Contacts of the helix formed by residues 213 - 224 (chain B) in PDB entry 5DQZ
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 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.6 53.2 - - - +
188B TYR* 5.4 4.3 - - + -
192B GLU* 4.0 17.0 - - - +
202B PRO* 3.3 11.0 - - + -
211B LYS* 3.1 2.4 - - - +
212B PRO* 1.3 92.2 - - + +
214B SER* 1.3 59.4 + - - +
216B VAL* 3.1 21.7 + - + -
217B TYR* 2.8 62.0 + - + +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PRO 3.2 2.4 + - - -
203B ALA 3.4 14.6 + - - -
205B GLY* 3.6 7.6 - - - -
208B HIS* 3.3 21.3 - - - +
209B THR* 3.5 9.5 + - - -
211B LYS* 2.8 37.0 + - - +
213B LEU* 1.3 76.0 - - - +
215B PHE* 1.3 58.6 + - - +
217B TYR* 3.1 16.2 + - - +
218B ASP* 2.9 29.8 + - - +
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 3.4 19.3 - - - -
119B MET* 4.3 6.7 - - + -
195B ILE* 3.5 30.5 - - + -
200B TYR* 4.2 11.2 - + + -
201B ALA 3.8 3.4 - - - +
202B PRO 2.9 16.4 + - - +
204B ILE 3.3 21.5 - - - +
205B GLY* 3.8 3.5 - - - -
206B PHE* 3.8 25.6 - + - -
214B SER* 1.3 72.8 - - - +
216B VAL* 1.3 65.9 + - - +
218B ASP* 3.2 7.0 + - + +
219B ILE* 3.0 55.5 + - + +
268B ILE* 4.0 24.2 - - + -
271B VAL* 5.0 0.2 - - + -
272B LEU* 4.1 16.4 - - + -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.9 42.2 - - + +
191B THR* 3.9 9.4 - - + +
192B GLU* 4.1 17.5 - - + +
195B ILE* 3.6 15.9 - - + -
202B PRO* 3.7 28.9 - - + -
213B LEU* 3.2 23.8 - - + +
215B PHE* 1.3 77.7 - - - +
217B TYR* 1.3 58.0 + - + +
220B ALA* 2.9 34.4 + - - +
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.7 41.5 - + - +
208B HIS* 3.6 32.3 - + + +
211B LYS* 4.3 19.7 - - + +
212B PRO* 6.0 1.2 - - - +
213B LEU* 2.8 53.5 + - + +
214B SER* 3.1 11.9 + - - +
216B VAL* 1.3 77.5 - - + +
218B ASP* 1.3 56.8 + - - +
221B ASP* 2.9 41.8 + - - +
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B MET* 3.8 22.4 - - + +
205B GLY* 3.6 3.8 - - - -
206B PHE* 2.7 36.0 + - - +
207B VAL* 3.1 15.3 + - - +
208B HIS* 2.9 33.7 + - - -
214B SER 2.9 13.4 + - - +
215B PHE* 3.2 10.9 + - + +
217B TYR* 1.3 76.6 - - - +
219B ILE* 1.3 64.5 + - - +
221B ASP* 3.2 5.4 + - - +
222B ILE* 3.1 27.2 + - - +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B MET* 4.9 1.6 - - + -
191B THR* 3.8 20.0 - - + -
195B ILE* 4.2 5.4 - - + -
215B PHE* 3.0 49.1 + - + +
218B ASP* 1.3 80.6 - - - +
220B ALA* 1.3 64.6 + - - +
222B ILE* 3.1 34.6 + - + +
223B ILE* 3.8 6.4 + - - +
264B LEU* 4.0 11.7 - - + -
267B LEU* 3.8 19.8 - - + +
268B ILE* 3.8 29.2 - - + -
271B VAL* 4.5 9.9 - - + -
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.6 19.5 - - + +
188B TYR* 3.4 32.8 - - + -
191B THR* 4.0 10.9 - - - +
216B VAL 2.9 20.8 + - - +
217B TYR 4.1 0.2 - - - +
219B ILE* 1.3 79.3 - - - +
221B ASP* 1.3 56.5 + - - +
223B ILE* 3.1 6.1 + - - +
224B LYS* 2.9 30.8 + - - +
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 3.1 42.1 + - - +
141B GLU* 3.9 9.2 - - - +
188B TYR* 3.9 9.2 + - - -
208B HIS* 3.2 25.7 + - + -
217B TYR* 2.9 25.4 + - - +
218B ASP* 3.2 6.0 + - - +
220B ALA* 1.3 77.0 - - - +
222B ILE* 1.3 62.4 + - - +
223B ILE 3.4 0.3 + - - -
224B LYS* 3.3 39.2 + - - +
225B PHE* 4.7 2.1 + - - -
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B MET* 3.8 42.0 - - + +
122B LEU* 4.1 23.1 - - + +
123B ARG* 3.7 28.2 - - + +
218B ASP 3.1 14.8 + - - +
219B ILE* 3.3 21.1 - - + +
220B ALA 3.1 0.6 - - - -
221B ASP* 1.3 79.1 - - - +
223B ILE* 1.3 69.2 + - + +
225B PHE 5.4 0.3 + - - -
226B ASP* 3.8 12.0 - - - +
267B LEU* 4.4 13.5 - - + -
271B VAL* 3.9 20.6 - - + -
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 4.0 24.2 - - + -
191B THR* 5.3 0.9 - - - +
219B ILE 4.1 5.8 - - - +
220B ALA* 3.7 8.1 - - - +
222B ILE* 1.3 90.1 - - + +
224B LYS* 1.3 66.4 + - - +
225B PHE 3.3 2.7 - - - -
226B ASP* 3.1 17.3 + - + +
227B THR* 2.8 38.0 + - - +
260B THR* 4.2 21.1 - - + +
264B LEU* 4.3 17.7 - - + -
267B LEU* 4.3 16.4 - - + -
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 5.3 0.4 - - - +
149B TYR* 5.0 5.9 + - - -
180B ILE* 6.2 0.2 - - + -
184B THR* 4.2 28.2 + - + +
187B LEU* 3.7 15.0 - - + -
188B TYR* 3.8 13.2 + - + +
220B ALA 2.9 16.0 + - - +
221B ASP* 3.3 32.2 + - - +
222B ILE 3.7 1.6 - - - -
223B ILE* 1.3 76.5 - - - +
225B PHE* 1.3 83.6 + - + +
227B THR 3.3 0.3 + - - -
228B VAL* 3.0 31.8 + - + -
229B VAL* 3.3 28.6 + - + -
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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