Contacts of the helix formed by residues 206 - 220 (chain A) in PDB entry 6R7Y
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 GLU 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 5.1 3.8 - - - +
201A ARG* 3.0 37.5 + - + +
205A GLY* 1.3 78.8 - - - -
207A THR* 1.3 62.1 + - - +
208A ILE 3.4 0.4 - - - -
209A ALA* 3.8 4.7 - - - +
210A LEU* 3.0 27.9 + - - +
272A TRP* 3.7 29.1 - - + -
274A THR* 3.7 30.0 - - + +
546A SER* 3.9 11.8 + - - -
547A GLU 4.0 7.7 + - - +
548A PRO* 4.1 14.8 - - + +
549A SER* 4.6 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY 3.7 0.6 - - - -
206A GLU* 1.3 76.0 - - - +
208A ILE* 1.3 69.3 + - + +
210A LEU* 3.2 5.2 + - + +
211A TYR* 3.2 19.8 + - - +
494A THR* 3.7 25.1 + - + +
498A TYR* 4.8 3.1 + - + +
547A GLU* 2.5 41.4 + - - +
549A SER* 3.5 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 4.9 0.9 - - + -
204A PHE* 3.4 35.6 + - + +
206A GLU 3.4 0.2 - - - -
207A THR* 1.3 79.2 - - + +
209A ALA* 1.3 61.0 + - - +
211A TYR* 3.4 4.8 + - + +
212A PHE* 3.2 41.7 + - + -
491A TYR* 3.7 34.5 - - + +
494A THR* 3.7 14.4 - - + -
537A MET* 4.0 19.3 - - + -
544A PRO* 4.2 18.2 - - + -
545A PHE 5.7 2.5 - - - +
547A GLU 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 3.7 10.7 - - - +
200A ILE* 3.9 18.1 - - + +
201A ARG* 3.7 25.4 - - + +
204A PHE* 5.1 0.2 - - - +
205A GLY 3.4 20.2 + - - +
206A GLU* 3.6 5.3 + - - +
207A THR 3.2 0.6 - - - -
208A ILE* 1.3 81.5 - - - +
210A LEU* 1.3 57.0 + - - +
212A PHE* 3.4 0.9 + - - +
213A GLY* 2.8 25.5 + - - -
272A TRP* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU 3.0 16.1 + - - +
207A THR* 3.2 7.4 + - + +
209A ALA* 1.3 75.0 - - - +
211A TYR* 1.3 59.5 + - - +
213A GLY* 3.7 1.2 - - - +
214A PHE* 2.8 29.3 + - - +
261A TRP* 3.9 9.9 - - + -
265A CYS* 3.9 15.9 - - - -
268A MET* 4.3 18.6 - - + -
269A THR* 4.0 13.2 - - + -
272A TRP* 3.7 27.1 - - + -
498A TYR* 4.0 5.1 + - - +
549A SER* 4.1 8.3 - - - +
551A ASN* 3.8 33.0 - - - +
552A ILE* 4.1 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR 3.2 9.9 + - - +
208A ILE* 3.8 8.3 - - + +
209A ALA 3.3 0.2 - - - -
210A LEU* 1.3 79.1 - - - +
212A PHE* 1.3 77.9 + + - +
214A PHE* 3.0 2.2 + - - +
215A LEU* 2.7 42.5 + - + +
491A TYR* 5.2 0.7 - - - -
494A THR* 4.5 13.5 - - + -
497A ASP* 3.2 45.5 + - + -
498A TYR* 3.4 35.1 + + + +
500A GLU* 5.6 0.7 - - - -
501A LEU* 4.0 17.0 - - + +
529A GLU* 4.4 2.6 + - - +
533A ASP* 2.5 37.5 + - + -
702A CA 3.5 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 3.8 30.7 - + - -
195A GLN* 3.7 16.9 + - - +
197A ILE* 5.3 1.6 - - + -
200A ILE* 4.5 19.3 - - + -
204A PHE* 5.9 0.4 - + - -
208A ILE* 3.2 34.8 + - + +
209A ALA 4.0 3.8 - - - +
211A TYR* 1.3 93.6 - + - +
213A GLY* 1.3 58.6 + - - +
215A LEU* 4.0 11.1 - - + +
216A GLU* 3.1 28.9 + - - +
530A VAL* 4.3 7.0 - - - -
533A ASP* 3.7 44.6 - - + -
534A ALA* 3.7 7.6 - - - -
537A MET* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.2 26.8 - - - +
209A ALA 2.8 18.0 + - - -
210A LEU 3.7 1.8 - - - -
212A PHE* 1.3 78.0 - - - +
214A PHE* 1.3 57.2 + - - +
216A GLU* 3.6 3.3 + - - +
217A TYR* 2.9 29.1 + - - +
261A TRP* 3.9 7.1 - - - -
268A MET* 4.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU 2.8 18.5 + - - +
211A TYR* 3.0 6.9 + - - +
213A GLY* 1.3 75.1 - - - +
215A LEU* 1.3 59.6 + - - +
217A TYR* 3.7 3.5 - + - +
218A PHE* 2.9 45.8 + + + +
258A LEU* 5.1 7.0 - - + -
261A TRP* 3.5 54.7 - + + -
498A TYR* 3.6 25.6 - + + +
501A LEU* 3.8 24.0 - - + -
552A ILE* 4.8 6.7 - - + -
559A PHE* 4.0 37.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 2.7 44.3 + - + +
212A PHE* 4.0 13.5 - - + +
213A GLY 3.3 0.2 - - - -
214A PHE* 1.3 70.0 - - - +
216A GLU* 1.3 57.4 + - - +
218A PHE* 3.4 1.4 + - + -
219A THR* 2.7 44.6 + - - +
501A LEU* 3.8 34.1 - - + -
526A ASN* 4.2 11.9 - - + +
529A GLU* 3.9 13.9 - - + +
530A VAL* 3.8 37.9 - - + +
533A ASP* 4.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TYR* 4.0 17.0 - - - +
195A GLN* 3.2 54.0 + - + +
197A ILE* 3.3 29.6 - - - +
212A PHE 3.1 15.7 + - - +
213A GLY 3.9 2.9 - - - +
215A LEU* 1.3 76.8 - - - +
217A TYR* 1.3 61.9 + - - +
219A THR* 3.8 5.3 + - - -
220A PHE* 3.4 39.0 + - + -
530A VAL* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLY 2.9 19.9 + - - +
214A PHE* 3.7 7.2 - + - +
215A LEU 3.2 0.2 - - - -
216A GLU* 1.3 78.8 - - - +
218A PHE* 1.3 68.3 + + + +
220A PHE* 3.3 16.6 + + + +
221A ALA* 3.3 13.9 + - + +
257A ILE* 3.4 36.8 + - + +
260A LEU* 3.2 36.1 - - + +
261A TRP* 3.6 38.6 - + + -
264A GLY* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 2.9 37.1 + + + +
215A LEU* 3.4 5.4 + - - +
217A TYR* 1.3 78.6 - + - +
219A THR* 1.3 64.1 + - - +
221A ALA* 3.4 9.1 + - - +
222A LEU* 3.5 36.1 + - + +
257A ILE* 4.1 24.0 - - + -
258A LEU* 5.8 4.0 - - + -
501A LEU* 4.1 36.1 - - + -
504A GLN* 5.2 2.5 - - + -
505A PHE* 3.4 44.6 - + + -
526A ASN* 4.2 7.2 - - - -
559A PHE* 4.6 8.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 2.7 26.0 + - - +
216A GLU* 4.0 7.3 - - - -
217A TYR 3.2 0.2 - - - -
218A PHE* 1.3 76.5 - - - +
220A PHE* 1.3 62.9 + - + +
221A ALA 3.1 6.0 + - - -
222A LEU* 3.5 11.5 + - - +
223A ILE* 3.5 14.2 + - - +
523A VAL* 4.7 8.3 - - + +
526A ASN* 3.3 38.7 + - + +
527A PHE* 3.6 33.7 - - + -
530A VAL* 4.4 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 6.1 5.6 - - + -
193A LYS 4.8 13.2 - - - -
194A TYR* 3.5 40.4 - + - -
216A GLU* 3.4 32.4 + - + +
217A TYR* 3.3 12.2 + + + +
219A THR* 1.3 80.1 - - + +
221A ALA* 1.3 57.4 + - - +
222A LEU 3.8 0.2 - - - -
223A ILE* 3.9 28.7 - - + +
224A PRO* 4.4 7.4 - - - +
253A TRP* 5.5 1.4 - - - -
527A PHE* 4.8 14.6 - + - -
----------------------------------------------------------
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