Contacts of the helix formed by residues 207 - 224 (chain L) in PDB entry 6GYS
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 THR 207 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205L PHE 4.0 1.2 - - - +
206L LYS* 1.3 92.6 - - + +
208L CYS* 1.3 61.1 + - - +
209L SER* 2.6 16.5 + - - +
210L GLU* 2.4 42.6 + - + +
211L LYS* 3.4 26.9 + - - +
301L SER* 5.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 208 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195L PRO* 4.1 15.9 - - - -
207L THR* 1.3 73.9 - - - +
209L SER* 1.3 58.8 + - - +
210L GLU 3.4 0.2 - - - -
211L LYS* 3.4 30.9 + - - +
212L LEU* 2.9 32.2 + - - +
292L LEU* 5.3 1.6 - - + -
482L HIS* 3.8 28.6 + - + +
483L ASP* 3.0 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207L THR* 2.6 25.1 + - - +
208L CYS* 1.3 77.0 - - - +
210L GLU* 1.3 58.1 + - - +
212L LEU* 3.6 11.4 - - - +
213L ARG* 2.8 30.0 + - - +
289L TYR* 3.8 11.9 - - - -
292L LEU* 4.8 23.9 - - - +
293L ARG* 5.4 2.2 - - - -
301L SER* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L LYS 4.8 0.9 - - - +
204L PHE* 2.6 36.8 - - - +
205L PHE* 3.7 3.1 - - + -
206L LYS* 2.6 40.7 + - - +
207L THR* 2.4 32.8 + - + +
209L SER* 1.3 66.9 + - - +
211L LYS* 1.3 59.1 + - - +
213L ARG* 3.2 36.5 + - - +
214L PHE* 3.0 28.4 + - - +
341L TYR* 3.2 14.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L LEU* 3.7 31.8 - - + +
194L ASN 2.6 21.1 + - - +
195L PRO* 2.1 39.0 + - - +
197L THR* 3.7 23.1 + - + +
205L PHE* 3.6 26.2 - - + -
206L LYS 5.7 0.4 - - - -
207L THR 3.4 18.6 + - - +
208L CYS* 3.4 22.1 + - - +
209L SER 3.3 0.4 - - - -
210L GLU* 1.3 78.4 - - - +
212L LEU* 1.3 57.0 + - + +
214L PHE* 3.5 6.0 + - - +
215L LEU* 2.9 29.5 + - - +
482L HIS* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L LEU 5.5 2.2 - - - +
193L TRP* 3.6 37.0 - - + -
208L CYS 2.9 21.1 + - - +
209L SER* 3.2 9.1 + - - +
211L LYS* 1.3 76.8 - - + +
213L ARG* 1.3 59.7 + - - +
215L LEU* 3.7 6.8 - - + +
216L VAL* 2.8 34.1 + - - +
285L THR* 4.3 11.4 - - + +
288L ALA* 4.0 11.4 - - + +
289L TYR* 3.7 36.1 - - + +
292L LEU* 4.0 20.9 - - + -
482L HIS* 4.6 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209L SER 2.8 11.8 + - - +
210L GLU* 3.2 40.3 + - - +
212L LEU* 1.3 73.2 - - - +
214L PHE* 1.3 60.4 + - - +
216L VAL* 4.0 2.6 - - - +
217L ASP* 3.0 30.1 + - - +
289L TYR* 3.5 28.2 - - + -
324L LEU* 3.9 23.1 - - + +
325L ARG 4.8 8.3 - - - -
326L GLY* 6.1 1.8 - - - -
333L PRO* 4.2 13.1 - - - +
337L THR* 5.2 1.4 + - - -
338L PHE* 3.9 15.8 - - - -
341L TYR* 2.4 44.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L VAL* 4.0 14.4 - - + -
192L LEU* 3.8 31.4 - - + -
205L PHE* 4.2 13.5 - + + -
210L GLU 3.0 17.4 + - - +
211L LYS 3.5 2.9 - - - +
213L ARG* 1.3 79.0 - - - +
215L LEU* 1.3 59.5 + - - +
217L ASP* 3.3 2.3 + - - +
218L PHE* 2.9 30.6 + + + +
338L PHE* 4.2 10.3 - + - -
341L TYR* 3.5 33.2 - + + -
342L TYR* 3.4 39.7 - + - -
345L VAL* 3.6 37.0 - - + -
346L PHE* 5.6 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L VAL* 4.1 13.9 - - + -
189L SER* 3.8 29.8 - - - +
192L LEU* 3.8 21.5 - - + +
193L TRP* 3.5 46.7 - - + +
211L LYS 2.9 18.3 + - - +
212L LEU* 3.2 10.9 + - + +
214L PHE* 1.3 76.0 - - - +
216L VAL* 1.3 60.4 + - - +
218L PHE* 3.4 3.6 + - + -
219L GLN* 2.9 36.0 + - + +
279L PHE 4.7 1.8 - - - +
285L THR* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212L LEU 2.8 19.1 + - - +
213L ARG* 4.1 5.8 - - - +
215L LEU* 1.3 76.2 - - - +
217L ASP* 1.3 56.9 + - - +
219L GLN* 3.3 7.0 + - - +
220L LEU* 2.9 44.1 + - + +
282L PRO 5.7 0.2 - - - +
285L THR* 3.7 29.4 - - + +
286L LEU* 3.8 24.7 - - + +
289L TYR* 3.8 26.9 - - + -
323L ILE* 5.7 2.2 - - + +
324L LEU* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213L ARG 3.0 19.7 + - - +
214L PHE 3.7 1.8 - - - +
216L VAL* 1.3 77.7 - - - +
218L PHE* 1.3 56.4 + - - +
220L LEU* 3.3 12.0 + - - +
221L ARG* 3.0 25.1 + - - +
228L PHE* 3.8 16.1 - - - -
231L ARG* 3.5 23.3 + - - -
324L LEU* 4.6 6.5 - - + +
332L TYR* 4.0 8.3 + - - -
338L PHE* 3.5 34.8 - - + +
342L TYR* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L PRO* 4.5 7.0 - - + -
185L LEU* 3.6 25.6 - - + -
188L VAL* 3.7 35.0 - - + -
214L PHE* 2.9 22.1 + + + +
215L LEU* 3.9 7.2 - - + +
216L VAL 3.3 0.2 - - - -
217L ASP* 1.3 78.2 + - - +
219L GLN* 1.3 58.3 + - - +
221L ARG* 3.3 1.7 + - + +
222L SER* 2.8 46.0 + - - -
342L TYR* 3.7 31.0 - + + +
346L PHE* 3.5 24.5 - + - -
358L TYR* 3.5 35.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L LEU* 3.7 16.8 - - + -
189L SER* 3.8 7.1 + - - +
215L LEU* 2.9 24.2 + - + +
216L VAL* 3.3 5.7 + - - +
218L PHE* 1.3 72.6 - - - +
220L LEU* 1.3 62.2 + - - +
222L SER* 4.0 5.4 - - - -
223L TYR* 2.9 45.1 + - + +
279L PHE 3.4 5.5 + - - -
280L ILE* 3.4 35.3 + - - +
282L PRO* 3.2 25.2 - - + +
285L THR* 3.3 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216L VAL* 2.9 34.7 + - + +
217L ASP* 3.5 12.3 - - - +
218L PHE 3.3 0.2 - - - -
219L GLN* 1.3 76.6 - - + +
221L ARG* 1.3 55.1 + - - +
223L TYR* 5.2 0.2 - - - -
224L LEU* 2.7 63.1 + - + +
231L ARG* 3.7 21.3 - - + -
234L ILE* 4.7 15.3 - - + -
272L LEU* 4.8 12.1 - - + -
282L PRO* 6.5 0.4 - - + -
286L LEU* 6.6 0.2 - - + -
323L ILE* 4.6 19.7 - - + -
324L LEU* 4.9 5.8 - - + -
332L TYR* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217L ASP 3.0 13.8 + - - +
218L PHE* 3.6 8.5 - - - +
219L GLN 3.3 0.4 - - - -
220L LEU* 1.3 76.7 - - - +
222L SER* 1.3 59.1 + - - +
224L LEU 4.0 1.1 - - - -
225L ASN* 2.8 58.9 + - - +
226L LEU 3.5 3.8 - - - +
231L ARG* 3.1 34.2 - - - +
342L TYR* 4.3 6.3 - - - +
356L ARG* 6.1 0.6 - - - +
357L GLU* 2.4 33.9 + - - +
358L TYR* 3.3 43.3 - - + +
360L ASN 3.3 23.3 + - - -
362L CYS* 3.3 21.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L LEU* 3.4 38.0 - - - +
218L PHE* 2.8 36.7 + - - -
219L GLN* 3.6 4.9 - - - -
220L LEU 3.2 0.2 - - - -
221L ARG* 1.3 79.8 - - - +
223L TYR* 1.3 60.4 + - - +
225L ASN* 4.0 7.5 + - - +
358L TYR* 5.2 4.0 - - - -
407L MET* 4.8 3.3 - - - +
409L PHE* 4.5 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L LEU* 3.9 22.9 - - + +
219L GLN* 2.9 31.8 + - + +
222L SER* 1.3 79.1 - - - +
224L LEU* 1.3 68.7 + - + +
225L ASN 3.9 0.7 - - - -
271L ALA 5.0 0.2 - - - +
272L LEU* 3.7 20.6 - - + -
273L LEU 5.0 1.8 - - - -
275L GLN* 4.2 13.1 + - + +
280L ILE* 2.9 32.7 + - - +
282L PRO* 3.7 29.0 - - + +
366L TYR* 4.2 0.3 - - - -
407L MET* 3.1 55.0 - - - +
408L ASN* 3.6 28.9 - - + +
409L PHE* 4.6 12.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220L LEU* 2.7 44.5 + - + +
221L ARG* 3.9 2.0 - - - +
223L TYR* 1.3 79.5 - - + +
225L ASN* 1.3 52.7 + - - +
226L LEU* 2.6 31.6 + - + +
231L ARG* 4.9 0.3 - - - -
234L ILE* 5.5 7.0 - - + -
239L LEU* 6.3 0.7 - - + -
251L TYR* 5.0 6.3 - - + -
270L LEU* 3.7 34.1 - - + -
271L ALA 3.7 20.0 - - - +
272L LEU* 3.8 31.0 - - + -
366L TYR* 3.5 24.5 - - + -
----------------------------------------------------------
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