Contacts of the strand formed by residues 220 - 227 (chain D) in PDB entry 4BGG
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 GLY 220 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D LYS* 3.5 1.9 - - - +
217D GLY 3.0 29.2 + - - +
218D ARG 3.3 5.0 + - - -
219D TYR* 1.3 87.6 - - - +
221D GLU* 1.3 66.8 + - - +
236D ILE 3.3 10.3 - - - -
238D SER* 4.0 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D CYS* 4.5 5.6 - - - -
215D GLY 3.3 9.9 - - - +
216D LYS* 4.3 12.3 - - + +
219D TYR* 4.0 2.1 - - - -
220D GLY* 1.3 77.8 - - - +
222D VAL* 1.3 63.8 + - - +
223D TRP* 3.0 34.2 + - + +
234D VAL 3.7 0.7 - - - +
235D LYS* 3.4 3.8 - - - +
236D ILE* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D CYS* 3.7 2.8 - - - -
214D VAL* 2.9 40.6 + - + +
215D GLY* 2.9 17.2 + - - +
219D TYR* 4.1 15.7 - - + +
221D GLU* 1.3 78.8 - - - +
223D TRP* 1.3 70.7 + - - +
233D ALA* 4.7 2.0 - - + -
234D VAL 3.2 9.2 - - - +
235D LYS* 4.1 19.7 - - + -
1000D 844 3.9 49.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU* 3.8 30.3 - - + -
211D LEU 4.2 4.5 - - - -
212D GLU* 3.2 34.3 - - - -
213D CYS* 3.5 27.5 - - + -
214D VAL* 4.3 5.2 - - - -
221D GLU* 3.0 36.0 + - + +
222D VAL* 1.3 80.2 - - - +
224D ARG* 1.3 63.2 + - - +
233D ALA* 3.4 7.4 - - - +
234D VAL* 2.8 46.8 + - + +
236D ILE* 3.7 24.5 - - + +
285D TYR* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU 3.9 0.5 - - - -
211D LEU* 2.9 54.2 + - - +
212D GLU* 2.7 53.2 + - + +
214D VAL* 4.3 3.9 - - + +
223D TRP* 1.3 74.5 - - - +
225D GLY* 1.3 61.0 + - - +
231D ASN* 3.3 32.4 + - - +
232D VAL 3.7 3.6 - - - +
285D TYR* 3.4 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 5.8 0.7 - - - -
209D THR 3.1 15.3 - - - -
210D LEU* 4.4 2.0 - - - -
211D LEU* 4.1 7.0 - - - -
223D TRP 3.8 1.4 + - - -
224D ARG* 1.3 74.9 - - - +
226D SER* 1.3 59.8 + - - -
231D ASN* 3.3 10.0 - - - +
232D VAL* 2.8 41.3 + - - -
234D VAL* 4.9 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D ASP 4.1 0.5 - - - +
208D ILE* 3.3 8.2 - - - -
209D THR* 2.9 42.8 + - - -
211D LEU* 4.0 18.8 - - - +
225D GLY* 1.3 72.6 - - - -
227D TRP* 1.3 62.4 + - - +
229D GLY* 4.1 17.5 + - - -
230D GLU 3.5 8.2 + - - -
231D ASN* 4.7 1.9 + - - +
232D VAL* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D VAL* 5.0 13.2 + - - +
207D ASP* 3.0 40.6 - - + +
208D ILE* 4.3 6.1 - - + -
226D SER* 1.3 76.0 + - - +
228D GLN* 1.3 102.3 + - + +
229D GLY 3.1 0.4 - - - -
230D GLU* 2.8 32.1 + - + +
232D VAL* 4.1 30.5 - - + -
266D ILE* 4.3 26.9 - - + -
282D ILE* 6.3 0.7 - - + -
----------------------------------------------------------
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