Contacts of the helix formed by residues 214 - 228 (chain H) in PDB entry 3EXF
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 ARG 214 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H ALA* 6.3 0.8 - - - +
148H TRP* 3.8 6.3 + - - -
172H ASN* 3.6 34.1 - - - +
174H LEU* 3.1 38.6 - - - +
175H MET* 3.9 23.8 - - + +
213H SER* 1.3 84.6 + - - +
215H PRO* 1.3 69.3 - - + +
216H VAL 2.8 7.8 + - - -
217H GLY* 2.9 16.3 + - - -
218H HIS* 3.4 36.5 + - + +
313H ILE* 4.4 18.0 - - - +
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Residues in contact with PRO 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H ASN* 5.7 0.4 - - - +
211H SER* 3.7 11.4 - - - +
212H HIS* 3.4 20.4 - - + +
213H SER* 4.4 2.2 - - - -
214H ARG* 1.3 96.9 - - + +
216H VAL* 1.3 61.6 + - - -
217H GLY 3.2 0.4 - - - -
218H HIS* 3.1 20.7 + - + +
219H CYS* 3.1 24.8 + - - -
262H VAL* 3.8 17.9 - - + +
263H GLU* 4.3 1.1 - - - -
264H GLY* 4.0 24.9 - - - +
314H PRO* 5.0 7.2 - - + -
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Residues in contact with VAL 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H TRP* 3.8 21.8 - - + -
201H GLU* 4.0 14.1 - - + -
211H SER* 3.8 23.6 + - - +
212H HIS 3.8 5.6 - - - -
213H SER 3.0 32.7 + - - +
214H ARG 2.8 5.5 + - - -
215H PRO* 1.3 72.8 - - - +
217H GLY* 1.3 60.6 + - - +
219H CYS* 3.1 6.8 + - - +
220H LEU* 3.0 38.4 + - + +
235H VAL* 4.5 8.7 - - + -
236H ILE 4.9 0.4 - - - +
237H ASN* 3.9 18.6 - - + +
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Residues in contact with GLY 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H TRP* 3.5 27.0 - - - +
214H ARG 2.9 10.8 + - - -
216H VAL* 1.3 76.2 - - - +
218H HIS* 1.3 61.1 + - - +
220H LEU* 3.1 8.2 + - - +
221H GLU* 2.9 30.5 + - - +
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Residues in contact with HIS 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ARG* 3.4 48.1 + - + +
215H PRO* 3.1 23.6 + - + +
217H GLY* 1.3 75.1 - - - +
219H CYS* 1.3 58.5 + - - +
221H GLU* 3.7 23.6 - - - -
222H ALA* 3.0 23.6 + - - +
313H ILE* 4.9 4.7 - - + +
314H PRO* 4.0 18.5 + - - +
315H GLN* 5.8 1.3 - - - -
316H VAL* 3.5 20.8 - - + +
319H ILE* 3.9 15.6 - - + +
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Residues in contact with CYS 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H VAL* 4.0 15.3 - - + -
211H SER* 4.4 8.7 - - - -
215H PRO 3.1 19.1 + - - -
216H VAL 3.1 6.7 + - - +
218H HIS* 1.3 73.4 - - - +
220H LEU* 1.3 58.6 + - - +
221H GLU 3.0 1.6 - - - -
222H ALA* 3.0 6.2 + - - +
223H ALA* 2.7 37.2 + - - +
235H VAL* 3.7 22.8 - - + +
262H VAL* 3.8 33.4 - - - -
319H ILE* 4.0 9.2 - - - -
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Residues in contact with LEU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H TRP* 3.5 35.0 - - + -
201H GLU* 4.1 24.0 - - + +
202H ARG* 4.9 17.5 - - + -
216H VAL* 3.0 30.5 + - + +
217H GLY* 3.2 9.2 - - - +
219H CYS* 1.3 77.9 - - - +
221H GLU* 1.3 63.0 + - - +
223H ALA* 3.2 7.5 + - - +
224H ALA* 3.1 22.0 + - - +
235H VAL* 4.6 8.1 - - + -
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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 GLY 2.9 13.8 + - - +
218H HIS* 3.6 22.4 - - - +
220H LEU* 1.3 76.7 - - - +
222H ALA* 1.3 63.2 + - - +
224H ALA* 3.1 17.3 + - - +
225H VAL* 3.2 18.2 + - + +
316H VAL* 3.5 21.9 - - + +
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Residues in contact with ALA 222 (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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218H HIS 3.0 18.4 + - - +
219H CYS* 3.0 7.2 + - - +
221H GLU* 1.3 76.7 - - - +
223H ALA* 1.3 57.2 + - - +
225H VAL* 3.4 7.4 + - - +
226H LEU* 2.9 33.3 + - - +
316H VAL* 3.9 26.7 - - + +
319H ILE* 4.4 13.7 - - + -
320H ILE* 4.0 14.7 - - + +
323H ILE* 5.4 3.6 - - + -
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Residues in contact with ALA 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ARG* 4.0 27.9 + - - +
219H CYS 2.7 20.9 + - - +
220H LEU 3.3 6.5 - - - +
222H ALA* 1.3 72.7 - - - +
224H ALA* 1.3 59.9 + - - +
226H LEU* 3.7 0.7 - - - +
227H SER* 2.9 31.4 + - - -
231H VAL 4.5 0.7 - - - +
233H CYS* 4.1 28.9 - - + -
235H VAL* 4.1 4.9 - - + -
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Residues in contact with ALA 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ARG* 5.0 3.1 - - - +
220H LEU 3.1 12.5 + - - +
221H GLU* 3.1 11.6 + - - +
223H ALA* 1.3 77.0 - - - +
225H VAL* 1.3 64.6 + - + +
226H LEU 3.4 0.2 + - - -
227H SER* 3.6 9.4 + - - -
228H LYS* 3.3 30.1 + - - +
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Residues in contact with VAL 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H GLU* 3.3 17.5 - - + +
222H ALA* 3.4 11.2 - - - +
224H ALA* 1.3 79.4 - - + +
226H LEU* 1.3 61.8 + - + +
228H LYS* 3.5 20.8 + - - +
229H GLU* 4.2 2.4 + - - +
316H VAL* 4.9 5.8 - - + -
320H ILE* 3.9 22.4 - - + -
324H LYS* 6.3 0.7 - - - +
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Residues in contact with LEU 226 (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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222H ALA 2.9 18.3 + - - +
223H ALA* 3.2 6.5 + - - +
225H VAL* 1.3 78.1 - - + +
227H SER* 1.3 55.7 + - - +
228H LYS 3.0 2.2 - - - -
229H GLU* 2.7 30.8 + - + +
231H VAL* 3.3 37.9 + - + +
233H CYS* 3.8 17.3 - - - -
320H ILE* 4.3 26.9 - - + -
323H ILE* 3.6 42.2 - - + -
324H LYS* 4.6 20.4 - - + +
329H ILE* 6.1 0.2 - - + -
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Residues in contact with SER 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ARG* 2.9 26.4 + - - -
223H ALA 2.9 10.5 + - - -
224H ALA* 3.8 7.9 - - - -
225H VAL 3.5 0.2 - - - -
226H LEU* 1.3 77.2 - - - +
228H LYS* 1.3 57.8 + - - +
229H GLU 3.0 0.4 - - - -
230H GLY* 2.9 17.7 + - - -
231H VAL 3.2 10.9 + - - +
232H GLU* 2.8 22.2 + - - +
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Residues in contact with LYS 228 (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 ALA* 3.3 25.4 - - - +
225H VAL* 3.6 12.8 - - - +
226H LEU 3.0 1.4 - - - -
227H SER* 1.3 76.7 - - - +
229H GLU* 1.3 59.1 + - - +
230H GLY 3.5 0.4 - - - -
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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