Contacts of the helix formed by residues 211 - 225 (chain B) in PDB entry 6CP3
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 LYS 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLN* 1.3 80.4 - - - +
212B ARG* 1.3 66.3 + - - +
213B SER* 4.1 11.8 + - - +
214B THR* 3.6 24.5 + - - +
215B VAL* 3.4 21.8 + - - +
237B THR* 3.6 1.0 - - - +
152E LYS* 3.4 26.1 - - - +
294E GLU* 3.2 20.6 - - - +
327E ALA 4.5 6.5 - - - +
328E HIS* 2.7 52.7 + - + +
329E LEU 4.7 0.2 - - - -
330E ASP* 3.0 29.5 + - - -
356E ARG* 5.7 3.9 - - - +
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Residues in contact with ARG 212 (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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117B ILE* 4.2 22.0 - - - +
210B GLN 3.9 0.6 + - - -
211B LYS* 1.3 71.4 - - - +
213B SER* 1.3 58.3 + - - +
215B VAL* 3.1 3.6 + - - -
216B ALA* 2.9 23.0 + - - +
235B ALA* 5.9 1.4 - - - +
237B THR* 3.2 35.8 + - - +
239B SER* 3.5 16.9 + - - +
240B GLU* 3.1 28.9 + - - +
121E PRO* 4.8 10.3 + - + +
122E PRO 3.9 17.8 + - - +
123E SER* 5.1 3.8 - - - +
124E PHE* 3.6 28.2 - - - +
127E GLN* 3.5 30.3 - - + +
294E GLU* 2.8 31.0 + - + +
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Residues in contact with SER 213 (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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211B LYS* 3.3 15.3 + - - +
212B ARG* 1.3 76.2 - - - +
214B THR* 1.3 63.5 + - - +
216B ALA* 3.5 8.0 - - - +
217B GLN* 2.9 41.1 + - - +
127E GLN* 3.8 16.4 - - - -
128E SER 5.0 9.2 - - - -
152E LYS* 4.8 6.4 + - - -
294E GLU* 4.4 0.8 + - - -
297E THR* 4.1 8.5 - - - -
330E ASP* 5.6 1.4 + - - -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 6.6 0.2 - - + -
210B GLN* 4.1 21.5 - - + +
211B LYS* 3.6 38.2 + - - +
212B ARG 3.2 0.6 - - - -
213B SER* 1.3 79.9 + - - +
215B VAL* 1.3 56.2 + - - +
217B GLN* 3.3 11.1 + - - +
218B LEU* 2.9 33.8 + - + +
600B ATP 5.6 3.8 - - - +
356E ARG* 5.0 14.9 + - - +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 5.8 1.3 - - + -
207B ALA* 3.7 27.4 - - + -
210B GLN* 4.1 9.6 - - + +
211B LYS 3.4 15.0 + - - +
212B ARG 3.1 7.2 + - - +
214B THR* 1.3 76.4 - - - +
216B ALA* 1.3 56.7 + - - +
218B LEU* 3.8 8.8 - - + +
219B VAL* 2.9 29.6 + - + +
233B ILE* 4.0 25.8 - - + -
235B ALA* 4.1 11.0 - - + -
237B THR* 4.0 12.8 - - + -
124E PHE* 3.5 19.3 - - + -
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Residues in contact with ALA 216 (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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212B ARG 2.9 13.2 + - - +
213B SER* 3.5 9.2 - - - +
214B THR 3.2 0.2 - - - -
215B VAL* 1.3 78.2 - - - +
217B GLN* 1.3 57.4 + - - +
219B VAL* 3.3 4.0 + - - +
220B GLN* 3.0 26.7 + - - +
124E PHE* 3.3 15.4 - - + +
127E GLN* 3.8 34.3 - - + +
128E SER 4.5 3.4 - - - +
129E THR* 4.1 14.7 - - + +
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Residues in contact with GLN 217 (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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213B SER* 2.9 28.0 + - - +
214B THR* 3.8 8.5 - - - +
216B ALA* 1.3 76.1 - - - +
218B LEU* 1.3 57.5 + - - +
220B GLN* 3.3 8.1 + - - +
221B THR* 2.8 33.4 + - - +
128E SER 4.8 4.3 + - - +
129E THR 4.2 17.9 - - - +
130E SER* 4.8 1.1 - - - +
131E ALA* 3.3 36.1 - - - +
357E LEU* 5.5 6.7 - - - +
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Residues in contact with LEU 218 (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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178B THR* 4.5 11.2 - - + -
182B LEU* 4.2 25.6 - - + -
205B TYR* 3.6 50.3 - - + +
210B GLN* 5.5 1.1 - - - +
214B THR* 2.9 24.4 + - + +
215B VAL* 3.8 8.5 - - + +
216B ALA 3.2 0.2 - - - -
217B GLN* 1.3 75.4 - - - +
219B VAL* 1.3 60.6 + - + +
221B THR* 3.3 6.1 + - - -
222B LEU* 2.9 49.2 + - + +
233B ILE* 4.2 6.7 - - + -
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Residues in contact with VAL 219 (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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109B VAL* 3.8 29.2 - - + -
215B VAL* 2.9 23.0 + - + +
216B ALA* 3.7 4.5 - - - +
218B LEU* 1.3 79.2 - - + +
220B GLN* 1.3 55.6 + - - +
222B LEU* 3.3 2.4 + - - -
223B GLU* 2.9 39.1 + - - +
228B MET* 3.8 19.6 - - + +
233B ILE* 4.1 16.4 - - + -
124E PHE* 3.9 15.3 - - + -
129E THR* 6.6 0.2 - - + -
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Residues in contact with GLN 220 (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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216B ALA 3.0 15.8 + - - +
217B GLN* 3.6 4.5 - - - +
219B VAL* 1.3 77.9 - - - +
221B THR* 1.3 55.8 + - - +
223B GLU* 3.3 14.8 + - - +
224B GLN* 2.9 52.9 + - - +
129E THR* 3.3 47.2 + - - +
130E SER* 5.5 2.7 - - - -
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Residues in contact with THR 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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182B LEU* 4.1 14.1 - - + -
186B LEU* 4.8 3.1 - - + -
217B GLN* 2.8 22.7 + - - +
218B LEU* 3.6 8.6 - - - -
219B VAL 3.2 0.2 - - - -
220B GLN* 1.3 77.3 - - - +
222B LEU* 1.3 62.7 + - - +
223B GLU 3.1 0.2 - - - -
224B GLN* 3.1 19.3 + - - +
225B HIS* 3.3 25.4 + - + +
435B TYR* 3.6 41.1 + - + +
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Residues in contact with LEU 222 (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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182B LEU* 3.7 24.7 - - + -
185B ILE* 4.1 18.6 - - + -
186B LEU* 3.7 16.8 - - + -
205B TYR* 5.3 0.7 - - + -
218B LEU* 2.9 37.8 + - + +
219B VAL 3.3 0.9 + - - -
221B THR* 1.3 76.4 - - - +
223B GLU* 1.3 58.1 + - - +
225B HIS 5.0 0.2 - - - +
226B ASP 4.3 0.7 - - - -
227B ALA* 2.8 47.7 + - + +
228B MET* 3.2 22.9 + - + +
231B SER* 4.0 19.7 - - - +
233B ILE* 4.5 10.1 - - + -
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Residues in contact with GLU 223 (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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120B LYS* 3.4 24.9 + - - -
219B VAL* 2.9 25.3 + - - +
220B GLN* 4.0 16.8 + - - +
221B THR 3.1 0.2 - - - -
222B LEU* 1.3 77.2 - - - +
224B GLN* 1.3 64.7 + - - +
226B ASP* 3.8 10.0 + - - +
228B MET* 3.8 29.5 - - + +
159Z ARG* 4.2 18.3 + - - -
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Residues in contact with GLN 224 (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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220B GLN* 2.9 37.9 + - - +
221B THR* 3.1 13.1 + - - +
223B GLU* 1.3 80.1 - - - +
225B HIS* 1.3 76.6 + - + +
226B ASP* 3.2 5.8 + - - +
435B TYR* 6.1 0.7 - - - -
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Residues in contact with HIS 225 (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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186B LEU* 3.7 38.7 - - + +
189B LYS* 3.4 32.3 + - - +
221B THR* 3.3 22.9 + - + +
224B GLN* 1.3 91.8 + - + +
226B ASP* 1.3 71.6 + - - +
227B ALA 3.6 0.9 - - - -
435B TYR* 3.8 37.9 + + + +
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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