Contacts of the helix formed by residues 81 - 86 (chain M) in PDB entry 2RCR
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 PRO 81 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L ILE 5.6 0.7 - - - +
276L PRO* 5.4 4.5 - - + -
277L GLY* 5.3 9.9 - - - +
80M ASN* 1.4 92.1 - - + +
82M ALA* 1.3 70.8 + - - +
83M VAL 3.0 0.5 + - - -
84M PHE* 3.1 7.2 + - + -
85M LEU* 2.7 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L TRP* 4.0 4.3 - - + +
273L ALA* 2.7 39.7 - - + +
276L PRO* 3.9 27.8 - - + +
80M ASN* 3.7 1.6 - - + +
81M PRO* 1.3 77.2 - - - +
83M VAL* 1.3 60.5 + - + +
85M LEU* 3.2 2.8 + - - +
86M ARG* 2.8 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77M ALA* 3.0 43.3 - - + +
78M GLY* 5.6 0.2 - - - -
79M TRP* 3.7 12.3 - - - +
80M ASN 3.6 8.7 + - - +
81M PRO 3.0 1.2 + - - -
82M ALA* 1.3 78.4 - - + +
84M PHE* 1.3 56.7 + - - +
85M LEU 2.7 1.4 + - - -
86M ARG* 2.6 60.5 + - - +
87M ASP* 3.1 9.0 - - - +
91M PHE* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M GLY* 5.2 8.3 - - - -
73M PHE* 3.8 37.5 - + - -
77M ALA* 6.4 1.1 - - + -
80M ASN 3.3 15.8 + - - +
81M PRO* 3.1 4.8 + - + +
83M VAL* 1.3 80.1 - - + +
85M LEU* 1.3 69.0 + - + +
86M ARG 3.5 0.4 - - - -
87M ASP 4.7 0.7 - - - -
88M LEU* 3.6 35.2 - - + +
91M PHE* 4.3 9.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266L TRP* 3.1 32.9 - - + -
273L ALA* 4.0 17.8 - - - +
274L ASN 6.0 0.7 - - - +
275L ILE* 5.3 9.0 - - + +
81M PRO* 2.7 49.2 + - + +
82M ALA* 3.4 6.7 - - - +
83M VAL 2.7 1.8 + - - -
84M PHE* 1.3 84.6 - - + +
86M ARG* 1.3 59.0 + - - +
87M ASP 4.9 1.6 - - - -
88M LEU* 5.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266L TRP* 3.0 28.0 + - - +
267L VAL* 4.4 26.3 - - + +
268L LYS* 5.6 2.8 - - - +
272L TRP* 3.6 31.9 - - - +
273L ALA* 3.8 21.8 - - + +
82M ALA* 2.8 12.1 + - - +
83M VAL* 2.6 55.3 + - - +
85M LEU* 1.3 72.0 - - - +
87M ASP* 1.3 81.1 + - - +
90M PHE* 5.4 0.7 - - - -
----------------------------------------------------------
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