Contacts of the strand formed by residues 221 - 225 (chain C) in PDB entry 1U75
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 GLU 221 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ASP* 5.0 14.4 - - + +
187C TYR* 3.5 12.3 + - - -
213C LEU* 3.8 30.1 - - + -
214C GLU 3.6 8.5 - - - +
215C LYS* 3.3 35.3 + - + +
220C ASN* 1.3 74.0 - - - +
222C GLN* 1.3 59.3 + - - +
233C PRO* 3.4 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 4.1 2.6 + - - -
187C TYR* 3.3 30.8 - - + +
188C GLU* 2.9 25.3 + - - +
212C LYS 3.6 1.2 - - - +
213C LEU* 3.6 7.8 - - - -
214C GLU 3.1 33.3 + - - +
216C ASN* 2.7 37.3 - - + +
221C GLU* 1.3 75.3 - - - +
223C TRP* 1.3 62.8 + - - +
224C ASP* 3.0 31.6 + - - +
230C MET* 3.3 9.7 - - + +
231C MET 3.9 10.5 - - - +
232C LEU* 5.2 0.2 - - - -
233C PRO* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C TRP* 3.2 43.0 - - + -
212C LYS* 3.7 2.2 - - - -
213C LEU* 3.4 55.5 - - + +
222C GLN* 1.3 71.1 - - - +
224C ASP* 1.3 62.5 + - - +
230C MET* 3.2 4.3 - - - -
231C MET* 2.8 54.3 + - + +
232C LEU 4.2 4.0 - - - -
233C PRO* 4.2 13.8 - - + +
236C TYR* 3.6 59.1 - + + +
240C GLN* 5.4 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 4.3 10.0 + - - -
210C ASP 3.7 0.3 - - - +
211C TRP* 3.5 4.7 - - - -
212C LYS* 3.0 33.3 + - - +
214C GLU* 3.4 36.9 - - - +
216C ASN* 5.9 0.7 - - - +
222C GLN* 3.0 33.0 - - - +
223C TRP* 1.3 78.1 - - - +
225C SER* 1.3 64.6 + - - +
229C TYR 3.4 13.3 - - - +
230C MET* 3.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLU* 3.2 28.6 + - - -
210C ASP 3.3 17.5 - - - -
211C TRP* 3.7 16.1 - - - -
224C ASP* 1.3 77.8 - - - +
226C LYS* 1.3 58.2 + - - +
227C SER* 3.0 6.0 + - - -
228C GLY* 3.0 19.4 + - - -
229C TYR* 3.1 29.9 + - - +
----------------------------------------------------------
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