Contacts of the helix formed by residues 211 - 222 (chain H) in PDB entry 6CAJ
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 GLY 211 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181G ALA* 3.8 19.9 - - - +
128H HIS* 3.3 25.1 + - - -
180H ASP* 5.6 0.9 - - - -
183H VAL* 5.8 0.5 - - - +
209H LYS* 2.9 2.6 + - - +
210H ILE* 1.3 79.9 - - - +
212H THR* 1.3 59.8 + - - +
213H ASN 3.5 0.7 - - - -
214H GLN* 3.7 17.0 + - - +
215H MET* 3.6 17.8 - - - +
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Residues in contact with THR 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H HIS* 3.9 10.1 + - - -
195H VAL* 4.4 4.0 - - + -
206H ILE* 3.8 15.3 - - + -
208H ASN* 3.4 23.2 + - + +
209H LYS 2.8 17.0 + - - -
211H GLY* 1.3 76.8 - - - +
213H ASN* 1.3 59.9 + - - +
215H MET* 3.4 5.3 + - - +
216H ALA* 2.9 27.9 + - - +
226H PHE* 3.7 24.0 - - + -
274H ASP* 3.0 12.5 + - - -
276H THR* 3.4 16.8 - - - +
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Residues in contact with ASN 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G GLY* 3.5 20.7 - - - +
185G TYR 5.2 0.2 - - - +
218G CYS* 5.4 0.2 - - - -
210H ILE 4.6 2.0 - - - +
211H GLY 3.5 0.4 - - - -
212H THR* 1.3 73.2 - - - +
214H GLN* 1.3 57.3 + - - +
216H ALA* 3.3 1.8 + - - +
217H VAL* 2.9 42.5 + - - +
243H GLN* 3.3 19.6 + - - +
274H ASP* 2.6 24.0 + - + +
275H TYR 2.9 25.9 + - - +
276H THR* 4.0 7.6 + - - +
277H ALA 5.1 0.4 - - - +
280H LEU* 4.1 13.1 - - - +
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Residues in contact with GLN 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G ASP 4.0 3.2 + - - +
181G ALA* 3.5 36.8 - - - +
183G VAL* 3.3 17.4 - - + +
184G GLY* 4.7 4.8 - - - +
214G GLN* 2.9 38.1 + - + +
218G CYS* 4.0 24.2 - - - -
153H THR* 5.9 0.2 - - - +
180H ASP* 4.0 15.2 + - - -
183H VAL* 4.2 8.6 - - + +
210H ILE 5.1 0.6 + - - -
211H GLY* 3.7 17.0 + - - +
213H ASN* 1.3 79.0 - - - +
215H MET* 1.3 59.7 + - - +
217H VAL* 3.9 0.7 - - - +
218H CYS* 2.9 36.7 + - - -
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Residues in contact with MET 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU* 3.7 28.7 - - + -
127H THR 4.6 4.0 - - - +
128H HIS* 4.0 21.3 - - - +
153H THR* 3.4 27.4 - - + +
183H VAL* 3.8 19.7 - - + -
187H MET* 3.4 8.7 - - + +
193H VAL* 3.7 14.8 - - + -
195H VAL* 3.7 29.4 - - - -
211H GLY 3.6 12.6 - - - +
212H THR* 3.4 6.4 + - - +
213H ASN 3.2 0.2 - - - -
214H GLN* 1.3 82.0 - - - +
216H ALA* 1.3 56.1 + - - +
219H ALA* 2.9 30.0 + - - +
226H PHE* 4.8 1.6 - - + -
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Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H THR 2.9 17.0 + - - +
213H ASN 3.8 3.8 - - - +
215H MET* 1.3 74.8 - - - +
217H VAL* 1.3 59.4 + - - +
219H ALA* 3.3 3.4 + - - +
220H LYS* 2.9 29.1 + - - +
226H PHE* 4.3 23.0 - - + -
276H THR* 3.7 27.4 - - + -
280H LEU* 4.0 19.3 - - + +
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Residues in contact with VAL 217 (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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217G VAL* 3.7 22.0 - - + +
218G CYS* 4.1 17.9 - - + -
221G ALA* 3.8 28.0 - - + -
213H ASN* 2.9 36.0 + - - +
214H GLN 3.9 3.4 - - - +
216H ALA* 1.3 77.3 - - - +
218H CYS* 1.3 56.7 + - - +
220H LYS* 3.3 6.7 + - - +
221H ALA* 2.9 27.9 + - + +
280H LEU* 3.9 15.3 - - + -
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Residues in contact with CYS 218 (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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214G GLN* 4.0 31.4 - - - -
217G VAL* 4.1 21.1 - - + -
218G CYS* 5.4 0.7 - - - -
183H VAL* 4.3 6.3 - - - +
184H GLY* 4.1 17.3 - - - -
187H MET* 3.3 30.9 - - + +
214H GLN* 2.9 26.1 + - - +
215H MET* 4.7 0.2 - - - -
217H VAL* 1.3 77.5 - - - +
219H ALA* 1.3 57.2 + - - +
221H ALA* 4.0 1.0 - - - +
222H GLN* 3.1 24.1 + - + +
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Residues in contact with ALA 219 (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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187H MET* 3.7 20.6 - - + +
193H VAL* 4.1 11.9 - - + -
215H MET 2.9 18.6 + - - +
216H ALA* 3.7 7.0 - - - +
217H VAL 3.2 0.2 - - - -
218H CYS* 1.3 76.2 - - - +
220H LYS* 1.3 59.1 + - - +
222H GLN 3.4 0.2 - - - -
223H ASN 2.8 6.2 + - - -
224H LYS* 2.6 48.9 + - + +
226H PHE* 4.7 7.9 - - + -
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Residues in contact with LYS 220 (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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319D GLU* 5.5 11.7 + - - +
216H ALA 2.9 17.2 + - - +
217H VAL* 3.8 4.0 - - - +
219H ALA* 1.3 75.7 - - - +
221H ALA* 1.3 63.6 + - - +
223H ASN* 3.2 22.8 + - - +
224H LYS 5.0 4.3 + - - -
279H SER 3.2 27.6 + - - -
280H LEU* 3.7 33.1 - - + +
281H ILE 5.8 1.0 + - - -
282H THR* 5.5 5.5 + - - -
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Residues in contact with ALA 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E ASN* 4.2 4.9 - - - +
217G VAL* 3.8 24.9 - - + -
217H VAL* 2.9 17.2 + - + +
218H CYS* 4.1 3.4 - - - +
220H LYS* 1.3 77.2 - - - +
222H GLN* 1.3 70.7 + - + +
223H ASN* 3.4 5.4 + - - +
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Residues in contact with GLN 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E ASN* 2.4 50.6 + - - +
184H GLY 6.1 0.4 - - - +
187H MET* 3.8 24.5 - - + -
188H GLU* 3.9 26.6 + - - +
218H CYS* 3.1 20.2 + - + +
221H ALA* 1.3 87.1 - - + +
223H ASN* 1.3 66.7 + - - +
224H LYS* 3.1 15.9 + - + +
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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