Contacts of the strand formed by residues 209 - 215 (chain E) in PDB entry 6IWQ
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 SER 209 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E THR* 1.3 76.5 + - - +
210E SER* 1.3 63.3 + - - +
211E VAL* 4.0 2.5 - - - -
238E TYR 2.9 7.1 + - - +
239E LEU* 3.8 4.7 - - - +
240E ALA* 2.8 31.9 + - - +
241E GLU 3.7 1.9 + - - +
294E GLY* 4.0 1.7 - - - -
296E VAL* 3.2 27.7 - - - +
298E ILE* 3.4 26.4 - - - +
311E TYR* 2.9 24.9 + - - -
315E VAL* 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E SER* 1.3 73.4 - - - +
211E VAL* 1.3 61.3 + - - +
212E VAL* 3.8 1.5 + - - -
241E GLU* 3.1 34.3 + - - +
291E ALA* 3.9 18.8 + - - -
294E GLY* 2.7 33.3 + - - -
296E VAL 2.9 7.3 + - - +
297E LEU* 3.6 11.3 - - - +
298E ILE 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E SER 5.0 0.9 - - - +
210E SER* 1.3 75.8 - - - +
212E VAL* 1.3 59.7 + - - +
213E ILE* 4.5 12.6 - - + -
230E VAL* 4.3 17.5 - - + -
239E LEU* 4.0 18.6 - - + -
241E GLU 3.2 5.3 + - - -
242E ILE* 3.5 32.8 - - + -
243E VAL* 2.8 26.3 + - - +
298E ILE* 3.1 35.0 - - + +
300E LEU* 4.4 9.9 - - + -
310E TRP* 4.5 4.7 - - + -
311E TYR* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E SER 4.3 7.6 - - - +
211E VAL* 1.3 77.6 - - - +
213E ILE* 1.3 60.3 + - - +
214E VAL* 4.0 6.4 + - + +
243E VAL* 3.2 12.6 - - + +
245E ILE* 5.2 1.8 - - + -
287E GLY* 4.1 19.1 - - - +
291E ALA* 4.0 27.4 - - + -
297E LEU* 4.4 10.1 - - + -
298E ILE 2.9 6.4 + - - +
299E TYR* 3.1 42.0 - - + +
300E LEU 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E VAL* 4.5 9.6 - - + -
212E VAL* 1.3 75.8 - - - +
214E VAL* 1.3 63.4 + - - +
215E PHE* 3.9 1.6 + - - -
223E LEU* 4.1 15.3 - - + -
226E THR* 3.9 21.8 - - + -
227E VAL* 4.0 13.5 - - + +
230E VAL* 5.2 2.2 - - + -
242E ILE* 4.2 9.9 - - + -
243E VAL 3.0 5.4 + - - +
244E LEU* 3.4 26.1 - - + +
245E ILE* 2.9 21.5 + - - -
300E LEU* 3.5 22.7 - - + +
301E ASP 3.8 3.1 - - - +
302E ALA* 3.6 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E VAL* 4.0 7.1 - - + -
213E ILE* 1.3 76.3 - - - +
215E PHE* 1.3 68.4 + - - +
245E ILE* 3.5 21.1 - - + +
247E ASP* 4.3 9.6 - - + -
280E LEU* 4.7 20.5 - - + +
283E ALA* 3.5 29.2 - - + +
284E ARG* 4.0 37.5 - - + +
299E TYR* 5.4 0.7 - - + -
300E LEU 4.1 5.1 + - - +
301E ASP* 4.7 0.9 - - - -
302E ALA* 3.5 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E ILE 4.3 6.5 - - - -
214E VAL* 1.3 79.0 - - - +
216E HIS* 1.3 64.6 + - - +
217E ASN 4.2 3.8 - - - -
218E GLU* 4.2 8.1 - - + -
223E LEU* 4.2 21.8 - - + -
244E LEU* 4.0 19.1 - - + -
245E ILE 2.9 11.5 + - - -
246E ASP* 3.4 37.7 - - + -
247E ASP* 2.9 28.9 + - - +
249E SER* 3.4 20.4 - - - -
254E LEU* 4.0 22.4 - - + -
258E LEU* 4.1 20.0 - - + -
271E VAL* 4.5 2.2 - - + -
302E ALA* 3.8 19.7 - - + -
----------------------------------------------------------
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