Contacts of the helix formed by residues 214 - 219 (chain B) in PDB entry 1U2X
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 PHE 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.9 30.7 - - + -
97B VAL* 3.8 14.8 - - - +
98B ASN 4.1 2.9 - - - -
99B GLU* 3.6 46.4 - - + +
102B ASN* 3.8 12.3 - - - -
179B LEU 3.5 21.8 - - - -
181B ILE 5.3 0.2 - - - -
212B ALA* 3.9 16.7 - - + -
213B ARG* 1.3 77.3 - - - +
215B GLU* 1.3 68.0 + - - +
216B SER* 3.4 22.8 + - - -
217B ILE* 3.3 43.5 - - + +
218B SER* 3.8 4.0 + - - -
249B ARG* 3.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 1.3 75.8 - - - +
216B SER* 1.3 59.5 + - - +
218B SER* 2.6 30.0 + - - +
219B ARG* 3.1 31.1 + - - +
249B ARG* 3.4 28.5 + - - +
251B LYS 4.7 0.2 - - - +
252B TYR* 3.4 19.5 - - + -
253B SER* 2.7 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 2.9 38.0 + - - -
141B PHE* 3.2 23.9 - - - -
178B PRO* 3.8 16.3 - - - +
214B PHE* 3.4 9.1 + - - -
215B GLU* 1.3 79.7 - - - +
217B ILE* 1.3 60.3 + - - +
218B SER 3.2 0.8 + - - -
219B ARG* 4.0 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 3.4 17.9 - - + -
178B PRO* 3.6 26.5 - - + -
180B LYS* 3.8 50.2 + - + +
212B ALA 3.6 28.0 - - - +
213B ARG* 4.3 2.9 - - - -
214B PHE* 3.3 48.7 - - + +
216B SER* 1.3 76.5 + - - +
218B SER* 1.3 60.4 + - - +
219B ARG 3.5 1.3 - - - -
220B ILE* 3.4 17.7 - - - +
247B GLY* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ARG* 5.5 2.5 - - - -
214B PHE 3.8 8.2 + - - -
215B GLU 2.6 20.3 + - - -
217B ILE* 1.3 80.9 - - - +
219B ARG* 1.3 54.6 + - - +
220B ILE* 3.0 15.0 + - - +
247B GLY 3.3 23.1 - - - +
248B LEU* 3.7 1.7 - - - +
249B ARG* 3.5 24.0 - - - -
252B TYR* 2.6 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PRO* 4.2 1.6 - - - +
141B PHE* 3.6 17.7 - - + -
215B GLU* 3.1 39.5 + - - +
216B SER* 4.0 15.8 + - - +
217B ILE 3.5 2.8 - - - -
218B SER* 1.3 74.8 - - - +
220B ILE* 1.3 61.7 + - - +
221B GLU* 3.3 15.9 + - - +
252B TYR* 3.9 21.6 - - + +
253B SER* 4.2 1.4 - - - -
254B ASP* 3.1 47.1 + - - +
256B LYS* 4.1 1.8 - - - +
261B TYR* 3.0 44.0 + - + +
----------------------------------------------------------
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