Contacts of the helix formed by residues 240 - 250 (chain A) in PDB entry 1M6X
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 ASP 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 4.2 0.9 - - - -
235A ALA* 3.7 17.6 + - - +
237A GLY 4.9 2.0 - - - +
238A ARG 3.7 4.4 + - - +
239A ILE* 1.3 76.2 - - - +
241A PRO* 1.3 71.0 - - - +
242A LEU* 2.8 21.8 + - - +
243A VAL* 3.1 28.1 + - + +
244A TYR* 3.1 23.8 - - - -
418A TYR* 2.4 32.2 + - - -
422A ARG* 3.1 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TRP* 6.0 0.9 - - + -
180A PHE* 5.7 0.2 - - - -
183A LEU* 3.6 24.2 - - + -
187A ILE* 4.2 22.4 - - + -
232A PHE* 4.7 12.8 - - + -
233A PHE* 3.1 40.8 - - + +
235A ALA* 3.3 19.3 - - + -
239A ILE* 4.0 2.2 - - + +
240A ASP* 1.3 82.5 - - - +
242A LEU* 1.3 53.4 + - - +
244A TYR* 2.9 5.5 + - - +
245A LEU* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 3.7 30.3 - - + -
232A PHE* 4.1 4.3 - - + +
233A PHE* 3.4 26.5 - - - +
234A SER* 3.2 32.1 - - - +
240A ASP* 2.8 11.0 + - - +
241A PRO* 1.3 72.7 - - - +
243A VAL* 1.3 56.1 + - - +
245A LEU* 3.4 5.3 - - + +
246A ASP* 2.8 28.9 + - - +
414A TYR* 4.0 13.9 - - + +
415A LEU* 3.6 14.3 - - + +
418A TYR* 3.5 36.3 - - + -
419A ILE* 4.5 1.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
240A ASP* 3.3 37.2 - - + +
241A PRO 2.9 1.0 + - - -
242A LEU* 1.3 74.6 - - - +
244A TYR* 1.3 71.5 + - + +
246A ASP* 3.0 10.8 + - + +
247A GLU* 2.9 37.1 + - + +
418A TYR* 4.8 6.1 - - + -
419A ILE* 4.4 8.3 - - + -
422A ARG* 4.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.3 30.8 - - + +
163A ASN* 4.5 8.1 + - - -
176A THR* 4.9 1.1 - - - +
179A GLN* 3.6 47.9 + - + -
180A PHE* 3.7 19.8 - - + +
183A LEU* 3.8 18.4 - - + -
238A ARG 4.9 4.0 + - - -
239A ILE* 4.2 10.7 - - + +
240A ASP 3.1 36.6 - - - -
241A PRO 2.9 8.6 + - - +
243A VAL* 1.3 82.0 - - + +
245A LEU* 1.3 57.9 + - - +
247A GLU* 3.8 9.7 - - + +
248A PHE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 3.7 30.0 - - + -
203A PHE* 4.9 10.1 - - + -
215A ILE* 3.6 32.8 - - + -
232A PHE* 3.9 26.5 - - + -
241A PRO 2.7 13.8 + - - +
242A LEU* 3.4 10.8 - - + +
244A TYR* 1.3 76.5 - - - +
246A ASP* 1.3 57.8 + - - +
248A PHE* 3.3 6.0 + - + +
249A LEU* 2.9 44.9 + - + +
411A VAL* 6.1 1.1 - - + -
415A LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU 2.8 14.1 + - - +
243A VAL* 3.1 11.0 - - - +
245A LEU* 1.3 76.5 - - - +
247A GLU* 1.3 72.9 + - - +
248A PHE 3.1 0.3 + - - -
249A LEU* 3.2 2.6 + - - +
250A ARG* 3.0 35.5 + - - +
399A ARG* 3.0 31.1 + - - -
400A TYR* 2.6 31.6 + - - +
415A LEU* 4.0 9.4 - - + +
419A ILE* 3.5 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 5.7 1.9 - - - +
175A LYS* 5.8 1.8 + - - +
176A THR* 2.9 18.4 + - + +
243A VAL* 2.9 28.9 + - + +
244A TYR* 3.8 12.8 - - + +
246A ASP* 1.3 83.4 - - - +
248A PHE* 1.3 61.7 + - - +
250A ARG* 3.0 30.5 + - - -
251A ASN* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 3.2 9.8 - - + +
177A LEU* 3.7 15.0 - - + -
180A PHE* 3.6 42.2 - + + -
244A TYR 2.9 18.8 + - - +
245A LEU* 3.4 5.8 - - + +
247A GLU* 1.3 73.9 - - - +
249A LEU* 1.3 94.8 + - + +
251A ASN* 2.9 14.9 + - - +
252A SER* 3.1 30.9 + - - -
274A LEU* 3.7 34.1 - - + -
275A LEU* 3.5 31.6 - - + -
403A TRP* 4.1 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 5.8 1.3 - - + -
245A LEU* 2.9 26.0 + - + +
246A ASP 3.7 1.1 - - - +
248A PHE* 1.3 95.6 - - + +
250A ARG* 1.3 59.0 + - - +
251A ASN 3.3 3.6 + - - -
252A SER 3.3 4.7 - - - +
274A LEU* 5.5 1.1 - - + -
400A TYR* 3.6 25.3 - - + +
402A ALA* 4.8 3.3 - - - +
403A TRP* 2.9 42.6 + - + +
407A ILE* 3.6 34.3 - - + -
411A VAL* 6.4 1.8 - - + -
412A LEU* 4.6 6.5 - - + -
415A LEU* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASP* 3.0 29.0 + - - +
247A GLU* 3.0 37.1 + - - +
248A PHE 3.0 0.8 + - - -
249A LEU* 1.3 75.3 - - - +
251A ASN* 1.3 70.4 + - - +
399A ARG* 3.5 50.2 - - - +
400A TYR* 3.6 22.2 - - + +
401A PRO* 6.4 0.9 - - - -
----------------------------------------------------------
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