Contacts of the strand formed by residues 203 - 208 (chain A) in PDB entry 3CBG
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 VAL 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.3 28.7 - - - +
157A LEU* 3.9 20.2 - - + -
197A LEU* 3.9 2.9 - - + +
200A ASP* 3.1 31.5 - - + +
201A GLU* 3.3 0.7 - - - -
202A ARG* 1.3 87.3 - - + +
204A ARG* 1.3 63.9 + - - +
205A ILE* 3.6 22.1 + - + +
217A ALA* 3.9 17.7 - - + +
218A LEU 3.2 11.7 - - - +
219A LYS* 4.2 4.5 - - - -
220A LYS* 4.1 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 1.3 71.1 - - - +
205A ILE* 1.3 61.8 + - - +
216A LEU 3.6 1.6 - - - +
218A LEU* 2.9 56.0 + - + +
220A LYS* 3.7 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN 5.6 0.7 - - - +
197A LEU* 3.9 31.2 - - + +
198A ALA* 4.1 16.2 - - + +
203A VAL* 3.6 26.8 + - + +
204A ARG* 1.3 78.8 - - - +
206A SER* 1.3 64.6 + - - +
207A VAL* 4.5 14.8 - - + -
215A THR* 4.1 15.3 - - + -
216A LEU 3.0 6.7 - - - +
217A ALA* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 1.3 80.1 - - - +
207A VAL* 1.3 63.9 + - - +
208A ILE* 3.3 24.1 + - - +
214A MET 3.9 0.2 - - - +
215A THR* 3.5 2.1 - - - -
216A LEU* 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 3.9 26.9 - - + -
172A LEU* 4.9 15.3 - - + -
205A ILE* 4.5 17.0 - - + -
206A SER* 1.3 72.6 + - - +
208A ILE* 1.3 67.7 + - - +
209A PRO* 3.7 10.6 - - + +
214A MET 3.8 2.2 - - - -
215A THR* 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 4.4 20.0 - - + -
206A SER* 3.3 32.3 - - - +
207A VAL* 1.3 76.8 - - - +
209A PRO* 1.3 66.8 - - + +
210A LEU* 3.0 29.3 + - + -
213A GLY* 3.6 2.0 - - - -
214A MET* 2.8 47.5 + - + +
216A LEU* 4.2 18.6 - - + -
----------------------------------------------------------
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