Contacts of the helix formed by residues 214 - 220 (chain B) in PDB entry 6TXC
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 SER 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.8 7.2 - - - +
148B LYS 2.8 18.3 + - - -
149B GLN 3.2 18.5 + - - -
151B GLY 4.6 1.3 - - - -
164B ARG* 3.0 33.0 + - - +
210B HIS* 3.7 20.3 + - - -
211B GLY 3.0 15.8 + - - +
213B PHE* 1.3 74.3 - - - +
215B HIS* 1.3 65.6 + - - -
217B PHE* 3.3 19.9 + - - +
218B ASP* 3.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN 5.1 2.0 - - - -
164B ARG* 3.9 20.2 + - - -
210B HIS* 3.8 11.5 + + - -
213B PHE 2.9 1.8 + - - -
214B SER* 1.3 75.6 - - - +
216B MET* 1.3 59.8 + - - +
217B PHE 3.2 1.1 - - - -
218B ASP* 3.3 15.7 + - - +
219B GLY* 3.0 28.6 + - - -
220B ARG* 5.4 0.2 - - - +
233B HIS* 3.9 26.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PRO 3.8 13.9 - - - +
213B PHE* 3.1 24.8 + - + +
215B HIS* 1.3 78.1 - - - +
217B PHE* 1.3 61.1 + - + +
220B ARG* 2.8 32.1 + - - +
221B PHE* 3.0 13.4 + - + +
383B ASP* 3.7 36.2 + - + +
386B ILE* 3.6 24.9 - - + -
387B THR* 3.1 29.4 - - - +
390B PHE* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLY* 3.7 18.4 - - - +
212B PRO* 3.4 36.5 + - + +
214B SER 3.3 9.1 + - - +
215B HIS 3.2 0.6 - - - -
216B MET* 1.3 81.5 - - - +
218B ASP* 1.3 61.5 + - + +
221B PHE* 3.5 28.7 - + + -
222B ILE* 3.0 54.7 + - + +
231B TRP* 4.5 5.4 - - - -
390B PHE* 4.8 5.6 - + - -
409B ILE* 3.8 22.2 - - + -
413B ILE* 3.8 19.7 - - + -
419B TYR* 3.9 12.3 - + - -
422B LEU* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS* 4.7 0.2 - - - -
211B GLY 6.2 0.9 - - - +
214B SER 3.9 3.2 + - - +
215B HIS* 3.3 27.8 + - - +
217B PHE* 1.3 80.0 - - + +
219B GLY* 1.3 65.7 + - - +
223B PRO* 3.3 21.1 - - - +
231B TRP* 4.0 31.5 - - + +
232B THR* 4.2 2.9 - - - -
233B HIS* 3.0 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B HIS 3.0 17.9 + - - -
218B ASP* 1.3 83.9 + - - +
220B ARG* 1.3 62.0 + - - +
223B PRO* 3.7 12.6 - - - +
470B ARG* 5.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B HIS 5.4 0.2 - - - +
216B MET* 2.8 21.4 + - - +
219B GLY* 1.3 77.6 - - - +
221B PHE* 1.3 64.7 + - - +
222B ILE 3.7 0.9 - - - -
223B PRO* 3.7 4.4 - - - +
224B LEU* 3.3 28.7 + - + +
375B GLN* 5.1 3.0 - - - +
380B ASN* 3.6 28.4 + - - +
383B ASP* 3.7 25.9 + - - +
384B THR* 3.0 32.9 - - - +
387B THR* 3.7 21.5 - - + +
501B ASP* 3.2 35.5 + - - -
503B ILE* 5.5 1.2 - - - +
----------------------------------------------------------
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