Contacts of the strand formed by residues 210 - 214 (chain D) in PDB entry 4UC5
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 HIS 210 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LYS* 6.0 3.6 - - + +
111C ASN* 5.6 8.6 + - + +
119C PHE* 3.5 64.6 - + + +
176D GLU* 3.1 21.3 + - - +
208D SER* 5.2 0.4 - - - -
209D HIS* 1.3 79.2 - - - +
211D PHE* 1.3 67.4 + - - +
222D ILE* 3.9 30.7 - - + -
223D VAL 3.2 3.8 - - - -
224D HIS* 3.2 48.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 5.7 1.8 - - + -
149D MET* 3.7 29.8 - - + -
173D VAL* 4.3 9.4 - - + -
176D GLU* 3.8 35.0 - - + +
177D LEU* 3.9 23.6 - - + -
180D GLY* 5.3 1.3 - - - -
210D HIS* 1.3 78.9 - - - +
212D LEU* 1.3 75.4 + - - +
213D SER* 3.9 18.8 - - - -
222D ILE* 3.7 3.1 - - - +
223D VAL* 2.8 57.7 + - + +
225D THR* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 3.7 27.6 - - + -
111C ASN* 5.4 2.9 - - - +
121C ILE* 4.3 14.4 - - + -
125C LEU* 5.3 2.5 - - + -
148C ASP* 3.7 18.3 + - - +
150C ILE* 3.4 38.9 - - + +
151C THR* 3.7 31.0 - - + -
154C TYR* 5.3 3.1 - - + -
149D MET* 3.9 10.6 - - - +
173D VAL* 5.5 1.2 - - - +
211D PHE* 1.3 80.6 - - - +
213D SER* 1.3 63.2 + - - +
221D ALA 3.4 5.6 - - - +
222D ILE* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE* 3.8 10.7 - - - +
149D MET 2.5 27.6 + - - -
150D ILE* 4.0 7.2 - - - -
153D GLN* 4.2 8.3 - - - +
211D PHE* 3.9 6.9 + - - -
212D LEU* 1.3 75.5 - - - +
214D VAL* 1.3 69.6 + - - +
220D SER* 3.5 4.3 - - - -
221D ALA* 2.6 39.0 + - - -
223D VAL* 3.7 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 4.6 2.4 - - - +
214C VAL* 3.8 25.6 - - + -
220C SER* 4.2 11.9 - - - -
21D PRO* 4.9 4.9 - - + -
150D ILE* 4.0 29.8 - - + -
153D GLN* 2.9 33.6 + - + +
213D SER* 1.3 89.3 + - - +
215D THR* 1.3 71.0 + - - +
218D GLY* 3.8 23.8 - - - +
219D HIS 3.0 8.1 - - - +
221D ALA* 4.0 4.7 - - - +
223D VAL* 5.4 0.3 - - - +
----------------------------------------------------------
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