Contacts of the helix formed by residues 239 - 249 (chain A) in PDB entry 3R6O
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 239 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR 5.5 0.9 - - - -
236A MET* 4.3 13.6 + - - -
237A THR 3.9 2.0 + - - -
238A LEU* 1.3 74.5 - - - +
240A PHE* 1.3 57.5 + - - -
241A ALA 3.3 3.1 - - - -
242A GLU* 3.0 20.4 + - - -
243A VAL* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 3.7 25.4 - - + -
142A VAL* 3.6 29.3 - - + +
163A TYR* 4.1 1.6 - + - -
214A PHE* 3.4 36.8 - + + -
215A GLU 3.4 25.8 - - - -
217A PHE* 4.0 10.5 - + - -
233A THR* 3.8 29.2 - - + -
236A MET* 3.9 8.9 - - + +
239A GLY* 1.3 70.6 - - - +
241A ALA* 1.3 61.6 + - - +
243A VAL* 3.4 6.1 + - - +
244A VAL* 3.1 27.9 + - - +
261A THR* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 3.7 32.8 - - + +
156A ALA* 3.7 7.0 - - - +
214A PHE* 3.7 25.1 - - + -
239A GLY 3.3 0.8 - - - -
240A PHE* 1.3 78.2 - - - +
242A GLU* 1.3 59.5 + - + +
244A VAL* 3.3 4.3 + - - +
245A GLU* 3.0 27.2 + - - +
403A CL 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 3.2 41.8 + - - +
237A THR 4.1 5.0 - - - +
238A LEU* 3.9 26.5 - - + +
239A GLY* 3.0 31.5 + - - +
241A ALA* 1.3 74.5 - - + +
243A VAL* 1.3 56.9 + - - +
245A GLU* 3.6 9.7 - - - +
246A THR* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.8 28.9 - - + -
91A ASN* 3.8 4.9 - - - +
142A VAL* 5.5 0.9 - - + -
236A MET* 4.2 7.2 - - + -
238A LEU* 3.3 30.3 - - + +
239A GLY 2.8 12.7 + - - +
240A PHE* 3.5 10.1 - - - +
242A GLU* 1.3 71.2 - - - +
244A VAL* 1.3 60.1 + - + +
246A THR* 3.3 3.2 + - - -
247A VAL* 2.8 37.9 + - + +
259A ILE* 3.8 31.2 - - + -
261A THR* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 4.6 13.7 - - + -
144A ILE* 4.8 2.9 - - + -
151A ILE* 3.6 29.6 - - + -
156A ALA* 3.8 24.2 - - + +
159A HIS* 5.0 2.9 - - + -
160A VAL* 4.0 24.9 - - + -
214A PHE* 4.7 1.1 - - + -
240A PHE 3.1 14.7 + - - +
241A ALA 3.3 6.7 + - - +
243A VAL* 1.3 74.9 - - + +
245A GLU* 1.3 53.8 + - - +
247A VAL* 4.3 0.2 - - - +
248A SER* 2.8 40.9 + - - -
253A LEU* 4.7 6.0 - - + +
259A ILE* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG* 5.4 0.3 - - - -
151A ILE 3.5 24.8 + - - +
152A GLU* 4.7 10.0 - - - +
153A ARG* 2.9 63.0 + - - +
156A ALA* 5.0 0.6 - - - +
241A ALA 3.0 16.8 + - - +
242A GLU* 3.6 8.3 - - - +
244A VAL* 1.3 78.1 - - - +
246A THR* 1.3 59.8 + - - +
248A SER* 3.6 1.2 + - - -
249A ALA* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 6.1 0.9 - - + +
110A VAL* 5.7 8.5 - - + +
238A LEU* 3.7 25.7 - - + +
242A GLU* 2.8 24.3 + - - +
243A VAL* 4.1 2.0 - - - -
245A GLU* 1.3 74.5 + - - +
247A VAL* 1.3 69.5 + - + +
249A ALA* 3.4 16.8 + - + +
250A THR* 4.1 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 4.2 22.9 - - + -
88A LEU* 3.7 29.8 - - + -
110A VAL* 4.7 10.5 - - + -
243A VAL* 2.8 31.6 + - + +
244A VAL 4.3 1.6 - - - +
246A THR* 1.3 73.1 - - + +
248A SER* 1.3 60.6 + - - +
250A THR* 3.2 7.0 + - - -
251A ILE* 3.0 32.2 + - + +
253A LEU* 4.3 17.3 - - + -
259A ILE* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 3.3 13.8 - - - -
150A ARG 2.8 23.8 + - - -
151A ILE* 3.0 44.6 + - - +
244A VAL 2.8 23.5 + - - -
245A GLU 3.6 2.3 + - - -
247A VAL* 1.3 75.5 - - - +
249A ALA* 1.3 63.7 + - - +
250A THR 3.1 0.7 - - - -
251A ILE 3.2 14.8 - - - -
253A LEU* 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG* 2.7 42.1 + - + +
245A GLU* 2.9 21.4 + - + +
246A THR* 3.4 12.8 - - + +
247A VAL 3.2 0.4 - - - -
248A SER* 1.3 78.1 - - - +
250A THR* 1.3 66.1 + - + +
----------------------------------------------------------
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