Contacts of the strand formed by residues 211 - 214 (chain G) in PDB entry 2BM8
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 LEU 211 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G MET* 3.9 40.2 - - + -
173G VAL* 4.2 12.8 - - + -
177G LEU* 4.4 16.8 - - + -
183G PHE* 4.8 7.4 - - + -
207G PHE* 2.9 17.4 + - + +
208G ARG* 3.7 11.6 - - - +
210G VAL* 1.3 81.8 - - + +
212G SER* 1.3 60.8 + - - +
229G LEU* 4.0 16.2 - - + -
230G ARG* 3.3 31.2 - - - +
231G ARG* 3.7 6.5 - - + +
232G VAL* 5.0 2.9 - - - -
37H PRO* 5.6 0.3 - - - +
38H LEU* 3.1 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G LEU* 1.3 74.5 - - - +
213G MET* 1.3 60.7 + - - +
214G ASP 3.5 0.7 + - - -
229G LEU* 3.2 4.9 - - - -
230G ARG* 2.9 35.0 + - - +
232G VAL* 3.5 16.4 - - - +
35H ASP* 2.8 43.0 + - - +
36H TRP 3.7 11.9 - - - -
37H PRO* 5.3 1.6 - - - -
38H LEU* 3.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G SER* 1.3 72.0 - - - +
214G ASP* 1.3 61.8 + - - +
215G MET* 3.3 14.7 + - + -
218G ALA* 3.7 18.6 - - + -
226G ARG* 3.9 28.9 - - + +
228G VAL 3.5 8.7 - - - +
229G LEU* 4.0 6.5 - - + -
34H ARG 3.3 2.1 - - - +
36H TRP* 2.9 42.3 + - + +
38H LEU* 3.5 15.8 - - + +
41H TRP* 3.6 34.8 - - + +
44H ALA* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G TYR* 2.6 34.6 + - + -
212G SER 3.5 2.8 + - - -
213G MET* 1.3 69.6 - - - +
215G MET* 1.3 59.7 + - - +
216G LEU* 3.0 13.2 + - - +
217G TYR* 3.3 9.7 + - - +
218G ALA* 3.0 28.3 + - - +
228G VAL* 3.0 25.0 + - + +
230G ARG* 3.8 15.0 + - + +
34H ARG* 2.9 38.0 + - - +
35H ASP* 5.0 3.1 - - - -
----------------------------------------------------------
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