Contacts of the helix formed by residues 59 - 65 (chain F) in PDB entry 2CHT
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 ALA 59 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D TSA 3.3 30.9 - - + +
47F LEU* 3.7 16.0 - - + +
57F PHE* 4.5 0.2 - - + -
58F PRO* 1.3 79.8 - - - +
60F LYS* 1.3 60.9 + - - +
62F VAL* 3.2 20.2 + - - +
63F ARG* 4.1 2.6 + - - +
73F VAL* 3.9 17.6 - - + +
75F CYS* 3.3 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D TSA 3.0 17.1 + - - +
17F GLU* 3.0 26.5 + - - -
21F LEU* 3.7 19.4 - - + +
56F VAL* 3.8 19.5 - - + -
57F PHE* 3.1 14.9 + - + +
58F PRO 2.9 1.2 + - - -
59F ALA* 1.3 74.6 - - - +
61F ALA* 1.3 62.7 + - - +
63F ARG* 3.0 29.2 + - + +
64F GLU* 3.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 3.4 33.1 - - + +
24F THR* 3.8 18.4 - - + -
25F LYS* 4.1 8.4 - - + +
28F LEU* 4.7 2.2 - - + -
58F PRO 2.7 20.3 + - - +
60F LYS* 1.3 72.6 - - - +
62F VAL* 1.3 62.4 + - - +
64F GLU* 2.9 33.8 + - - +
65F LEU* 3.8 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 3.9 22.7 - - + -
45F MET* 4.0 14.4 - - + -
47F LEU* 4.0 8.1 - - + -
58F PRO 4.7 0.7 - - - +
59F ALA* 3.3 22.7 - - - +
60F LYS 3.0 0.4 + - - -
61F ALA* 1.3 75.1 - - - +
63F ARG* 1.3 56.2 - - + +
65F LEU* 2.8 36.4 + - + +
68F TRP* 4.0 27.9 - - + +
71F VAL 4.9 2.9 - - - +
73F VAL* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D LEU 5.7 2.6 + - - -
206D TSA 4.3 15.9 + - - +
59F ALA 4.7 4.7 - - - +
60F LYS* 3.0 17.2 + - + +
62F VAL* 1.3 79.1 - - + +
64F GLU* 1.3 59.4 + - + +
65F LEU 3.2 8.4 + - - +
66F SER* 5.4 0.5 - - - -
68F TRP 5.4 5.6 - - - +
69F GLN* 4.2 39.5 + - - +
73F VAL* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 3.6 31.6 - - - +
25F LYS* 3.8 34.8 - - + +
60F LYS* 4.3 11.5 - - + +
61F ALA* 2.9 30.2 + - - +
63F ARG* 1.3 76.5 - - + +
65F LEU* 1.3 61.0 + - - +
66F SER* 3.7 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LYS* 4.3 17.9 - - + +
28F LEU* 3.8 32.3 - - + -
29F GLU* 3.7 33.2 - - + +
32F ILE* 4.3 10.1 - - + -
61F ALA 4.3 3.8 - - - +
62F VAL* 2.8 21.2 + - + +
63F ARG 3.8 6.7 - - - +
64F GLU* 1.3 77.2 - - - +
66F SER* 1.3 65.7 + - - +
67F GLY 3.5 0.3 + - - -
68F TRP* 3.2 47.4 + - + +
69F GLN 4.5 0.5 + - - -
----------------------------------------------------------
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