 23.6 + + + +
230A ILE* 2.9 43.2 + - + +
264A VAL* 4.4 2.9 - - + -
495A MET* 3.2 39.5 - - + -
520A LEU* 4.9 2.7 - - + -
523A LEU* 6.0 0.2 - - + -
524A CYS* 4.4 9.4 - - - -
526A PHE* 4.3 8.7 - + - -
539A LEU* 5.6 2.9 - - + -
541A PRO* 3.8 31.6 - - + -
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 3.0 44.0 + - + +
224A MET* 3.3 18.5 + - + +
226A PHE* 1.3 77.2 - - + +
228A SER* 1.3 63.7 + - - +
229A HIS 3.3 0.2 - - - -
230A ILE* 3.7 10.7 - - + +
231A ASP* 3.2 29.5 + - - +
272A HIS* 3.4 40.5 + - + +
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Residues in contact with SER 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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224A MET 3.2 8.8 + - - -
225A SER* 3.0 18.8 + - - -
226A PHE 3.0 0.6 - - - -
227A THR* 1.3 81.5 + - - +
229A HIS* 1.3 64.8 + - - +
231A ASP* 3.2 16.9 + - - +
232A GLU* 3.2 21.7 + - - +
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Residues in contact with HIS 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* 3.1 29.2 + - - -
226A PHE* 2.9 15.4 + + + +
228A SER* 1.3 79.3 - - - +
230A ILE* 1.3 65.9 + - - +
231A ASP 3.0 0.3 + - - -
232A GLU* 3.1 20.6 + - - +
233A LEU* 2.9 29.3 + - + +
523A LEU* 3.2 39.8 - - + +
539A LEU* 3.4 27.8 - - + +
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Residues in contact with ILE 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 PHE* 2.9 50.5 + - + +
227A THR* 3.7 14.4 - - + +
228A SER 3.4 0.2 - - - -
229A HIS* 1.3 75.2 - - - +
231A ASP* 1.3 51.4 + - - +
233A LEU* 3.5 8.5 + - + +
234A TYR* 2.7 31.9 + - - +
262A VAL* 4.2 16.8 - - + +
264A VAL* 4.0 19.5 - - + -
272A HIS* 4.0 18.4 - - + -
274A THR* 4.0 12.8 - - + -
497A MET* 4.6 5.6 - - - -
516A PHE* 3.7 15.5 - - + -
520A LEU* 4.6 9.9 - - + -
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A THR* 3.2 14.6 + - - +
228A SER* 3.4 11.3 - - - +
229A HIS 3.0 0.8 - - - -
230A ILE* 1.3 74.3 - - - +
232A GLU* 1.3 60.6 + - - +
234A TYR* 3.0 5.4 + - - +
235A GLU* 2.8 38.5 + - + +
272A HIS* 3.2 18.2 + - - -
274A THR* 3.2 31.8 - - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 3.2 15.7 + - - +
229A HIS* 3.1 23.3 + - - +
231A ASP* 1.3 76.6 - - - +
233A LEU* 1.3 66.7 + - + +
235A GLU* 3.0 8.5 + - - +
236A SER* 2.8 26.7 + - - -
523A LEU* 6.0 1.0 - - - +
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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
----------------------------------------------------------
229A HIS* 2.9 22.7 + - + +
230A ILE* 3.5 7.4 - - + +
232A GLU* 1.3 73.9 - - + +
234A TYR* 1.3 61.9 + - - +
236A SER* 3.8 1.5 - - - -
237A ALA* 3.2 19.1 + - - +
515A HIS* 5.6 0.2 - - - -
516A PHE* 3.3 34.3 - - + -
519A ASP* 3.3 39.0 - - + +
520A LEU* 3.6 42.6 - - + +
523A LEU* 4.2 22.4 - - + -
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Residues in contact with TYR 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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230A ILE 2.7 18.7 + - - +
231A ASP* 3.0 11.6 + - - +
233A LEU* 1.3 75.5 - - - +
235A GLU* 1.3 89.3 + - - +
238A LYS* 3.0 32.4 + - - +
260A TRP* 2.7 86.9 + + - +
261A GLY* 4.1 0.4 - - - -
262A VAL* 4.0 9.2 - - + -
274A THR* 3.4 38.1 - - + -
275A GLY* 3.1 14.6 - - - -
276A ASP* 4.9 1.2 + - - -
516A PHE* 4.1 8.7 - - + -
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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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231A ASP* 2.8 25.9 + - + +
232A GLU* 3.7 5.8 - - - +
234A TYR* 1.3 93.5 - - - +
236A SER* 1.3 69.6 + - - +
238A LYS* 2.9 39.4 + - - +
239A LYS* 3.5 14.0 + - - +
274A THR* 4.6 1.4 + - - -
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Residues in contact with SER 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 GLU 2.8 20.8 + - - -
233A LEU* 3.8 4.3 - - - -
235A GLU* 1.3 73.8 - - - +
237A ALA* 1.3 63.7 + - - +
238A LYS 3.0 0.3 + - - -
239A LYS* 3.0 26.7 + - - +
240A GLN* 4.1 6.1 + - - +
515A HIS* 3.6 16.8 + - - -
519A ASP* 3.6 17.2 + - - -
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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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233A LEU 3.2 13.0 + - - +
236A SER* 1.3 77.7 + - - +
238A LYS* 1.3 62.1 + - - +
240A GLN* 3.2 15.3 + - - +
260A TRP* 3.6 27.6 - - + -
512A LYS* 3.5 33.3 - - - +
515A HIS* 3.7 21.2 - - + -
516A PHE* 4.1 5.4 - - + +
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Residues in contact with LYS 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 TYR* 3.0 42.1 + - - +
235A GLU* 2.9 29.1 + - - +
237A ALA* 1.3 76.2 - - - +
239A LYS* 1.3 61.2 + - + +
240A GLN 3.2 1.9 + - - -
241A SER* 4.6 3.1 + - - -
258A ASP 5.2 7.8 + - - +
260A TRP* 3.5 19.2 - - + +
512A LYS* 3.7 14.6 - - - -
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Residues in contact with LYS 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* 3.9 13.0 - - - +
236A SER* 3.0 17.8 + - - +
238A LYS* 1.3 78.3 - - + +
240A GLN* 1.3 64.2 + - - +
241A SER* 3.2 14.6 + - - -
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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