Contacts of the helix formed by residues 273 - 277 (chain A) in PDB entry 6ICV
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 LEU 273 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.5 22.8 - - + +
83A MET* 3.8 24.5 - - - -
86A ALA* 4.2 25.4 - - + -
91A ALA* 4.4 7.0 - - + -
92A SER* 3.1 27.6 - - - +
93A VAL* 4.3 4.7 - - + -
96A PHE* 3.9 18.8 - - + -
98A MET* 4.7 9.2 - - - -
108A LEU* 4.3 7.5 - - + +
121A LEU* 4.4 8.5 - - + -
123A VAL* 4.8 5.8 - - + -
127A LEU* 6.4 0.2 - - + -
175A TYR* 4.8 1.2 - - - -
271A ILE 3.7 0.2 + - - -
272A PRO* 1.3 72.6 - - + +
274A TRP* 1.3 65.1 + - - +
275A ASP* 3.2 5.7 + - - -
276A MET* 3.1 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.6 30.7 - - + -
123A VAL* 3.9 21.5 - - + +
256A ASN* 3.3 37.7 - - - -
271A ILE* 3.6 24.0 - - + -
272A PRO 2.6 9.1 + - - -
273A LEU* 1.3 74.9 - - - +
275A ASP* 1.3 73.0 + - - +
276A MET 2.9 5.7 + - - -
277A CYS* 3.1 21.8 + - - +
286A THR* 3.0 40.4 + - + +
295A CYS* 5.8 2.0 - - + -
297A CYS* 3.7 18.2 - - + -
311A ILE* 3.4 26.0 - - + +
71C ILE* 3.9 11.9 - - + -
73C HIS* 3.5 27.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 2.8 34.7 + - - -
254A ARG* 2.9 41.8 + - + +
271A ILE 3.1 29.6 + - - +
273A LEU 4.0 5.2 + - - -
274A TRP* 1.3 90.2 - - + +
276A MET* 1.3 64.4 + - - +
277A CYS 3.2 0.7 - - - -
601A SAH 3.3 13.3 - - - +
73C HIS* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 3.7 10.8 - - - +
79A PHE* 4.2 21.3 - - + -
82A LEU* 5.0 4.9 - - + -
98A MET* 4.6 7.6 - - + -
106A PHE* 3.5 41.5 - - + +
107A GLY* 3.4 22.1 - - - +
108A LEU* 3.5 20.4 - - + -
178A THR* 4.9 2.9 - - - +
254A ARG* 3.3 24.9 - - - -
273A LEU* 3.1 23.0 + - - +
274A TRP 2.9 1.2 + - - -
275A ASP* 1.3 83.3 + - - +
277A CYS* 1.3 62.9 + - - +
278A ASN 3.4 0.3 + - - -
601A SAH 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.0 19.3 - - - +
120A PHE* 5.1 0.2 - - - -
121A LEU* 3.9 24.2 - - - -
274A TRP* 3.1 20.5 + - - +
275A ASP 3.9 2.3 - - - +
276A MET* 1.3 77.1 - - - +
278A ASN* 1.3 59.9 + - - +
309A ILE* 4.1 22.9 - - - +
311A ILE* 3.8 33.4 - - + -
313A TYR* 2.7 23.7 + - - -
601A SAH 3.7 2.1 - - - +
73C HIS* 4.0 1.6 + - - -
----------------------------------------------------------
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