Contacts of the strand formed by residues 212 - 218 (chain A) in PDB entry 5UMS
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 GLY 212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLN* 4.2 1.7 - - - -
207A CYS* 2.9 39.1 + - - +
210A PRO 3.5 0.6 + - - -
211A ARG* 1.3 78.3 - - - +
213A ARG* 1.3 63.4 + - - -
214A TYR* 3.7 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU* 3.0 56.8 + - - +
205A LEU 3.4 5.5 + - - +
206A GLN* 3.5 42.2 + - - +
212A GLY* 1.3 72.5 - - - -
214A TYR* 1.3 66.9 + - - +
227A GLY* 4.2 8.7 - - - -
228A LYS* 3.6 31.5 + - - +
281A GLU* 5.6 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU* 4.2 0.9 - - - -
205A LEU* 2.9 37.6 + - - +
207A CYS* 3.6 20.9 - - - -
210A PRO* 3.8 32.8 - - + +
211A ARG 4.2 5.1 + - - -
212A GLY* 3.6 21.8 - - - -
213A ARG* 1.3 78.0 - - - +
215A ASP* 1.3 63.4 + - - +
225A LEU* 3.7 33.2 - - + -
226A HIS 3.5 5.8 - - - -
227A GLY* 3.4 36.3 - - - -
230A PHE* 4.0 22.7 - - - -
232A TYR* 4.2 18.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 4.2 11.5 - - + +
202A PHE 3.2 7.0 - - - +
203A ARG* 3.3 24.7 + - - +
204A GLU* 2.9 33.3 + - - +
214A TYR* 1.3 75.1 - - - +
216A ILE* 1.3 62.3 + - - +
217A ARG* 4.0 5.0 + - + +
224A HIS 3.4 1.1 - - - +
225A LEU* 3.6 3.1 - - - -
226A HIS* 2.9 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A CYS 4.1 0.2 - - - +
201A ILE* 3.4 2.5 - - - -
202A PHE* 2.7 46.4 + - + +
205A LEU* 3.5 30.1 - - + -
207A CYS* 5.5 0.9 - - - -
214A TYR* 4.2 1.1 + - + +
215A ASP* 1.3 74.8 - - - +
217A ARG* 1.3 62.8 + - - +
218A ILE* 3.9 23.7 + - + -
223A LEU* 4.0 23.8 - - + -
224A HIS 3.5 2.0 - - - -
225A LEU* 3.6 25.4 - - + -
257A ILE* 5.4 2.5 - - + -
273A LEU* 4.4 10.5 - - + -
275A LEU* 3.9 19.5 - - + -
314A VAL* 6.1 1.6 - - + -
318A MET* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA* 4.3 1.8 - - + -
200A CYS 3.8 3.8 - - - -
201A ILE* 3.9 32.4 - - + +
215A ASP* 5.0 4.1 + - + +
216A ILE* 1.3 74.5 - - - +
218A ILE* 1.3 62.5 + - - +
219A TYR* 3.7 29.3 + - + -
223A LEU* 3.3 5.9 - - - +
224A HIS* 2.8 66.9 + - + +
226A HIS* 3.3 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA* 3.5 5.0 - - - +
199A ILE* 2.8 41.6 + - + -
200A CYS* 2.9 38.3 + - - +
202A PHE* 4.1 17.3 - - + -
216A ILE* 3.9 22.9 - - + +
217A ARG* 1.3 72.3 - - - +
219A TYR* 1.3 63.0 + - - +
223A LEU* 4.1 6.5 - - + -
236A TYR* 3.4 8.3 - - - +
317A VAL* 4.3 4.3 - - + -
318A MET* 4.5 11.4 - - - -
321A LEU* 3.4 42.0 - - + -
----------------------------------------------------------
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