Contacts of the strand formed by residues 219 - 223 (chain C) in PDB entry 1X1O
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 219 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS* 2.9 51.8 - - + +
196B TYR* 3.6 11.7 - - + -
198C LYS* 4.3 14.4 - - + +
199C VAL 3.0 4.7 + - - +
200C GLU* 3.4 49.5 - - + +
201C VAL* 3.4 4.9 + - - +
217C ALA* 3.4 11.9 - - - +
218C ASP* 1.3 94.7 - - - +
220C ILE* 1.3 62.1 + - - +
241C VAL* 4.9 1.8 - - - -
242C PRO* 3.3 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C GLU* 4.2 2.9 - - - -
201C VAL* 3.3 17.9 - - + +
203C VAL* 3.4 35.0 - - + -
209C LEU* 3.5 25.4 - - + -
212C ALA* 4.8 4.5 - - + -
213C LEU* 5.1 3.6 - - + -
217C ALA* 5.8 2.7 - - + -
219C LEU* 1.3 77.2 - - - +
221C LEU* 1.3 67.6 + - - +
222C LEU* 3.7 11.5 + - + +
241C VAL* 4.1 13.0 - - + -
242C PRO 3.3 9.9 + - - +
243C LEU* 3.2 31.6 - - + -
244C GLU* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 4.4 21.8 - - + -
172C LYS* 6.2 0.7 - - - -
200C GLU* 4.1 9.8 + - + +
201C VAL 2.9 16.9 + - - +
202C GLU* 3.2 28.8 - - + +
203C VAL* 3.0 30.0 + - - +
220C ILE* 1.3 72.7 - - - +
222C LEU* 1.3 63.8 + - - +
223C ASP* 5.0 0.7 - - + +
244C GLU* 3.0 50.0 - - + +
246C SER* 3.3 32.3 - - - +
266C SER* 4.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.2 10.3 - - + -
209C LEU* 4.4 8.1 - - + -
220C ILE* 3.7 27.6 - - + +
221C LEU* 1.3 70.1 - - - +
223C ASP* 1.3 58.2 + - - +
224C ASN 3.6 0.3 + - - -
225C PHE* 3.9 30.6 + - + +
230C LEU* 4.9 22.2 - - + +
233C ALA* 4.1 25.6 - - + -
234C VAL* 6.5 0.2 - - + -
243C LEU* 5.0 11.9 - - + -
244C GLU 2.8 18.8 + - - +
245C ALA* 3.9 9.3 - - + +
246C SER* 2.8 33.2 + - - +
262C VAL* 5.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C GLU* 4.3 6.2 - - - +
202C GLU* 4.9 22.7 - - + +
203C VAL 3.1 20.5 + - - +
204C ARG* 3.7 31.9 - - + +
221C LEU* 3.5 1.4 + - + -
222C LEU* 1.3 68.7 - - - +
224C ASN* 1.3 95.2 + - - +
225C PHE* 3.2 9.9 + - - -
246C SER* 3.6 8.9 + - - -
247C GLY* 4.2 9.0 + - - -
----------------------------------------------------------
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