Contacts of the strand formed by residues 218 - 223 (chain A) in PDB entry 3R6O
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 ASP 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A THR* 5.0 4.9 - - - +
217A PHE* 1.3 73.4 - - - +
219A PHE* 1.3 63.4 + - - +
231A GLY 3.4 5.6 - - - +
232A SER* 3.1 30.8 + - - -
286A HIS* 5.5 1.4 - - - -
287A SER* 3.6 19.1 + - - -
288A ALA 4.2 1.4 + - - -
402A CL 3.5 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.2 33.0 - + - -
138A ILE* 3.7 36.1 - - + -
139A GLU* 4.9 0.4 - - - -
140A ILE* 3.8 32.1 - - + -
165A LEU* 4.6 0.4 - - + -
217A PHE 4.0 5.8 - - - -
218A ASP* 1.3 79.9 - - - +
220A GLU* 1.3 63.3 + - - +
230A SER* 3.5 2.3 + - - -
231A GLY* 2.8 57.8 + - - +
232A SER 3.8 2.9 - - - -
233A THR* 4.0 7.6 - - + -
262A GLY 5.2 1.3 - - - -
264A PRO* 3.7 24.9 - - + -
286A HIS* 3.3 11.7 - - - +
287A SER* 4.0 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.2 9.4 - - - +
219A PHE* 1.3 77.1 - - - +
221A LEU* 1.3 61.8 + - - +
222A ARG* 2.3 49.8 + - + -
227A LEU* 3.9 11.7 - - + +
229A GLN 3.3 11.7 - - - +
230A SER* 4.6 5.1 + - - +
284A GLU 5.4 0.4 - - - +
285A ALA* 3.3 0.7 - - - -
286A HIS* 2.9 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.6 27.4 - - + -
138A ILE* 3.8 28.7 - - + +
167A ASN* 3.2 30.5 - - - +
220A GLU* 1.3 75.0 - - - +
222A ARG* 1.3 66.2 + - - +
223A ILE* 4.0 10.8 - - + -
227A LEU* 3.8 2.8 - - - +
228A ARG* 2.8 41.5 + - + -
229A GLN* 2.9 25.4 + - + +
283A ILE* 3.7 19.3 - - + -
284A GLU 3.4 4.0 - - - +
285A ALA* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 2.3 42.1 + - - +
221A LEU* 1.3 79.6 - - - +
223A ILE* 1.3 68.0 + - - +
225A GLY* 2.9 28.5 + - - -
226A GLU 2.9 14.8 - - - +
227A LEU* 3.7 26.2 - - + +
228A ARG 4.2 0.7 - - - +
283A ILE* 3.5 0.9 - - - -
284A GLU* 2.7 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.7 14.4 - - + -
221A LEU* 4.0 5.6 - - + -
222A ARG* 1.3 78.8 - - - +
224A ASN* 1.3 78.9 + - - +
226A GLU* 2.9 26.1 + - - +
228A ARG* 3.4 47.2 + - + +
275A ARG 5.0 0.2 - - - +
277A LEU* 3.6 27.4 - - + -
278A ARG* 5.8 0.2 + - - -
281A ASP* 3.6 35.9 - - + +
282A VAL 3.2 5.2 - - - +
283A ILE* 4.2 11.0 - - + -
----------------------------------------------------------
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