Contacts of the helix formed by residues 243 - 254 (chain A) in PDB entry 4ACR
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 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A HIS* 5.3 0.2 + - - -
241A PRO 4.0 1.0 + - - -
242A LEU* 1.3 76.7 - - - +
244A PRO* 1.3 71.7 - - - +
245A GLU* 3.3 14.1 - - - -
246A CYS* 3.2 12.0 + - - +
247A SER* 3.0 26.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
242A LEU 4.6 0.9 - - - +
243A GLY* 1.3 81.3 - - - +
245A GLU* 1.3 74.6 + - - +
247A SER* 3.2 9.0 + - - -
248A ARG* 2.9 38.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
243A GLY* 4.2 8.6 - - - -
244A PRO* 1.3 90.6 - - - +
246A CYS* 1.3 63.6 + - + +
248A ARG* 3.7 16.1 - - - +
249A ALA* 2.9 29.5 + - - +
442A VAL* 4.2 14.6 - - + +
443A GLU* 3.6 30.6 - - + +
444A VAL* 5.6 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.7 0.2 - - - -
242A LEU* 4.0 25.1 - - - -
243A GLY* 3.2 20.3 + - - +
245A GLU* 1.3 84.0 - - + +
247A SER* 1.3 59.2 + - - +
249A ALA* 3.3 4.4 + - - +
250A VAL* 2.9 37.4 + - - +
279A CYS* 2.0 60.3 - - + +
442A VAL* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA* 4.2 11.9 + - - +
81A SER* 4.4 2.3 + - - -
82A HIS* 3.9 37.0 - - - +
242A LEU* 6.1 0.2 - - - -
243A GLY 3.0 13.1 + - - -
244A PRO* 3.2 12.3 + - - -
246A CYS* 1.3 76.8 - - - +
248A ARG* 1.3 57.5 + - - +
250A VAL* 3.3 7.1 + - - +
251A MET* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG 4.7 12.4 + - - -
61A ILE* 3.3 41.8 - - + +
78A ALA* 6.3 0.2 - - - -
244A PRO* 2.9 24.6 + - - +
245A GLU* 3.7 14.8 - - - +
247A SER* 1.3 77.3 - - - +
249A ALA* 1.3 57.8 + - - +
251A MET* 3.3 2.4 + - - -
252A LYS* 2.9 25.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
245A GLU 2.9 18.8 + - - +
246A CYS 3.7 4.0 - - - +
248A ARG* 1.3 76.3 - - - +
250A VAL* 1.3 58.4 + - - +
252A LYS* 3.3 9.6 + - - +
253A LEU* 2.9 26.7 + - - +
271A TYR* 4.3 1.0 + - - -
275A VAL* 4.1 13.5 - - + +
441A GLU* 3.4 25.8 - - + +
442A VAL* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 3.7 32.8 - - - +
82A HIS* 4.7 1.6 - - - +
85A LEU* 3.7 31.2 - - + -
242A LEU* 5.7 0.7 - - + -
246A CYS* 2.9 22.6 + - - +
247A SER* 3.6 7.2 - - - +
248A ARG 3.2 0.2 - - - -
249A ALA* 1.3 74.5 - - - +
251A MET* 1.3 59.5 + - - +
253A LEU* 3.0 9.9 + - + +
254A VAL* 2.9 38.6 + - + +
275A VAL* 4.0 16.6 - - + -
276A LEU* 5.1 2.2 - - + -
279A CYS* 4.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.6 20.6 - - + -
62A CYS* 3.7 25.8 - - - -
74A GLU* 3.8 16.4 - - + +
77A LEU* 3.6 45.3 - - + +
78A ALA* 3.7 21.8 - - + -
81A SER* 3.9 13.0 + - - +
247A SER 2.9 17.1 + - - +
248A ARG* 3.6 5.8 - - - +
250A VAL* 1.3 75.7 - - - +
252A LYS* 1.3 62.2 + - - +
254A VAL 4.7 0.2 - - - +
255A TYR* 3.3 19.0 + - - +
256A CYS* 3.1 24.5 + - - -
259A CYS* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 4.2 19.3 - - + +
63A PRO* 4.5 15.1 - - + +
248A ARG 2.9 16.6 + - - +
249A ALA* 3.5 10.3 - - - +
250A VAL 3.2 0.2 - - - -
251A MET* 1.3 77.6 - - - +
253A LEU* 1.3 57.4 + - - +
256A CYS* 3.5 22.2 - - + +
271A TYR* 3.3 13.1 + - - +
416A TRP* 3.2 20.6 + - - -
417A ASN 5.1 0.8 + - - -
418A GLY* 3.6 27.5 + - - +
419A MET* 4.6 4.4 - - - +
441A GLU* 4.8 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 2.9 13.8 + - - +
250A VAL* 3.0 10.1 + - + +
252A LYS* 1.3 78.9 - - - +
254A VAL* 1.3 74.6 + - + +
267A PRO* 3.7 23.1 - - + +
271A TYR* 3.5 34.3 - - + -
272A CYS* 3.8 36.8 - - + +
275A VAL* 4.1 22.2 - - + -
276A LEU* 5.2 6.7 - - + -
416A TRP* 3.3 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 4.7 5.8 - - - -
84A GLU* 4.4 11.0 - - - +
250A VAL* 2.9 26.1 + - + +
253A LEU* 1.3 98.5 - - + +
255A TYR* 1.3 92.4 + - + +
256A CYS 3.4 0.7 + - - -
257A ALA* 4.0 9.2 + - - +
258A HIS* 3.7 14.6 + - + -
267A PRO* 5.6 7.0 - - + +
----------------------------------------------------------
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