Contacts of the helix formed by residues 221 - 238 (chain A) in PDB entry 5N9G
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 HIS 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 5.2 0.6 - - - +
219A GLY 5.4 0.4 + - - -
220A ARG* 1.3 72.6 - - - +
222A PRO* 1.3 71.0 - - + +
223A LEU 3.3 0.9 - - - +
224A PRO* 3.2 23.0 - - + +
225A VAL* 3.8 11.3 - - - +
265A ARG* 5.5 0.3 + - - -
285B PRO 3.2 20.5 + - - -
286B GLU* 3.1 26.0 + - + -
287B LEU* 4.6 4.7 - - - -
291C TYR* 3.6 17.2 + + + -
292C SER* 2.9 31.2 + - - -
293C SER* 4.8 2.4 - - - -
294C PHE* 5.9 5.0 - + - -
19D G 4.2 2.0 + - - -
20D C 2.9 45.1 + - - +
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Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.6 33.0 - - + -
169A LEU* 3.6 30.0 - - + +
172A LEU* 4.4 2.7 - - + -
217A VAL* 5.2 7.2 - - + -
220A ARG 3.3 7.1 - - - +
221A HIS* 1.3 84.7 - - + +
223A LEU* 1.4 65.8 + - - +
225A VAL* 3.1 24.2 + - + +
226A ILE* 3.4 9.9 + - - +
285B PRO* 4.5 11.9 - - + -
286B GLU* 4.3 16.2 - - + -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 5.1 4.5 - - + -
172A LEU* 4.3 19.9 - - + +
176A TYR* 3.6 50.9 - - + +
221A HIS* 3.3 0.6 - - - +
222A PRO* 1.4 81.1 - - + +
224A PRO* 1.4 68.1 - - + +
226A ILE* 3.0 17.4 + - + +
227A THR* 3.0 15.0 + - - +
259A PRO* 4.7 4.0 - - + -
289C THR 3.4 25.8 - - - +
291C TYR* 3.4 40.6 - - + +
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Residues in contact with PRO 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A HIS* 3.2 26.9 - - + +
223A LEU* 1.4 91.9 - - + +
225A VAL* 1.3 59.6 + - - +
227A THR* 3.4 8.2 + - - +
228A ALA* 3.1 24.4 + - - +
259A PRO* 3.8 11.2 - - + -
261A PRO* 3.9 18.6 - - + -
262A ALA* 3.6 32.0 - - + +
265A ARG* 4.0 6.7 - - + +
291C TYR* 3.6 22.2 - - + -
20D C 4.8 0.4 - - - +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 6.2 1.1 - - + -
208A VAL* 4.8 12.8 - - + -
211A ALA* 3.8 28.5 - - + -
216A LEU* 4.0 12.3 - - + +
217A VAL* 3.8 20.0 - - + -
220A ARG* 4.9 1.8 - - + -
221A HIS 3.8 15.0 - - - +
222A PRO* 3.1 10.0 + - + +
224A PRO* 1.3 74.6 - - - +
226A ILE* 1.4 58.7 - - + +
228A ALA* 3.4 3.1 + - - +
229A ALA* 2.9 28.4 + - + +
265A ARG* 3.7 32.1 - - + -
269A LEU* 5.2 2.0 - - + +
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.0 15.9 - - + -
172A LEU* 3.7 37.9 - - + +
173A VAL* 3.7 33.7 - - + +
176A TYR* 3.6 20.6 - - + -
177A CYS* 3.8 20.2 - - - -
204A THR* 4.3 3.1 - - - +
208A VAL* 4.1 12.6 - - + -
222A PRO 3.7 10.5 - - - +
223A LEU* 3.0 10.6 + - + +
225A VAL* 1.4 74.0 - - + +
227A THR* 1.4 53.9 + - - +
229A ALA 3.7 0.2 - - - -
230A THR* 2.8 33.7 + - - -
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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
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176A TYR* 2.9 29.2 + - - +
180A PHE* 4.5 5.6 - - + -
223A LEU 3.0 14.1 + - - -
224A PRO* 3.7 5.6 - - - +
225A VAL 3.4 0.2 - - - -
226A ILE* 1.4 73.7 - - - +
228A ALA* 1.4 63.7 + - - +
230A THR* 3.1 22.9 - - + +
231A PHE* 3.1 11.4 + - - +
247A LEU* 4.6 2.2 - - + -
251A CYS* 3.6 30.3 - - - -
257A ASP 4.9 0.2 - - - +
258A LEU* 4.5 0.4 - - + -
259A PRO* 3.5 22.4 - - + +
262A ALA* 4.0 11.4 - - + -
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Residues in contact with ALA 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 PRO 3.1 14.0 + - - +
225A VAL 3.8 4.0 - - - +
227A THR* 1.4 74.2 - - - +
229A ALA* 1.3 61.4 + - - +
231A PHE* 3.5 6.7 + - - +
232A LEU* 3.1 27.5 + - - +
247A LEU* 4.7 6.1 - - - -
262A ALA* 3.5 24.6 - - - +
265A ARG* 3.9 6.7 - - + +
266A LEU* 3.5 25.3 - - - +
269A LEU* 4.6 5.8 - - + -
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Residues in contact with ALA 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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204A THR* 3.8 5.8 + - - +
207A LEU* 3.5 26.2 - - + +
208A VAL* 3.7 25.6 - - + +
225A VAL* 2.9 18.1 + - + +
226A ILE 3.7 3.8 - - - +
228A ALA* 1.3 73.7 - - - +
230A THR* 1.4 59.7 + - - +
232A LEU 3.4 0.5 + - - -
233A ALA* 2.9 30.0 + - - +
269A LEU* 4.1 13.1 - - + +
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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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177A CYS* 3.8 20.0 - - - +
180A PHE* 3.4 38.5 - - + -
200A MET* 3.6 20.4 - - - +
204A THR* 3.5 17.6 + - - -
226A ILE 2.8 20.5 + - - +
227A THR* 3.1 20.4 - - - +
229A ALA* 1.4 67.9 - - - +
231A PHE* 1.3 58.8 + - - +
233A ALA* 3.4 2.1 + - - +
234A TRP* 3.0 29.8 + - - +
250A PHE* 3.8 3.6 - - + -
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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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227A THR 3.1 16.8 + - - +
228A ALA 3.7 2.0 - - - +
229A ALA 3.3 0.2 - - - -
230A THR* 1.3 76.3 - - - +
232A LEU* 1.4 57.6 + - - +
234A TRP* 3.2 8.7 + + - +
235A GLN* 2.9 56.6 + - + +
245A CYS 3.2 27.1 - - - -
246A SER* 3.5 11.9 - - - -
247A LEU* 3.4 35.2 - - + -
250A PHE* 3.4 37.9 - + + -
266A LEU* 3.7 33.9 - - + -
291A ARG* 5.7 0.7 - - - -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.9 11.9 - - + -
228A ALA 3.1 12.2 + - - +
229A ALA* 3.8 4.3 - - - +
231A PHE* 1.4 71.9 - - - +
233A ALA* 1.4 58.4 - - - +
235A GLN* 3.9 20.6 - - - +
236A SER* 3.0 32.2 + - - -
266A LEU* 3.6 26.0 - - + -
269A LEU* 3.9 23.3 - - + -
270A LEU* 3.8 22.2 - - + -
273A LEU* 3.9 27.1 - - + -
294A VAL* 4.3 4.0 - - + -
297A ILE* 3.7 19.6 - - + +
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Residues in contact with ALA 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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200A MET* 4.0 9.9 - - - +
203A ARG* 3.8 13.0 - - + -
204A THR* 3.7 28.3 - - - +
207A LEU* 3.6 5.8 - - + +
229A ALA 2.9 17.6 + - - +
230A THR 3.5 5.6 - - - +
232A LEU* 1.4 73.9 - - - +
234A TRP* 1.3 62.1 + - - +
236A SER* 2.9 20.1 + - - -
237A LEU* 3.1 19.8 + - + +
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Residues in contact with TRP 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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182A LEU* 4.2 7.2 - - + +
193A TYR* 2.8 52.8 + + + -
195A GLU* 4.0 12.8 - - + -
200A MET* 3.7 18.5 - - + -
230A THR 3.0 17.5 + - - +
231A PHE* 3.5 8.3 - + - +
233A ALA* 1.3 75.7 - - - +
235A GLN* 1.4 86.7 + - + +
237A LEU* 3.3 7.8 + - - +
242A ARG* 2.9 70.0 + - + +
245A CYS* 3.8 32.8 - - + -
250A PHE* 3.4 37.7 - + + -
253A LEU* 5.0 2.7 - - + -
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Residues in contact with GLN 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 PHE* 2.9 49.2 + - + +
232A LEU* 3.9 18.3 - - - +
234A TRP* 1.4 76.2 - - + +
236A SER* 1.3 58.7 + - - +
238A GLN 3.2 5.9 - - - +
239A PRO* 3.1 30.0 - - - +
242A ARG* 3.1 35.6 + - + +
243A LEU* 3.7 14.4 + - - +
245A CYS 3.1 18.8 + - - -
291A ARG* 3.8 8.9 + - - +
294A VAL* 3.8 23.3 - - + +
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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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203A ARG* 2.8 31.8 + - - -
232A LEU 3.0 15.9 + - - -
233A ALA* 2.9 18.7 + - - -
235A GLN* 1.3 76.6 - - - +
237A LEU* 1.3 59.3 + - - +
238A GLN 3.3 0.2 - - - -
239A PRO* 3.5 15.3 - - - +
294A VAL* 3.6 24.7 - - - +
295A LYS* 5.4 1.6 - - - +
297A ILE* 3.7 19.7 - - - +
298A GLY 4.8 0.4 + - - -
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Residues in contact with LEU 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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195A GLU* 3.6 40.1 - - + +
199A LYS* 3.9 42.8 - - + +
200A MET* 4.1 5.8 - - - +
203A ARG* 3.9 34.1 - - + +
233A ALA 3.1 23.7 + - - +
234A TRP* 3.7 4.7 - - - +
235A GLN 3.2 1.0 - - - -
236A SER* 1.3 79.6 - - - +
238A GLN* 1.4 72.7 + - - +
239A PRO* 3.9 2.5 - - - +
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Residues in contact with GLN 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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192A LYS 4.8 2.7 - - - +
195A GLU* 4.3 4.0 + - - +
234A TRP 3.8 3.0 + - - -
235A GLN 3.2 4.7 + - - -
237A LEU* 1.4 85.0 + - - +
239A PRO* 1.4 67.5 - - - +
240A ALA* 3.4 5.4 + - - +
241A ASP* 3.5 19.4 + - + +
242A ARG* 3.2 56.1 + - + +
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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
------------------------------------------------------------
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