Contacts of the helix formed by residues 215 - 233 (chain H) in PDB entry 4U0Z
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 LEU 215 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ALA* 1.4 75.4 - - - +
216H ARG* 1.4 58.4 + - - +
218H VAL* 3.2 8.9 + - - +
219H MET* 2.9 38.4 + - + +
429H LEU* 5.8 2.6 - - + +
432H ALA* 5.0 6.9 - - + +
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Residues in contact with ARG 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ALA 3.4 5.0 - - - +
215H LEU* 1.4 78.1 - - - +
217H ARG* 1.4 54.6 + - - +
219H MET* 3.5 7.9 + - - +
220H GLU* 3.2 43.6 + - - +
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Residues in contact with ARG 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ALA* 3.7 17.7 + - - +
215H LEU 3.3 0.4 - - - -
216H ARG* 1.4 76.3 - - - +
218H VAL* 1.4 58.6 + - - +
220H GLU* 4.3 4.0 - - - +
221H GLU* 3.2 28.9 + - - +
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Residues in contact with VAL 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ALA 3.5 10.5 + - - +
215H LEU* 3.2 12.7 + - - +
217H ARG* 1.4 76.6 - - - +
219H MET* 1.4 52.8 + - - +
221H GLU* 3.2 13.6 - - - +
222H THR* 2.7 43.6 + - + +
428H THR 5.8 4.0 - - - +
429H LEU* 5.0 15.7 - - + -
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Residues in contact with MET 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 2.9 26.2 + - + +
216H ARG* 3.5 8.5 + - - +
218H VAL* 1.4 75.1 - - - +
220H GLU* 1.4 62.6 + - + +
222H THR* 3.1 17.5 + - - +
223H TYR* 3.3 13.7 + - - +
382H MET* 6.5 0.2 - - + -
387H PRO* 5.8 4.3 - - + -
388H PRO* 5.1 16.8 - - + -
429H LEU* 4.0 26.7 - - - -
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H ARG* 3.2 29.4 + - - +
217H ARG* 4.6 4.7 - - - +
218H VAL 3.4 0.2 - - - -
219H MET* 1.4 77.5 - - - +
221H GLU* 1.3 61.9 + - - +
223H TYR* 3.4 13.3 - - + +
224H TYR* 3.2 28.7 - - + -
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Residues in contact with GLU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H ARG 3.2 17.6 + - - +
218H VAL* 3.2 20.1 - - - +
220H GLU* 1.3 76.6 - - - +
222H THR* 1.4 64.9 + - + +
223H TYR 3.2 0.8 + - - -
224H TYR* 3.3 10.1 + - - +
225H HIS* 2.9 28.3 + - - +
240H LEU* 5.4 4.1 - - + +
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Residues in contact with THR 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H VAL* 2.7 29.4 + - + +
219H MET* 3.1 20.1 + - - +
221H GLU* 1.4 81.6 - - + +
223H TYR* 1.4 58.5 + - - +
225H HIS* 3.7 21.6 - - + +
226H HIS* 2.9 28.9 + - - +
390H THR* 4.8 1.6 + - - -
428H THR* 5.5 11.7 - - + -
429H LEU* 5.5 8.5 - - + +
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Residues in contact with TYR 223 (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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219H MET 3.3 11.6 + - - +
220H GLU* 3.4 13.5 - - + +
221H GLU 3.2 0.4 - - - -
222H THR* 1.4 77.1 - - - +
224H TYR* 1.4 77.9 + + - +
226H HIS* 3.4 15.1 + - - +
227H ILE* 3.4 30.4 + - + +
247H LEU* 5.0 3.1 - - + -
268H HIS* 2.7 42.1 + + - -
271H MET* 3.3 45.9 - - + +
272H LYS* 3.6 25.9 + - - +
275H ASN* 5.1 7.0 - - - -
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Residues in contact with TYR 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220H GLU* 3.2 31.0 - - + -
221H GLU* 3.3 9.5 + - - +
223H TYR* 1.4 89.0 - + - +
225H HIS* 1.3 57.1 + - - +
227H ILE* 3.5 9.2 + - - +
228H TYR 3.2 21.0 + - - -
240H LEU* 3.3 24.2 - - + +
243H ILE* 4.1 4.4 - - + +
244H ARG* 3.9 33.9 - - + -
247H LEU* 3.7 43.1 + - + +
248H GLU* 3.6 27.1 - - - +
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Residues in contact with HIS 225 (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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221H GLU* 2.9 18.7 + - - +
222H THR* 3.7 22.2 - - + +
224H TYR* 1.3 73.0 - - - +
226H HIS* 1.4 66.2 + - - +
228H TYR* 3.0 15.4 + - - +
229H HIS* 3.1 50.6 + + - -
240H LEU* 3.9 14.6 - - + +
390H THR* 3.7 25.2 - - + +
392H ARG* 4.2 21.6 + - - +
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Residues in contact with HIS 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H THR 2.9 21.8 + - - +
223H TYR* 3.4 6.5 + - - +
225H HIS* 1.4 71.4 - - - +
227H ILE* 1.4 56.6 + - - +
229H HIS* 3.6 1.6 + - - +
230H THR* 3.0 48.3 + - + +
267H MET* 4.4 0.9 - - + -
271H MET* 3.5 23.6 - - + +
374H ARG* 4.9 11.1 + - + +
375H LEU* 4.1 22.4 - - + -
378H ASN* 3.3 23.7 + - - -
388H PRO* 5.6 3.1 - - + -
389H ILE 3.3 23.8 + - - -
390H THR* 3.3 26.5 - - + +
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Residues in contact with ILE 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H TYR* 3.4 43.7 + - + +
224H TYR* 3.7 6.3 - - - +
225H HIS 3.3 0.6 - - - -
226H HIS* 1.4 72.6 - - - +
228H TYR* 1.4 66.1 + - - +
229H HIS 3.2 0.2 + - - -
230H THR* 3.3 7.5 + - - +
231H VAL* 3.1 29.8 + - + +
243H ILE* 4.1 16.8 - - + -
247H LEU* 3.9 18.4 - - + -
264H VAL* 4.3 22.9 - - + +
267H MET* 4.1 22.4 - - + -
268H HIS* 4.8 5.8 - - - +
271H MET* 3.8 23.8 - - - -
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Residues in contact with TYR 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H TYR 3.2 5.5 + - - -
225H HIS* 3.0 10.3 + - - +
227H ILE* 1.4 75.1 - - - +
229H HIS* 1.3 90.5 + + - +
231H VAL* 3.5 3.2 - - + +
232H ALA* 3.0 37.7 + - + +
236H ASN 5.4 0.2 - - - -
238H LEU 3.3 26.5 - - - -
239H THR* 4.2 2.0 - - - -
240H LEU* 3.7 44.4 - - + -
243H ILE* 3.6 18.8 - - + +
393H LYS* 3.6 22.8 - - + +
394H GLU* 5.5 0.4 - - - -
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Residues in contact with HIS 229 (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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225H HIS* 3.1 57.6 + + - -
228H TYR* 1.3 96.3 - + - +
230H THR* 1.4 59.0 + - - +
232H ALA* 4.4 2.0 - - - -
233H ILE* 2.9 34.7 + - - +
390H THR* 3.8 10.4 - - + +
391H ILE 3.4 19.3 - - - +
392H ARG* 3.6 19.3 + - + -
393H LYS* 3.1 34.4 + - + -
394H GLU* 3.5 13.9 + - - -
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Residues in contact with THR 230 (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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226H HIS* 3.0 34.4 + - - +
227H ILE* 3.4 13.2 - - - +
229H HIS* 1.4 74.8 - - - +
231H VAL* 1.3 57.3 + - - +
233H ILE* 3.3 10.6 - - - +
234H GLU* 4.3 1.6 + - - -
267H MET* 3.6 36.7 - - + +
371H ARG* 3.7 15.3 + - - +
374H ARG* 2.9 54.2 + - - +
390H THR* 5.4 0.4 - - - +
391H ILE 4.7 1.8 + - - -
501H APC 4.9 0.2 + - - -
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Residues in contact with VAL 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227H ILE* 3.1 26.6 + - + +
228H TYR* 3.5 7.6 - - - +
230H THR* 1.3 76.7 - - - +
232H ALA* 1.4 60.7 + - + +
233H ILE 3.3 0.4 - - - -
234H GLU* 3.0 19.8 + - - -
235H GLY 3.4 1.0 + - - -
236H ASN* 3.2 39.0 + - + +
238H LEU* 5.9 0.2 - - + -
243H ILE* 4.4 5.6 - - + -
263H GLU* 4.1 30.4 - - + +
264H VAL* 4.3 11.4 - - + +
267H MET* 3.8 28.7 - - + -
371H ARG* 4.6 7.0 - - - +
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Residues in contact with ALA 232 (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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228H TYR* 3.0 30.5 + - + +
229H HIS 4.0 2.5 - - - +
231H VAL* 1.4 70.8 - - + +
233H ILE* 1.4 55.2 + - - +
234H GLU 3.1 5.4 - - - -
235H GLY* 2.9 23.0 + - - -
236H ASN 3.7 21.7 + - - +
393H LYS* 3.7 36.0 - - + +
396H ARG* 5.6 0.5 - - - -
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Residues in contact with ILE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229H HIS 2.9 16.1 + - - +
230H THR* 3.3 22.9 - - - +
232H ALA* 1.4 74.4 - - - +
234H GLU* 1.3 55.4 + - - +
235H GLY 3.4 0.2 - - - -
374H ARG* 3.4 25.8 - - - +
391H ILE* 3.7 25.1 - - + +
392H ARG 3.3 27.4 - - - +
393H LYS* 4.6 7.9 - - - +
396H ARG* 3.4 55.5 + - + +
399H TYR* 4.0 13.5 - - + -
400H TYR* 4.3 7.4 + - + -
501H APC 4.9 2.0 - - - +
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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
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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