Contacts of the strand formed by residues 212 - 216 (chain B) in PDB entry 5E5R
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 THR 212 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 5.0 2.2 - - - +
295A HIS* 4.7 6.5 + - + +
296A VAL* 4.1 25.4 - - + -
129B ARG* 3.9 28.5 + - + +
130B SER 4.3 4.7 - - - +
132B VAL* 4.2 12.6 - - + -
142B LEU* 5.0 8.7 - - + +
143B LEU 5.6 0.2 + - - -
157B TRP* 5.7 2.0 - - - -
192B GLY 3.6 1.6 - - - +
193B ASN* 4.3 0.2 - - - -
194B TYR* 2.5 46.5 + - - +
210B SER 4.5 0.2 + - - -
211B PRO* 1.3 72.8 - - - +
213B PRO* 1.3 75.2 - - + +
214B LEU* 3.6 4.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG 4.3 9.6 - - - +
131B THR* 3.5 37.2 - - + -
132B VAL 3.2 22.7 + - - -
192B GLY 3.3 6.7 - - - +
193B ASN* 3.5 21.1 - - - +
211B PRO* 3.5 10.8 - - + +
212B THR* 1.3 86.6 - - + +
214B LEU* 1.3 60.3 + - - +
215B VAL* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 5.8 2.2 - - + -
132B VAL* 3.2 16.6 - - + +
134B VAL* 4.7 23.8 - - + -
140B VAL* 5.6 0.9 - - + -
142B LEU* 3.8 26.9 - - + -
183B ILE* 4.8 5.2 - - + -
186B VAL* 5.7 3.1 - - + -
190B ASP* 3.3 32.3 - - + +
191B VAL* 3.4 8.5 - - + +
192B GLY* 2.9 26.7 + - - +
194B TYR* 3.5 31.6 - - + -
212B THR* 4.7 5.2 - - + +
213B PRO* 1.3 74.5 - - - +
215B VAL* 1.3 65.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 5.2 8.7 - - - +
132B VAL 3.3 4.4 + - - +
133B SER* 3.9 24.5 - - - +
134B VAL* 3.0 31.8 + - - +
191B VAL* 4.1 18.2 - - + -
213B PRO* 6.4 0.7 - - + -
214B LEU* 1.3 79.8 - - - +
216B LEU* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B SER* 4.1 5.4 + - - -
134B VAL* 3.4 3.8 - - + +
136B GLU* 3.8 37.9 - - + +
186B VAL* 3.8 22.7 - - + -
188B PRO* 3.7 33.2 - - + +
191B VAL* 3.7 20.0 - - + +
214B LEU* 6.5 0.2 - - + -
215B VAL* 1.3 85.2 - - - +
217B ARG* 1.3 66.5 + - - +
218B SER* 3.9 4.5 + - - -
----------------------------------------------------------
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