Contacts of the helix formed by residues 197 - 214 (chain B) in PDB entry 3CRK
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 VAL 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B CYS* 3.3 3.1 + - - +
196B SER* 1.3 70.8 - - - +
198B SER* 1.3 57.9 + - - +
200B VAL* 3.1 4.3 + - - +
201B VAL* 2.9 33.5 + - + +
236B ILE* 3.4 18.2 + - + +
238B MET* 4.0 34.5 - - + -
245B LEU* 4.4 14.3 - - + +
277B VAL* 3.7 32.1 - - + -
284B LEU* 4.1 14.1 - - + -
286B ILE* 3.8 24.5 - - + -
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Residues in contact with SER 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 3.3 5.8 + - - -
197B VAL* 1.3 79.7 - - - +
199B ASP* 1.3 57.4 + - - +
201B VAL* 3.3 10.2 + - - +
202B LYS* 2.9 57.2 + - - +
224B ILE* 4.4 12.3 - - - +
226B GLU* 3.3 25.6 + - - -
236B ILE 4.7 0.6 + - - -
277B VAL* 5.3 2.7 - - - -
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Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 3.2 31.6 + - - +
198B SER* 1.3 81.4 + - - +
200B VAL* 1.3 58.0 + - + +
202B LYS* 3.4 16.9 + - - +
203B ASP* 3.0 40.2 + - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B CYS* 3.7 22.9 - - - -
196B SER 3.2 14.8 + - - +
197B VAL 3.1 6.8 + - - +
199B ASP* 1.3 75.1 - - + +
201B VAL* 1.3 65.0 + - - +
203B ASP* 3.4 7.4 + - - +
204B ALA* 3.0 23.7 + - - +
242B PRO* 4.0 15.7 - - + +
245B LEU* 3.9 18.4 - - + -
246B TYR* 3.6 38.3 - - + +
249B LEU* 4.1 2.7 - - + -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 2.9 31.9 + - + +
198B SER* 3.5 11.0 - - - +
200B VAL* 1.3 77.2 - - - +
202B LYS* 1.3 55.6 + - - +
205B TYR* 3.0 24.8 + - - +
222B LEU* 4.6 1.1 - - + -
224B ILE* 4.1 13.7 - - + -
249B LEU* 3.7 26.2 - - + +
253B PHE* 3.3 27.2 - - + -
275B ILE* 3.8 31.6 - - + -
277B VAL* 4.5 2.5 - - + -
286B ILE* 4.5 4.0 - - + -
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 2.9 38.8 + - - +
199B ASP* 3.4 16.6 + - - +
200B VAL 3.3 0.2 - - - -
201B VAL* 1.3 73.0 - - - +
203B ASP* 1.3 58.4 + - - +
205B TYR* 3.3 6.1 + - - +
206B ASP* 2.8 47.4 + - - +
222B LEU* 4.6 6.1 - - + -
224B ILE* 3.7 22.4 - - + -
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP* 3.0 26.0 + - - +
200B VAL* 3.7 8.2 - - - +
201B VAL 3.4 0.2 - - - -
202B LYS* 1.3 78.5 - - - +
204B ALA* 1.3 61.3 + - - +
206B ASP* 3.7 8.9 - - - +
207B MET* 3.2 29.7 + - + +
246B TYR* 3.9 13.7 - - + -
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Residues in contact with ALA 204 (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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200B VAL 3.0 17.9 + - - +
201B VAL 3.8 2.9 - - - +
203B ASP* 1.3 75.6 - - - +
205B TYR* 1.3 61.9 + - - +
207B MET 3.5 0.9 + - - -
208B ALA* 3.1 24.6 + - - +
246B TYR* 3.6 21.5 - - + -
249B LEU* 3.6 28.3 - - + -
250B PHE* 3.7 18.2 - - - +
253B PHE* 3.8 5.5 - - + -
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Residues in contact with TYR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL 3.0 17.5 + - - +
202B LYS* 3.3 3.3 + - - +
204B ALA* 1.3 75.2 - - - +
206B ASP* 1.3 70.1 + - - +
208B ALA* 3.2 0.7 + - - -
209B LYS* 2.7 74.5 + - + +
220B PRO 2.7 25.7 + - - -
221B ASP* 3.3 10.1 - - - -
222B LEU* 3.6 41.2 + - + -
253B PHE* 3.5 27.5 - + + -
257B MET* 3.4 26.6 - - + +
273B ILE* 4.7 3.1 - - + -
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LYS* 2.8 31.5 + - - +
203B ASP* 3.4 10.1 + - - +
205B TYR* 1.3 88.9 - - - +
207B MET* 1.3 64.1 + - + +
209B LYS* 3.8 7.0 - - - +
210B LEU* 3.2 26.6 + - - +
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Residues in contact with MET 207 (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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203B ASP 3.2 15.0 + - - +
204B ALA 3.9 1.3 - - - +
206B ASP* 1.3 78.7 - - + +
208B ALA* 1.3 64.5 + - - +
210B LEU* 3.4 24.6 - - + +
211B LEU* 3.2 29.8 + - + +
246B TYR* 3.1 31.0 - - + +
250B PHE* 3.7 13.7 - - + -
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA 3.1 17.9 + - - +
205B TYR 3.9 1.1 - - - +
207B MET* 1.3 73.2 - - - +
209B LYS* 1.3 56.0 + - - +
211B LEU* 3.1 5.4 + - - +
212B CYS* 2.8 34.7 + - - +
250B PHE* 3.6 10.7 - - + -
253B PHE* 3.7 19.5 - - + -
254B LYS* 3.9 22.1 - - + +
257B MET* 3.5 17.7 - - - +
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 2.7 61.1 + - + +
206B ASP* 3.8 8.5 - - - +
208B ALA* 1.3 70.8 - - - +
210B LEU* 1.3 53.4 + - + +
212B CYS* 3.1 2.6 + - - +
213B ASP* 2.8 49.5 + - - +
219B SER* 3.5 26.7 + - - +
220B PRO 4.0 2.6 + - - -
221B ASP* 4.0 13.3 + - - -
257B MET* 3.5 16.5 - - + +
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Residues in contact with LEU 210 (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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206B ASP 3.2 14.5 + - - +
207B MET* 3.4 31.4 - - + +
209B LYS* 1.3 80.3 - - + +
211B LEU* 1.3 61.3 + - + +
213B ASP* 3.0 26.0 + - - +
214B LYS* 3.0 24.9 - - + +
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Residues in contact with LEU 211 (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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207B MET* 3.2 14.1 + - + +
208B ALA* 3.1 7.2 + - - +
210B LEU* 1.3 80.3 - - + +
212B CYS* 1.3 59.6 + - - +
214B LYS* 3.8 3.5 - - - +
215B TYR* 3.2 29.3 + - - +
250B PHE* 3.5 33.7 - - + -
254B LYS* 4.0 19.1 - - + +
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Residues in contact with CYS 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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208B ALA 2.8 16.2 + - - +
209B LYS* 3.1 4.9 + - - +
211B LEU* 1.3 74.7 - - - +
213B ASP* 1.3 57.4 + - - +
214B LYS 3.1 4.3 - - - -
215B TYR* 3.1 1.6 + - - -
216B TYR* 2.8 57.2 + - - +
218B ALA 3.4 18.6 - - - -
219B SER* 4.1 7.9 - - - -
257B MET* 3.7 33.7 - - + -
258B ARG 4.9 0.2 - - - -
261B VAL* 3.9 10.1 - - - -
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Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 2.8 48.3 + - - +
210B LEU* 3.0 26.4 + - - +
212B CYS* 1.3 72.7 - - - +
214B LYS* 1.3 69.5 + - - +
215B TYR 3.5 0.4 - - - -
217B MET* 3.3 32.1 - - - +
218B ALA* 4.1 10.3 - - - +
219B SER* 4.1 14.2 + - - +
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Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.0 30.6 + - + +
211B LEU* 3.7 4.5 + - - +
212B CYS 3.1 1.0 - - - -
213B ASP* 1.3 89.5 + - - +
215B TYR* 1.3 59.0 + - - +
217B MET* 4.9 12.3 - - - +
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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
------------------------------------------------------------
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