Contacts of the helix formed by residues 206 - 211 (chain C) in PDB entry 7C17
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 ALA 206 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ASN 5.0 1.2 + - - -
194C LEU* 3.7 39.8 + - + +
196C VAL* 3.8 11.7 - - + -
204C LEU 3.9 0.4 + - - -
205C PRO* 1.3 70.8 - - - +
207C THR* 1.3 62.4 + - - +
208C ILE 3.2 2.7 - - - -
209C ILE* 3.3 21.2 - - - +
210C LEU* 3.3 14.9 + - + +
347C ILE* 6.1 0.2 - - + -
350C THR* 4.4 14.8 - - + -
429C MET* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C PRO* 3.3 1.8 - - - +
206C ALA* 1.3 76.5 - - - +
208C ILE* 1.3 63.0 + - - +
209C ILE 3.3 0.2 - - - -
210C LEU* 3.7 13.0 - - - -
211C ARG* 3.1 44.3 + - - +
220C ILE* 5.3 5.2 - - - -
350C THR* 4.7 15.2 - - - -
351C LEU* 5.0 7.9 - - - -
354C ASP* 4.1 25.6 - - - -
356C THR 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.0 24.2 - - + -
205C PRO* 3.6 16.7 + - - +
206C ALA 3.2 0.2 - - - -
207C THR* 1.3 80.4 - - - +
209C ILE* 1.3 59.5 + - - +
211C ARG* 4.0 3.9 + - - +
212C ALA* 4.1 9.2 + - - +
355C PRO* 5.0 9.2 - - + +
356C THR 5.7 2.2 - - - -
362C ALA* 4.1 32.3 - - - +
363C LEU* 5.0 1.0 - - - +
365C GLU* 4.8 9.6 - - + -
366C ILE* 5.4 7.4 - - + +
385C PHE* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LEU* 3.8 24.7 - - + -
186C PHE* 5.2 1.3 - - + -
196C VAL* 4.3 24.2 - - + -
198C ILE* 5.0 0.4 - - + -
205C PRO 4.5 0.4 + - - -
206C ALA 3.3 15.9 - - - +
208C ILE* 1.3 78.9 - - + +
210C LEU* 1.3 69.7 + - + +
211C ARG 3.5 0.2 - - - -
212C ALA* 3.7 13.8 + - - +
213C LEU* 4.1 12.1 - - - +
366C ILE* 5.5 8.3 - - + -
385C PHE* 4.0 20.2 - - + -
389C PHE* 3.7 31.9 - - + -
425C ILE* 5.1 21.3 - - + +
429C MET* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA* 3.3 26.2 + - + +
207C THR* 3.5 9.4 + - - +
208C ILE 3.4 0.2 - - - -
209C ILE* 1.3 78.4 - - + +
211C ARG* 1.3 59.3 + - - +
212C ALA 3.2 4.1 + - - -
213C LEU* 3.9 22.3 + - + +
215C TYR* 4.3 4.7 - - - +
220C ILE* 4.2 37.2 - - + +
224C PHE* 4.0 31.0 - - + -
347C ILE* 5.4 7.0 - - + -
350C THR* 5.7 1.6 - - - +
425C ILE* 4.5 15.3 - - + -
426C ILE* 5.6 4.9 - - + -
429C MET* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C THR* 3.1 32.5 + - - +
208C ILE 4.6 0.4 - - - -
209C ILE 3.5 0.2 - - - -
210C LEU* 1.3 75.9 - - - +
212C ALA* 1.3 60.0 + - - +
213C LEU 3.3 2.0 + - - -
214C ASN* 4.1 6.7 + - - -
215C TYR 4.3 13.7 - - - +
216C THR* 5.6 1.2 - - - +
217C THR* 3.6 32.0 - - - +
220C ILE* 4.8 11.0 - - + +
351C LEU* 3.5 26.3 - - - +
354C ASP* 5.2 0.8 - - - +
356C THR 4.0 7.8 + - - -
357C ASN* 2.7 72.6 + - - +
358C ASP 4.5 0.9 - - - +
359C ARG* 3.6 23.3 - - - +
362C ALA* 4.2 12.8 - - + -
----------------------------------------------------------
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