Contacts of the helix formed by residues 211 - 222 (chain C) in PDB entry 6AH0
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 PHE 211 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 5.3 9.5 - - - +
206C PRO* 4.6 11.6 - - - +
208C HIS* 3.3 11.8 + - - +
209C VAL 3.2 0.6 - - - -
210C ASN* 1.3 73.8 - - - +
212C SER* 1.3 62.8 + - - +
213C ASP 3.2 3.9 + - - +
214C GLU* 3.4 11.0 + - - -
215C VAL 4.1 3.6 + - - -
636C TYR* 6.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PRO 5.1 3.1 - - - -
208C HIS 3.4 6.8 + - - -
209C VAL* 3.2 13.3 + - - +
210C ASN 3.2 4.9 - - - -
211C PHE* 1.3 75.5 - - - +
213C ASP* 1.3 57.8 + - - +
215C VAL* 2.9 20.8 + - - +
216C THR* 2.9 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ASN 4.6 2.8 + - - -
211C PHE* 3.2 2.4 - - - +
212C SER* 1.3 77.1 - - - +
214C GLU* 1.3 61.9 + - - +
216C THR* 3.2 3.2 + - - +
217C ALA* 3.0 18.9 + - - -
615C PRO* 5.9 6.6 - - - +
616C SER 5.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C SER* 5.3 14.8 - - - +
205C THR* 5.5 3.6 - - - -
211C PHE 3.4 9.0 + - - -
212C SER 3.2 0.6 - - - -
213C ASP* 1.3 75.2 - - - +
215C VAL* 1.3 56.5 + - - +
217C ALA* 3.2 3.7 + - - +
218C GLY* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C THR* 4.7 18.1 - - - +
206C PRO 5.4 2.5 + - - -
211C PHE 4.1 3.4 + - - -
212C SER* 2.9 11.4 + - - +
214C GLU* 1.3 76.1 - - - +
216C THR* 1.3 55.8 + - - +
218C GLY* 3.2 2.5 + - - +
219C LEU* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C SER 2.9 12.9 + - - -
213C ASP* 3.2 4.6 + - - +
215C VAL* 1.3 76.0 - - - +
217C ALA* 1.3 56.5 + - - +
219C LEU* 3.2 3.0 + - - +
220C ARG* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ASP 3.0 14.0 + - - -
214C GLU* 3.2 3.6 + - - +
216C THR* 1.3 75.5 - - - +
218C GLY* 1.3 63.5 + - - +
220C ARG* 3.2 2.9 + - - +
221C ILE* 3.0 19.2 + - - -
479C THR* 4.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C THR* 5.3 8.8 - - - -
203C MET* 6.2 4.9 - - - -
214C GLU 2.9 14.5 + - - -
215C VAL* 3.2 4.0 + - - -
217C ALA* 1.3 75.2 - - - +
219C LEU* 1.3 56.6 + - - +
221C ILE* 3.2 2.6 + - - -
222C SER* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C THR* 6.0 3.6 - - - +
215C VAL 2.9 14.5 + - - -
216C THR* 3.2 4.2 + - - +
218C GLY* 1.3 74.7 - - - +
220C ARG* 1.3 64.1 + - - +
222C SER* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C THR 2.9 14.0 + - - -
217C ALA 3.2 3.1 + - - -
219C LEU* 1.3 79.0 - - - +
221C ILE* 1.3 62.1 + - - +
222C SER 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ALA 3.0 14.0 + - - -
218C GLY* 3.2 3.3 + - - -
220C ARG* 1.3 79.6 - - - +
222C SER* 1.3 58.7 + - - +
223C ASP 4.0 0.7 + - - -
495C ARG* 5.6 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASN* 4.8 12.1 - - - +
132C VAL 5.2 1.1 - - - +
133C THR* 5.3 4.3 - - - +
218C GLY 2.9 15.9 + - - -
219C LEU* 3.0 15.8 + - - +
220C ARG 3.8 3.5 - - - +
221C ILE* 1.3 78.3 - - - +
223C ASP* 1.3 64.4 + - - +
224C GLY 3.4 7.2 - - - +
----------------------------------------------------------
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