Contacts of the helix formed by residues 206 - 220 (chain B) in PDB entry 5CYO
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 ASP 206 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASP* 3.6 0.9 - - - +
205B GLU* 1.3 83.8 + - - +
207B SER* 1.3 57.4 + - - +
208B GLU* 3.1 12.2 + - - +
209B ASP* 2.5 40.0 + - - +
210B ARG* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP* 1.3 72.3 - - - +
208B GLU* 1.3 60.4 + - - +
210B ARG* 3.3 19.7 + - - +
211B LEU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP* 3.1 10.6 + - - +
207B SER* 1.3 75.1 - - - +
209B ASP* 1.3 66.6 + - - +
211B LEU* 3.3 7.6 + - - +
212B VAL* 3.2 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE 4.3 3.3 - - - +
204B ASP* 4.2 0.9 - - - -
205B GLU* 3.3 26.7 + - + +
206B ASP* 2.5 34.0 + - - +
208B GLU* 1.3 72.6 - - - +
210B ARG* 1.3 58.4 + - - +
212B VAL* 3.3 9.1 + - - +
213B ASN* 2.9 52.0 + - - +
272B ASN* 5.4 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LYS 5.3 2.8 + - - -
204B ASP* 3.2 43.5 + - - +
205B GLU 5.9 0.2 - - - -
206B ASP* 2.8 21.2 + - - +
207B SER* 3.3 21.5 + - - +
209B ASP* 1.3 76.5 - - - +
211B LEU* 1.3 53.2 + - - +
213B ASN 3.2 0.5 + - - -
214B GLU* 2.7 46.8 + - + +
217B ARG* 3.5 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B SER 2.9 16.3 + - - +
208B GLU* 3.6 7.6 - - - +
210B ARG* 1.3 76.2 - - - +
212B VAL* 1.3 65.1 + - + +
214B GLU* 3.5 14.8 + - - +
215B LYS* 3.5 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 3.2 15.5 + - + +
209B ASP* 3.6 11.4 - - - +
211B LEU* 1.3 76.6 - - + +
213B ASN* 1.3 64.8 + - - +
215B LYS* 3.2 21.1 + - - +
216B PHE* 3.5 5.2 + - - +
264B LEU* 6.3 0.4 - - + -
268B THR* 6.1 3.1 - - - -
269B HIS* 4.0 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TYR* 5.0 0.5 + - - -
199B PRO* 3.6 23.6 - - + +
200B GLN 5.6 0.2 + - - -
203B PHE 5.1 1.8 + - - -
204B ASP* 3.3 21.6 + - - +
209B ASP* 2.9 39.3 + - - +
212B VAL* 1.3 75.4 - - - +
214B GLU* 1.3 60.2 + - - +
216B PHE* 3.2 6.5 + - - +
217B ARG* 2.9 49.3 + - - +
269B HIS* 3.1 24.4 + - - -
272B ASN* 5.1 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 2.7 34.3 + - + +
211B LEU* 3.6 10.8 - - - +
213B ASN* 1.3 71.9 - - - +
215B LYS* 1.3 59.7 + - - +
217B ARG* 3.6 26.9 + - - +
218B GLU* 2.8 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU 3.5 7.3 + - - +
212B VAL* 3.2 14.0 + - - +
214B GLU* 1.3 81.1 - - - +
216B PHE* 1.3 62.0 + - - +
218B GLU* 3.7 11.9 + - - +
219B MET* 3.7 29.2 + - + +
264B LEU* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 4.1 7.9 - - + -
198B TYR* 3.4 39.3 - + - -
199B PRO* 3.5 20.0 - - + -
212B VAL 3.5 2.2 + - - -
213B ASN 3.2 10.3 + - - +
215B LYS* 1.3 81.0 - - - +
217B ARG* 1.3 61.9 + - - +
219B MET* 3.1 15.2 + - - +
220B ILE* 3.5 12.6 + - + +
222B PHE* 3.5 26.0 - + - -
261B LEU* 5.1 0.2 - - + -
264B LEU* 3.7 37.8 - - + +
265B LEU* 4.1 19.1 - - + -
269B HIS* 3.5 35.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B THR* 5.5 2.8 + - - +
197B VAL* 5.7 4.5 - - + +
199B PRO* 2.9 39.9 + - + +
201B LYS* 3.8 14.9 - - - +
204B ASP* 2.8 42.2 + - - -
210B ARG* 3.5 16.4 + - - +
213B ASN* 2.9 35.7 + - - +
214B GLU* 3.2 30.5 + - - +
216B PHE* 1.3 77.0 - - - +
218B GLU* 1.3 62.0 + - - +
219B MET 3.2 0.9 + - - -
220B ILE* 3.3 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 4.4 6.9 - - - +
214B GLU* 2.8 42.0 + - - +
215B LYS* 4.0 9.8 - - - +
216B PHE 3.3 0.2 - - - -
217B ARG* 1.3 76.0 - - - +
219B MET* 1.3 61.5 + - + +
220B ILE 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 2.9 29.2 + - - +
215B LYS* 3.7 18.4 + - + +
216B PHE 3.1 8.0 + - - +
217B ARG 3.1 1.2 - - - -
218B GLU* 1.3 78.8 - - + +
220B ILE* 1.3 60.2 + - - +
221B PRO 3.0 6.6 - - - +
222B PHE* 3.3 20.2 + - + -
257B GLU* 4.2 16.6 - - - +
260B TYR* 3.7 45.5 - - + -
264B LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 5.0 0.4 - - + -
166B PRO* 3.8 30.3 - - + -
183B LYS* 4.5 3.4 - - - +
187B THR* 3.5 15.1 + - - -
190B LEU* 4.0 16.2 - - + -
197B VAL* 3.7 19.3 - - + -
198B TYR 3.2 27.8 - - - +
199B PRO* 4.6 0.2 - - + -
216B PHE* 3.6 17.3 - - + +
217B ARG* 3.3 21.9 + - + +
218B GLU 4.3 4.0 - - - +
219B MET* 1.3 78.2 - - - +
221B PRO* 1.3 70.8 - - + +
222B PHE* 3.6 21.1 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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