Contacts of the strand formed by residues 208 - 213 (chain B) in PDB entry 3ER8
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 MET 208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.6 18.8 - - + -
175B LYS* 3.9 0.3 - - - -
176B TRP* 2.8 52.2 + - + +
178B CYS 5.8 2.7 - - - +
195B LYS* 3.5 27.1 - - + -
196B MET 3.3 17.7 - - - +
197B LEU* 4.3 6.7 - - + -
198B GLN* 3.4 9.8 + - - +
206B ALA* 3.1 20.2 - - + +
207B GLU* 1.3 77.2 - - - +
209B ARG* 1.3 68.6 + - - +
232B TYR* 3.8 15.9 - - + -
236B MET* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 5.0 0.8 - - - +
42B LEU* 4.2 17.8 - - - +
45B GLY* 5.9 3.8 - - - +
46B GLU* 5.8 0.4 + - - -
66B TYR* 6.0 0.2 + - - -
136B ILE* 6.1 2.2 - - - +
137B SER 3.7 4.6 + - - -
138B ASP* 2.3 42.8 + - - +
173B SER* 3.7 21.2 + - - +
174B LEU 3.5 10.0 + - - +
175B LYS* 3.0 18.6 - - - +
176B TRP* 4.9 0.4 - - - -
194B ASN 3.0 4.0 - - - +
195B LYS* 3.4 2.2 - - - -
196B MET* 2.6 66.1 + - + +
198B GLN* 3.5 17.3 + - + -
207B GLU* 3.4 31.5 + - - +
208B MET* 1.3 78.7 - - - +
210B LEU* 1.3 59.1 + - - +
211B LEU* 3.1 7.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B SER* 3.7 0.7 - - - -
174B LEU* 2.9 49.2 + - + +
175B LYS 5.7 0.7 - - - +
176B TRP* 4.1 16.4 - - + +
190B ILE* 4.1 16.8 - - + -
191B PRO* 3.4 42.6 - - + +
193B GLY* 3.3 43.5 - - - +
194B ASN 3.5 3.4 - - - +
195B LYS* 4.1 16.8 - - + +
208B MET 4.2 1.0 + - - -
209B ARG* 1.3 68.2 - - - +
211B LEU* 1.3 61.7 + - - +
212B SER* 3.5 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 4.5 7.6 - - + +
45B GLY 5.2 0.7 - - - +
48B PHE* 4.1 18.2 - - + -
49B PHE* 4.1 26.7 - - + -
52B LYS* 5.0 6.7 - - + -
172B SER 3.6 4.0 - - - +
173B SER* 3.3 28.5 - - - +
193B GLY* 3.1 0.3 - - - -
194B ASN 2.7 39.9 + - - +
196B MET* 3.8 30.3 - - + -
209B ARG* 3.8 22.0 - - + +
210B LEU* 1.3 71.4 - - - +
212B SER* 1.3 57.9 + - - +
213B ILE* 5.9 0.2 - - - -
371C LEU* 3.5 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 5.1 1.2 - - - -
171B ALA* 3.4 3.6 - - - +
172B SER* 2.9 56.3 + - - +
174B LEU* 4.2 0.7 - - - +
191B PRO* 4.2 5.4 - - - +
192B HIS 2.7 30.7 + - - -
193B GLY* 3.5 4.0 - - - -
210B LEU* 3.7 6.8 + - - +
211B LEU* 1.3 76.0 - - - +
213B ILE* 1.3 66.1 + - - +
214B TYR* 3.4 15.4 + - - -
371C LEU* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 5.8 1.6 - - + -
52B LYS* 5.4 6.7 - - + -
53B LEU* 4.7 13.5 - - + -
56B HIS* 5.5 4.7 - - + -
58B ILE* 5.6 7.4 - - + -
170B VAL 3.9 9.0 - - - +
171B ALA* 4.3 11.4 - - + -
212B SER* 1.3 78.4 - - - +
214B TYR* 1.3 71.4 + - - +
215B THR* 4.5 0.2 + - - -
220B ARG* 4.3 8.3 + - - -
364C ASN* 3.8 23.3 - - + +
367C SER* 3.2 35.2 - - - +
368C SER* 3.2 28.8 + - - +
371C LEU* 4.3 22.3 - - + +
----------------------------------------------------------
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