Contacts of the strand formed by residues 209 - 216 (chain F) in PDB entry 6H25
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 209 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F SER* 3.5 3.1 + - - -
187F LEU* 2.9 37.9 + - + +
195F TRP* 4.2 11.5 - - + -
207F ALA* 5.0 2.5 - - - -
208F ALA* 1.3 80.8 - - + +
210F GLY* 1.3 58.7 + - - +
228F SER 3.7 9.0 - - - +
229F GLY* 3.7 3.6 - - - -
230F GLU* 3.4 26.0 - - + +
231F GLY 4.6 10.8 - - - +
237F TRP* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F LEU 3.5 12.3 - - - -
186F SER* 4.1 4.3 - - - -
195F TRP* 5.3 1.1 - - - -
209F ALA* 1.3 74.1 - - - +
211F LEU* 1.3 59.7 + - - -
227F GLY* 3.2 1.9 - - - -
228F SER* 2.9 35.0 + - - +
237F TRP* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E MET* 4.7 3.4 - - + -
184F GLY* 3.3 0.2 - - - -
185F LEU* 2.5 64.1 + - + +
195F TRP* 4.8 8.0 - - + -
210F GLY* 1.3 74.4 - - - +
212F THR* 1.3 76.6 + - - +
213F VAL* 3.7 26.2 - - + -
225F LEU* 5.8 4.0 - - + -
226F LEU 4.0 0.7 - - - -
227F GLY* 3.7 11.7 - - - +
237F TRP* 3.5 35.0 - - + +
240F ALA* 4.4 23.3 - - + +
241F VAL* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F SER* 5.8 0.7 - - - -
158F LEU* 3.8 35.0 + - + +
159F ALA* 4.1 20.6 - - + +
162F LEU* 5.2 1.6 - - + -
183F CYS 3.6 11.7 - - - +
184F GLY* 3.7 5.8 - - - -
211F LEU* 1.3 81.5 + - - +
213F VAL* 1.3 68.9 + - - +
224F GLY 4.0 0.7 - - - +
225F LEU* 3.4 4.3 - - - +
226F LEU 3.1 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F LEU* 5.5 0.2 - - - -
182F GLY* 3.2 2.8 - - - -
183F CYS 2.9 35.5 + - - +
185F LEU* 4.7 3.6 - - + -
211F LEU* 3.7 17.9 - - + -
212F THR* 1.3 84.4 - - - +
214F ALA* 1.3 63.2 + - - +
215F LEU* 5.4 0.9 - - + -
222F VAL* 5.3 4.0 - - + -
224F GLY 3.7 4.9 - - - +
225F LEU* 3.8 22.0 - - + -
241F VAL* 4.6 16.8 - - + -
244F GLY* 3.9 35.0 - - - +
245F LEU* 4.4 11.0 - - + +
248F CYS* 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ALA* 5.2 1.8 - - + -
162F LEU* 3.7 28.3 - - + -
180F VAL* 4.0 14.1 - - + -
181F VAL 3.3 7.9 - - - +
182F GLY* 3.7 7.6 - - - -
213F VAL* 1.3 79.0 - - - +
215F LEU* 1.3 61.0 + - - +
222F VAL* 3.8 3.3 - - - +
223F ALA* 2.8 26.2 + - + +
224F GLY 3.2 16.6 + - - +
248F CYS* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F VAL* 5.0 0.9 - - - -
181F VAL* 3.0 25.2 + - - +
213F VAL* 5.4 1.1 - - + -
214F ALA* 1.3 76.1 - - - +
216F MET* 1.3 70.9 + - - +
217F PRO* 3.4 17.1 - - + +
220F ASN* 4.0 20.6 - - - +
221F GLN 3.3 17.0 - - - +
222F VAL* 3.9 9.6 - - + -
223F ALA* 4.0 2.5 - - - +
244F GLY 4.6 0.2 - - - +
245F LEU* 3.7 45.5 - - + +
248F CYS* 3.6 30.5 - - + +
249F GLN* 5.1 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E SER* 4.0 18.2 - - - +
132F PRO* 3.8 41.1 - - + +
133F ALA* 4.1 14.6 - - - -
177F TYR* 5.1 1.1 - - - -
178F ASP* 3.2 28.7 - - + +
179F LEU 3.3 16.2 - - - +
180F VAL* 4.3 9.9 - - + -
215F LEU* 1.3 72.5 - - - +
217F PRO* 1.3 61.6 - - - +
219F LEU* 4.9 18.4 - - + -
220F ASN* 2.9 28.2 + - - -
221F GLN* 3.2 19.7 + - + +
223F ALA* 4.7 9.2 - - + -
----------------------------------------------------------
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