Contacts of the helix formed by residues 227 - 247 (chain H) in PDB entry 6H25
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 SER 227 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLU* 5.7 0.4 - - - -
225H PRO 3.8 2.4 + - - -
226H VAL* 1.3 81.7 - - - +
228H LEU* 1.3 73.8 + - - +
229H ALA* 3.5 7.6 + - - +
230H ASP* 3.5 10.6 + - - +
231H ARG* 3.1 18.9 + - - +
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Residues in contact with LEU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E GLU* 3.8 42.5 + - + +
22E LEU* 4.2 20.9 - - + +
226H VAL 4.7 0.2 - - - -
227H SER* 1.3 78.2 + - - +
229H ALA* 1.3 60.9 + - + +
231H ARG* 3.2 9.7 + - + +
232H GLU* 2.9 36.7 + - - +
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Residues in contact with ALA 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227H SER* 3.5 4.7 + - - +
228H LEU* 1.3 77.7 - - + +
230H ASP* 1.3 66.1 + - - +
232H GLU* 3.2 21.0 - - - +
233H VAL* 3.0 29.3 + - + +
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Residues in contact with ASP 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H GLY* 3.2 24.7 - - - +
193H ALA* 4.9 0.2 - - - +
207H PRO* 3.3 26.0 - - - +
208H THR* 4.8 3.5 + - - +
226H VAL* 3.5 16.0 - - + +
227H SER* 3.5 16.1 + - - +
228H LEU 3.3 0.6 - - - -
229H ALA* 1.3 79.4 - - - +
231H ARG* 1.3 56.4 + - - +
233H VAL* 3.4 6.3 + - - +
234H ILE* 3.0 32.2 + - - +
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Residues in contact with ARG 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.3 47.9 + - + +
16E HIS* 3.5 36.8 + - - +
17E GLY* 3.4 27.3 - - - +
20E GLU* 3.9 16.5 + - - +
22E LEU* 3.8 23.6 - - + +
23E ARG 5.6 1.1 - - - +
226H VAL* 3.3 34.1 + - + +
227H SER 3.1 13.8 + - - +
228H LEU* 3.2 10.9 + - - +
230H ASP* 1.3 75.8 - - - +
232H GLU* 1.3 58.5 + - - +
234H ILE* 3.3 6.7 + - - +
235H SER* 2.9 31.6 + - - +
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Residues in contact with GLU 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 3.9 23.0 - - + +
228H LEU* 2.9 22.3 + - - +
229H ALA* 3.2 27.5 - - - +
231H ARG* 1.3 75.7 - - - +
233H VAL* 1.3 61.9 + - + +
235H SER* 3.1 10.1 + - - +
236H ARG* 2.9 38.1 + - + +
268H ILE* 3.9 5.3 - - + +
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Residues in contact with VAL 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H CYS* 3.8 36.6 - - + +
192H GLY 5.0 1.3 - - - -
193H ALA* 4.6 12.3 - - + +
229H ALA* 3.0 20.1 + - + +
230H ASP* 3.8 6.5 - - - +
232H GLU* 1.3 80.1 - - + +
234H ILE* 1.3 64.9 + - - +
236H ARG* 3.1 7.7 + - - +
237H LEU* 3.1 24.7 + - + +
260H TYR* 3.4 29.3 - - + +
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Residues in contact with ILE 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.6 27.8 - - + +
169H GLY* 5.7 0.9 - - - -
170H VAL* 4.2 15.9 - - + +
193H ALA* 3.9 22.0 - - + -
205H ILE* 3.7 26.4 - - + +
206H TYR 4.4 0.4 - - - -
207H PRO* 3.7 41.7 - - + -
226H VAL* 5.0 1.6 - - + -
230H ASP* 3.0 22.8 + - - +
231H ARG* 3.5 7.9 - - - +
233H VAL* 1.3 75.7 - - - +
235H SER* 1.3 60.9 + - - +
237H LEU* 3.3 5.8 + - - +
238H ARG* 3.3 20.4 + - - +
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Residues in contact with SER 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 5.6 1.1 - - - -
22E LEU* 5.4 3.6 - - - +
23E ARG 4.3 12.3 + - - -
24E VAL* 3.9 18.8 - - - +
26E GLY* 4.9 1.4 - - - -
170H VAL* 6.3 0.2 - - - -
231H ARG* 2.9 20.8 + - - +
232H GLU* 3.1 12.8 + - - -
234H ILE* 1.3 75.3 - - - +
236H ARG* 1.3 62.3 + - - +
237H LEU 3.4 0.2 - - - -
238H ARG* 4.0 7.6 - - - +
239H ASN* 3.1 31.4 + - - -
268H ILE* 3.2 16.9 - - - +
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Residues in contact with ARG 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H GLU* 2.9 27.4 + - + +
233H VAL* 3.1 6.4 + - - +
235H SER* 1.3 77.2 - - - +
237H LEU* 1.3 64.5 + - - +
239H ASN* 3.7 3.2 + - - +
240H CYS* 3.3 28.2 + - - -
260H TYR* 4.1 26.0 - - + -
263H SER* 2.3 52.8 + - - +
264H LEU* 3.9 14.9 - - - +
266H HIS* 2.5 21.8 + - - +
267H GLN* 4.0 3.8 + - - +
268H ILE* 3.7 35.8 - - + +
271H ILE* 5.0 0.2 - - - +
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Residues in contact with LEU 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H LEU* 3.9 22.7 - - + -
191H CYS* 5.3 2.5 - - + -
193H ALA* 3.9 28.9 - - + +
195H VAL* 5.7 5.2 - - + -
205H ILE* 4.1 18.6 - - + -
233H VAL* 3.1 19.4 + - + +
234H ILE 3.3 6.9 + - - +
236H ARG* 1.3 77.4 - - - +
238H ARG* 1.3 61.7 + - - +
240H CYS* 3.3 7.2 + - + +
241H ILE* 3.0 30.9 + - + +
256H ILE* 3.8 26.7 - - + +
260H TYR* 3.7 30.1 - - + -
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Residues in contact with ARG 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E VAL* 3.9 26.6 + - - +
25E ASP* 4.1 15.6 - - - +
55E HIS* 6.2 2.0 - - - -
217E GLN* 5.4 7.3 + - - +
170H VAL* 4.6 22.3 - - + +
171H LEU 5.3 1.8 + - - -
172H VAL* 3.7 27.8 - - + +
205H ILE* 3.9 14.1 - - + +
234H ILE 3.3 12.7 + - - +
235H SER* 4.0 8.1 - - - +
236H ARG 3.3 0.8 - - - -
237H LEU* 1.3 79.2 - - - +
239H ASN* 1.3 74.0 + - - +
241H ILE* 3.2 6.0 + - - +
242H ILE* 3.0 48.9 + - - +
272H LEU* 5.2 6.3 - - - +
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Residues in contact with ASN 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASP* 3.0 29.3 + - - +
235H SER 3.1 20.5 + - - +
236H ARG* 4.3 3.6 - - - +
237H LEU 3.4 0.4 - - - -
238H ARG* 1.3 98.1 + - - +
240H CYS* 1.3 57.3 + - - +
242H ILE* 3.4 8.4 + - - +
243H SER* 2.9 27.7 + - - -
268H ILE* 3.6 18.0 + - + +
271H ILE* 3.6 24.0 - - + +
272H LEU* 3.4 22.9 - - + +
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Residues in contact with CYS 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H ARG 3.3 15.7 + - - +
237H LEU* 3.3 11.6 + - + +
238H ARG 3.3 0.4 - - - -
239H ASN* 1.3 76.7 - - - +
241H ILE* 1.3 61.1 + - + +
243H SER* 2.6 23.7 + - - +
244H LEU* 2.9 22.0 + - + +
256H ILE* 5.5 3.4 - - + +
259H CYS* 3.6 41.5 - - + -
260H TYR* 4.5 3.6 - - - +
263H SER* 3.7 19.5 - - - -
271H ILE* 4.6 7.9 - - - -
280H ILE* 5.4 4.5 - - - -
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Residues in contact with ILE 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H VAL* 4.5 20.0 - - + -
195H VAL* 4.9 4.3 - - + -
203H ILE* 3.7 32.8 - - + -
205H ILE* 3.8 17.3 - - + -
237H LEU* 3.0 20.2 + - + +
238H ARG* 3.2 7.2 + - - +
240H CYS* 1.3 77.5 - - + +
242H ILE* 1.3 62.1 + - - +
244H LEU* 3.3 7.3 + - + +
245H VAL* 3.0 28.3 + - + +
251H LEU* 3.8 22.4 - - + -
256H ILE* 4.7 30.1 - - + -
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Residues in contact with ILE 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H VAL* 3.7 28.5 - - + -
173H GLN 5.6 1.6 - - - +
174H VAL* 6.0 1.3 - - + -
238H ARG* 3.0 43.9 + - - +
239H ASN* 3.6 10.3 - - - +
241H ILE* 1.3 76.3 - - - +
243H SER* 1.3 54.1 + - - +
245H VAL* 3.4 4.3 + - + +
246H THR* 2.6 45.2 + - - +
272H LEU* 5.0 18.4 - - + -
277H MET* 5.3 3.6 - - + -
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Residues in contact with SER 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H ASN 2.9 11.9 + - - -
240H CYS* 2.6 28.4 + - - +
242H ILE* 1.3 77.1 - - - +
244H LEU* 1.3 58.2 + - - +
246H THR* 3.4 1.4 + - - -
247H GLN* 3.0 34.8 + - - +
259H CYS* 5.4 0.3 - - - -
271H ILE* 4.6 9.7 - - - +
277H MET* 3.7 39.5 - - - -
280H ILE* 5.0 9.4 - - - +
281H VAL* 4.2 7.3 - - - +
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Residues in contact with LEU 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H CYS 2.9 21.9 + - - +
241H ILE* 3.7 7.4 - - + +
243H SER* 1.3 78.3 + - - +
245H VAL* 1.3 64.1 + - + +
247H GLN* 3.4 1.9 + - - +
248H ARG 3.1 17.7 + - - -
249H MET* 3.3 39.3 + - + +
250H MET 4.9 5.6 - - - +
251H LEU* 5.1 9.0 - - + -
255H SER* 3.7 22.7 - - - +
256H ILE* 4.6 17.0 - - + -
259H CYS* 3.6 32.8 - - + -
281H VAL* 4.6 15.5 - - + -
284H THR* 5.2 2.0 - - + -
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Residues in contact with VAL 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H VAL* 3.7 40.6 - - + -
175H SER* 4.6 2.7 - - - +
178H LEU* 3.9 30.4 - - + +
241H ILE 3.0 17.6 + - - +
242H ILE* 4.1 4.7 - - + +
244H LEU* 1.3 73.8 - - + +
246H THR* 1.3 65.4 + - - +
248H ARG* 3.4 11.0 + - - +
249H MET 5.1 2.7 - - - +
251H LEU* 3.7 21.5 - - + -
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Residues in contact with THR 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H ILE* 2.6 32.9 + - - +
243H SER* 3.6 4.4 - - - -
244H LEU 3.2 0.2 - - - -
245H VAL* 1.3 78.8 - - - +
247H GLN* 1.3 61.6 + - - +
248H ARG* 3.2 7.2 + - - +
277H MET* 3.9 23.1 - - + +
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Residues in contact with GLN 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.1 10.7 - - - +
243H SER 3.0 20.2 + - - +
244H LEU 3.4 2.7 + - - +
246H THR* 1.3 77.8 - - - +
248H ARG* 1.3 69.1 + - - +
249H MET* 3.6 2.2 - - + -
274H PRO* 5.3 1.2 + - - +
277H MET* 3.9 24.3 - - + +
278H GLU* 4.5 21.0 + - - +
281H VAL* 3.7 37.3 - - + +
285H ARG* 4.1 10.0 + - - -
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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
------------------------------------------------------------
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