Contacts of the helix formed by residues 224 - 235 (chain H) in PDB entry 1R4N
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 224 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329G ILE 5.9 0.4 - - - +
331G ASP* 3.7 31.9 - - + +
339G TYR* 4.4 13.7 - - + +
343G GLN* 5.1 5.4 - - - +
213H PHE* 5.7 2.9 - - + -
223H ARG* 1.3 87.6 - - + +
225H PRO* 1.3 77.0 - - + +
226H GLU* 3.8 19.7 - - + +
227H HIS* 2.8 49.9 + - + +
228H CYS 3.5 3.1 + - - -
273H ILE* 3.7 7.6 - - - +
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Residues in contact with PRO 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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224H LEU* 1.3 85.5 - - + +
226H GLU* 1.3 72.4 + - - +
228H CYS* 3.1 15.2 + - + +
229H ILE* 3.2 18.9 + - - +
273H ILE* 3.6 9.6 - - + -
274H ARG 3.2 27.6 - - - +
275H GLY* 3.2 30.7 - - - +
276H VAL* 3.7 14.8 - - + +
280H LEU* 3.7 10.1 - - + -
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Residues in contact with GLU 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H PHE* 3.8 25.4 - - + -
224H LEU* 3.8 15.8 - - + +
225H PRO* 1.3 98.6 - - - +
227H HIS* 1.3 58.5 + - + +
228H CYS 3.1 0.5 + - - -
229H ILE* 3.2 2.1 + - - +
230H GLU* 2.8 32.4 + - - +
280H LEU* 3.9 16.7 - - + +
284H VAL* 4.2 24.8 - - + +
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Residues in contact with HIS 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G ASP* 3.7 7.7 + - - -
213H PHE* 3.5 40.5 - + + -
214H PRO* 6.3 0.4 - - - +
217H THR* 4.8 9.0 + - - -
218H ILE* 3.7 16.1 - - + +
221H MET 4.7 0.2 + - - -
222H PRO* 4.0 18.9 - - + +
223H ARG* 3.2 44.6 + - - -
224H LEU* 2.8 45.3 + - + +
226H GLU* 1.3 72.0 - - - +
228H CYS* 1.3 62.9 + - - +
230H GLU* 4.2 4.7 - - - -
231H TYR* 3.5 17.7 + - - +
267H ARG* 3.9 3.4 + - - -
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Residues in contact with CYS 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H PRO* 4.6 4.9 - - - -
224H LEU 3.5 2.2 + - - -
225H PRO* 3.1 10.0 + - - +
226H GLU 3.1 0.6 - - - -
227H HIS* 1.3 76.2 - - - +
229H ILE* 1.3 69.5 + - - +
231H TYR* 2.9 12.8 + - - +
232H VAL* 3.0 14.8 + - - +
264H SER* 3.8 20.0 - - - +
267H ARG* 3.9 19.2 + - + +
268H ALA* 3.3 36.1 - - + +
271H TYR* 5.7 0.4 - - - -
273H ILE* 4.1 24.5 - - - -
276H VAL* 4.8 0.9 - - + -
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Residues in contact with ILE 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H PRO 3.2 12.7 + - - +
226H GLU 3.7 4.5 - - - +
228H CYS* 1.3 74.4 - - - +
230H GLU* 1.3 54.1 + - - +
231H TYR 2.6 12.6 + - - -
232H VAL* 2.7 14.9 + - - +
233H ARG* 3.0 9.7 + - + +
260H ILE* 4.2 1.6 - - + -
264H SER* 3.0 27.1 + - - +
276H VAL* 4.5 8.3 - - + -
280H LEU* 3.6 14.8 - - + +
281H THR* 3.3 52.3 - - + +
284H VAL* 3.4 37.2 - - + -
285H VAL* 4.1 9.2 - - + -
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Residues in contact with GLU 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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212H ASN* 5.4 1.9 + - - -
213H PHE* 3.8 23.1 + - + +
218H ILE* 3.8 26.3 - - + +
226H GLU 2.8 19.6 + - - +
227H HIS* 4.3 4.3 - - - +
229H ILE* 1.3 74.0 - - - +
231H TYR* 1.3 56.5 + - - +
233H ARG* 2.9 32.4 + - - -
234H MET* 2.9 42.6 + - + +
284H VAL* 3.7 9.5 - - + +
287H ARG* 2.9 32.5 + - - -
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Residues in contact with TYR 231 (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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448C TYR* 4.9 7.8 + - - -
218H ILE* 3.4 23.6 - - - +
219H ALA* 4.4 7.9 - - + -
227H HIS 3.5 7.8 + - - +
228H CYS 2.9 4.8 + - - +
229H ILE 2.6 4.9 + - - -
230H GLU* 1.3 72.0 - - - +
232H VAL* 1.3 71.4 + - + +
233H ARG 2.6 15.4 + - - -
234H MET* 5.0 0.2 - - - -
235H LEU* 2.9 51.0 + - + +
236H GLN* 3.2 36.6 + - + +
267H ARG* 2.9 53.7 + - - +
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Residues in contact with VAL 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 CYS 3.0 4.7 + - - +
229H ILE 2.7 5.7 + - - +
231H TYR* 1.3 79.5 - - + +
233H ARG* 1.3 55.8 + - - +
236H GLN* 3.6 23.8 - - - +
237H TRP* 3.6 19.6 + - - +
259H TRP* 4.0 9.0 - - + -
260H ILE* 3.5 28.3 - - + +
263H LYS* 3.3 33.9 - - + +
264H SER* 3.3 37.7 - - - +
267H ARG* 4.5 2.5 - - + -
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Residues in contact with ARG 233 (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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229H ILE 3.0 11.2 + - - +
230H GLU* 2.9 31.9 + - - +
231H TYR 2.6 5.9 + - - -
232H VAL* 1.3 76.2 - - - +
234H MET* 1.3 90.2 + - - +
235H LEU 3.1 2.6 + - - -
237H TRP* 3.9 3.1 - - - +
238H PRO* 3.3 19.9 - - - +
249H LEU* 3.7 27.7 - - + +
260H ILE* 4.7 3.4 - - + -
284H VAL* 4.6 1.6 - - - -
285H VAL* 3.9 43.8 + - + +
287H ARG* 4.4 17.2 - - - +
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Residues in contact with MET 234 (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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212H ASN* 5.5 7.2 - - - +
213H PHE 5.6 3.4 - - - +
215H MET* 5.2 14.1 - - - +
218H ILE* 4.3 21.8 - - + -
230H GLU* 2.9 47.5 + - + +
231H TYR* 5.0 0.2 - - - -
233H ARG* 1.3 90.8 - - - +
235H LEU* 1.3 74.5 + - + +
238H PRO* 4.0 10.3 - - - +
287H ARG* 5.0 3.6 - - - +
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Residues in contact with LEU 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H MET* 4.4 28.5 - - + -
218H ILE* 5.0 6.5 - - + -
219H ALA* 4.4 15.3 - - + -
231H TYR* 2.9 39.4 + - + +
233H ARG 3.1 1.0 + - - -
234H MET* 1.3 95.3 - - + +
236H GLN* 1.3 66.0 + - - +
237H TRP 3.2 2.0 - - - -
238H PRO* 3.0 14.2 - - + +
239H LYS* 3.1 17.1 + - - +
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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
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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