Contacts of the strand formed by residues 205 - 213 (chain E) in PDB entry 6DWZ
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 ARG 205 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E GLU* 2.9 27.6 + - - -
196E LEU 3.8 1.7 - - - +
197E HIS* 3.6 5.5 - - - +
198E TYR* 3.0 48.6 + - + +
199E HIS 4.5 0.6 + - - -
200E GLU* 3.3 28.8 - - - +
203E GLU* 2.2 42.6 + - + +
204E LEU* 1.3 78.0 - - - +
206E ASP* 1.3 57.9 + - - +
207E LEU* 4.1 1.4 + - + +
606E ASN* 3.3 28.3 + - + +
607E PHE* 3.2 37.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E THR* 4.6 4.9 - - - +
196E LEU 3.7 4.7 - - - -
197E HIS* 3.4 25.7 + - - +
204E LEU 4.0 1.4 + - - -
205E ARG* 1.3 69.6 - - - +
207E LEU* 1.3 61.3 + - - +
208E ILE* 5.9 1.3 - - - +
377E CYS* 3.8 21.3 - - - +
378E SER* 4.3 11.9 + - - +
570E ALA* 3.8 12.5 - - - +
573E ARG* 4.3 13.7 + - - -
602E SER* 4.0 3.6 + - - -
606E ASN* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E ILE* 5.7 2.0 - - + -
166E ILE* 3.9 23.3 - - + -
195E THR* 4.4 2.7 - - - -
196E LEU* 2.8 42.7 + - + +
198E TYR* 4.7 4.9 - - + +
205E ARG* 4.9 3.4 - - + +
206E ASP* 1.3 79.1 + - - +
208E ILE* 1.3 68.1 + - - +
209E LEU* 3.4 23.5 - - + +
235E PHE* 6.2 0.4 - - + -
599E PHE* 5.0 13.0 - - + +
602E SER* 3.8 17.0 - - - +
603E PHE* 4.2 10.8 - - + +
606E ASN* 3.3 27.8 - - + +
607E PHE* 4.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E VAL 4.0 8.7 - - - +
195E THR* 4.2 6.5 - - + -
206E ASP* 5.9 1.8 - - - +
207E LEU* 1.3 72.6 - - - +
209E LEU* 1.3 67.4 + - - +
210E GLY* 4.0 13.9 - - - +
211E LEU* 6.0 0.7 - - + -
574E THR* 3.3 38.8 - - + +
577E LEU* 4.0 25.1 - - + -
598E LEU* 4.1 23.3 - - + +
599E PHE* 3.5 24.2 - - - +
601E ASN* 6.4 0.2 - - + -
602E SER* 3.2 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E LYS* 4.7 2.6 - - - +
166E ILE* 5.0 6.3 - - + -
194E VAL* 3.1 16.2 + - + +
195E THR 4.3 1.3 - - - -
196E LEU* 3.5 31.4 - - + +
207E LEU* 3.4 32.9 + - + +
208E ILE* 1.3 78.2 - - - +
210E GLY* 1.3 60.6 + - - +
231E ILE* 3.9 14.1 - - + +
232E PHE* 3.2 37.9 - - + -
234E GLN* 5.4 0.9 - - - +
235E PHE* 4.1 33.2 - - + -
595E ASP* 4.4 4.2 - - - +
599E PHE* 3.5 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E GLY* 3.8 1.4 - - - -
194E VAL 3.1 28.0 + - - +
208E ILE* 3.6 8.7 - - - +
209E LEU* 1.3 83.1 - - - +
211E LEU* 1.3 60.8 + - - +
231E ILE* 3.3 23.4 - - - +
234E GLN* 6.2 0.2 - - - -
574E THR* 5.4 1.0 - - - +
595E ASP* 3.9 11.2 - - - -
599E PHE* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E TRP* 5.1 2.2 - - + -
191E PHE* 3.6 44.1 - - + -
192E LEU 3.3 11.2 - - - +
193E GLY* 3.7 4.3 - - - +
208E ILE* 6.0 0.7 - - + -
210E GLY* 1.3 73.9 - - - +
212E LYS* 1.3 61.6 + - - +
213E SER 4.2 0.7 + - - -
231E ILE* 4.3 0.2 - - - -
574E THR* 4.8 7.0 - - + -
575E PHE* 3.7 25.6 - - + -
578E ALA* 4.0 16.6 - - + -
582E ILE* 6.3 0.2 - - + -
591E GLN* 4.9 2.8 - - - +
594E VAL* 4.4 12.3 - - + -
595E ASP* 3.4 29.6 + - + +
598E LEU* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E PHE* 3.8 2.5 - - - -
192E LEU* 3.0 33.2 + - - +
211E LEU* 1.3 75.7 - - - +
213E SER* 1.3 70.3 + - - +
214E LEU* 3.8 1.6 + - - +
227E LYS* 4.4 22.6 - - + +
230E ALA* 3.4 34.4 - - + +
231E ILE* 3.9 21.7 - - + +
234E GLN* 4.0 21.3 - - - +
591E GLN* 6.0 2.9 - - + +
595E ASP* 6.1 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E ARG* 3.3 29.6 - - - +
190E ASN 3.8 3.4 - - - -
191E PHE* 3.5 22.6 - - - -
211E LEU 4.2 0.2 + - - -
212E LYS* 1.3 79.5 - - - +
214E LEU* 1.3 58.5 + - - +
215E ASP* 2.4 40.2 + - - +
227E LYS* 3.3 21.0 + - - -
591E GLN* 3.5 20.5 + - - +
----------------------------------------------------------
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