Contacts of the helix formed by residues 209 - 216 (chain B) in PDB entry 3PU3
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 PRO 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.6 17.7 - - + +
137B LEU* 4.2 18.2 - - + +
207B GLU 3.7 0.2 - - - -
208B PRO* 1.3 91.0 - - + +
210B ASP* 1.3 66.1 + - - +
211B ILE* 4.2 12.1 - - + -
212B VAL* 3.0 31.3 + - + +
213B LYS* 3.3 10.0 + - - +
258B TRP* 3.6 31.2 - - + -
312B THR* 5.1 2.9 - - + -
314B PHE* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B EDO 2.7 32.3 + - - -
134B GLY 5.4 1.3 - - - +
135B LEU 2.8 22.4 + - - +
136B GLY* 3.9 14.0 + - - +
208B PRO 3.6 1.8 + - - +
209B PRO* 1.3 69.9 - - - +
211B ILE* 1.3 61.7 + - - +
213B LYS* 3.2 16.8 + - - +
214B LYS* 3.1 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 3.8 30.7 + - + +
114B THR* 3.7 29.8 - - - +
115B LEU* 3.8 7.2 - - - +
118B MET* 4.1 19.1 - - + -
135B LEU* 4.5 4.0 + - + -
209B PRO* 4.2 6.7 - - + +
210B ASP* 1.3 80.1 - - - +
212B VAL* 1.3 64.7 + - + +
214B LYS* 3.4 12.9 + - + +
215B LEU* 3.1 40.8 + - + +
314B PHE* 3.8 29.8 - - + -
336B PHE* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B EDO 3.8 30.5 - - - +
208B PRO* 4.6 2.5 - - + -
209B PRO* 3.0 28.0 + - + +
211B ILE* 1.3 75.5 - - + +
213B LYS* 1.3 62.2 + - + +
215B LEU* 3.3 1.0 + - - +
216B SER* 2.9 29.3 + - - -
258B TRP* 3.5 22.4 - - + -
314B PHE* 4.1 10.8 - - + -
336B PHE* 3.8 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B EDO 6.6 0.2 - - - -
207B GLU* 2.7 42.1 + - - +
208B PRO* 3.4 37.0 - - + -
209B PRO 3.8 7.4 - - - +
210B ASP* 3.2 15.8 + - - +
212B VAL* 1.3 79.1 - - + +
214B LYS* 1.3 59.0 + - + +
215B LEU 3.6 0.2 + - - -
216B SER* 3.7 0.8 + - - -
219B GLU* 3.2 45.5 - - - +
220B ASN* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 5.7 7.9 - - - +
115B LEU* 4.8 27.5 - - + +
210B ASP* 3.1 29.6 + - - +
211B ILE* 3.7 22.9 - - + +
212B VAL 3.2 0.2 - - - -
213B LYS* 1.3 78.7 - - + +
215B LEU* 1.3 61.8 + - + +
220B ASN* 3.0 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B EDO 3.8 19.7 - - - -
115B LEU* 3.5 29.4 - - + -
118B MET* 3.8 38.4 - - + -
123B PHE* 4.7 6.1 - - + -
211B ILE* 3.1 26.0 + - + +
214B LYS* 1.3 77.7 - - - +
216B SER* 1.3 65.1 + - - +
217B TRP* 3.3 5.0 + - - -
220B ASN* 4.0 0.8 + - - -
221B TYR* 6.0 0.2 - - - -
336B PHE* 3.9 26.7 - - + -
337B LEU 4.0 1.1 - - - -
338B HIS* 3.2 29.2 - - + +
339B SER 4.6 1.0 + - - -
340B LEU* 4.6 7.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
22B EDO 5.2 5.9 + - - -
212B VAL* 2.9 20.9 + - - -
213B LYS* 3.7 0.6 + - - -
214B LYS 3.5 1.6 - - - -
215B LEU* 1.3 75.8 - - - +
217B TRP* 1.3 63.7 + - - +
218B VAL* 3.1 12.5 + - - +
219B GLU* 3.0 30.1 + - - +
220B ASN* 2.7 29.7 + - - +
221B TYR* 5.7 0.2 - - - -
336B PHE* 4.1 17.9 - - - +
337B LEU 3.3 7.1 + - - -
----------------------------------------------------------
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