Contacts of the helix formed by residues 242 - 249 (chain A) in PDB entry 4ECX
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 SER 242 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 3.8 30.3 - - - +
149A GLY* 5.3 2.2 - - - -
238A VAL* 3.3 20.1 - - - +
239A SER* 2.8 34.1 + - - -
241A GLY* 1.3 76.8 - - - +
243A VAL* 1.3 64.1 + - - +
244A PRO* 3.5 1.0 - - - -
245A GLN* 3.6 5.5 + - - +
246A LEU* 3.0 23.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
222A LEU* 3.9 31.2 - - + -
238A VAL* 4.5 4.3 - - + -
239A SER 3.7 11.0 - - - +
240A HIS* 3.2 18.1 + - - +
242A SER* 1.3 75.7 - - - +
244A PRO* 1.3 68.9 - - + +
246A LEU* 3.2 5.1 + - + -
247A PHE* 2.7 61.3 + - + +
302A CYS 4.4 2.5 - - - +
303A ARG* 4.2 7.0 - - - +
304A GLY* 4.0 18.4 - - - +
506A GOL 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS 3.9 5.2 - - - +
241A GLY* 3.3 17.0 - - - +
243A VAL* 1.3 95.2 - - + +
245A GLN* 1.3 64.5 + - + +
247A PHE* 4.9 0.4 - - + -
248A SER* 3.1 9.2 + - - -
506A GOL 2.6 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY* 5.8 2.7 + - - -
152A GLN* 4.3 15.4 + - - -
241A GLY 5.9 1.8 - - - +
242A SER* 3.6 7.2 + - - +
243A VAL 3.3 0.4 - - - -
244A PRO* 1.3 76.7 - - + +
246A LEU* 1.3 66.8 + - - +
248A SER* 2.8 25.0 + - - -
249A GLN* 4.1 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 3.5 31.6 - - + +
222A LEU* 5.4 0.4 - - + -
225A LEU* 4.1 20.6 - - + -
229A LEU* 4.5 9.9 - - + -
238A VAL* 4.1 34.8 - - + -
242A SER* 3.0 19.1 + - - +
243A VAL* 3.7 5.2 - - - +
245A GLN* 1.3 79.0 - - - +
247A PHE* 1.3 69.4 + - + +
248A SER 3.4 0.2 + - - -
249A GLN* 3.8 2.4 + - - +
250A MET* 3.4 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A VAL* 5.9 0.2 - - + -
222A LEU* 3.8 24.9 - - + -
225A LEU* 3.8 25.6 - - + -
243A VAL* 2.7 36.1 + - + +
244A PRO* 4.9 0.2 - - + -
246A LEU* 1.3 81.8 - - + +
248A SER* 1.3 63.8 + - - +
249A GLN 3.1 4.8 + - - -
250A MET* 3.3 16.4 + - + -
255A ILE* 4.7 7.2 - - + -
275A MET* 3.6 35.0 + - + -
276A GLY* 3.0 29.4 + - - +
301A MET* 3.3 29.4 - - + -
302A CYS 3.5 18.4 - - - +
304A GLY 4.4 0.4 - - - -
506A GOL 3.7 5.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
244A PRO 3.1 17.4 + - - -
245A GLN* 2.8 20.4 + - - -
247A PHE* 1.3 77.2 - - - +
249A GLN* 1.3 71.3 + - - +
274A TYR* 3.5 20.3 - - - +
276A GLY* 4.7 0.2 - - - -
277A GLU* 5.8 0.7 - - - +
506A GOL 3.3 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN 4.1 2.3 + - - +
246A LEU 3.8 5.1 + - - +
247A PHE 3.1 0.2 - - - -
248A SER* 1.3 93.9 + - - +
250A MET* 1.3 57.9 + - - +
251A PRO* 3.4 11.6 - - - +
274A TYR* 3.4 25.4 + - + -
----------------------------------------------------------
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