Contacts of the helix formed by residues 55 - 62 (chain D) in PDB entry 1F80
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 SER 55 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 4.1 1.1 - - - +
53D GLU* 4.0 2.0 + - - +
54D ILE* 1.3 77.7 - - - +
56D ASP* 1.3 58.9 + - - +
57D GLU* 3.5 10.5 + - - +
58D ASP* 3.0 32.9 + - - -
59D ALA* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.4 31.0 + - - +
68B ILE* 4.2 9.0 - - + -
69B GLY* 3.7 12.9 - - - +
73B SER* 2.6 40.0 + - - +
74B PHE* 2.9 29.0 + - - +
75B GLN* 5.2 1.0 - - - +
36D PN2 3.3 19.0 + - - +
55D SER* 1.3 73.4 - - - +
57D GLU* 1.3 61.7 + - - +
59D ALA* 3.3 4.2 + - - -
60D GLU 3.2 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 4.2 8.4 + - - +
70B ARG* 3.7 33.4 - - + +
55D SER* 2.9 11.1 - - - +
56D ASP* 1.3 79.3 - - - +
58D ASP* 1.3 69.3 + - - +
60D GLU* 3.1 15.4 + - - +
61D LYS* 3.3 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 4.4 1.4 - - - +
54D ILE* 3.4 20.9 - - + +
55D SER* 3.0 20.4 + - - +
57D GLU* 1.3 82.8 - - - +
59D ALA* 1.3 67.3 + - - +
61D LYS* 3.1 17.5 + - + +
62D ILE* 3.3 18.0 + - - +
71D TYR* 3.1 33.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 4.4 4.3 - - - +
36D PN2 3.0 50.3 + - + +
43D VAL* 4.1 20.6 - - + -
54D ILE* 3.7 6.9 - - + +
55D SER 2.8 12.4 + - - +
56D ASP* 3.4 8.3 - - - +
57D GLU 3.1 0.4 - - - -
58D ASP* 1.3 78.5 - - - +
60D GLU* 1.3 64.0 + - - +
62D ILE* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR 4.9 6.2 - - - +
68B ILE 3.9 14.7 - - - +
69B GLY* 3.9 0.9 - - - -
70B ARG* 2.8 42.5 + - + +
71B GLN* 4.5 8.8 + - - -
36D PN2 3.3 32.5 + - + +
56D ASP 3.2 1.8 + - - +
57D GLU 3.1 10.5 + - - +
59D ALA* 1.3 80.6 - - - +
61D LYS* 1.3 63.0 + - - +
63D ALA* 4.0 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU 3.3 6.9 + - - +
58D ASP* 3.1 14.7 + - + +
60D GLU* 1.3 80.5 - - - +
62D ILE* 1.3 65.2 + - + +
63D ALA* 2.8 11.4 + - - +
67D ASP* 4.0 19.9 - - + +
70D ASN* 6.0 5.5 - - - +
71D TYR* 5.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 3.5 3.3 - - - -
36D PN2 2.9 48.4 + - + +
43D VAL* 4.8 3.1 - - + -
46D LEU* 4.6 11.9 - - + -
54D ILE* 4.5 26.2 - - + -
58D ASP 3.3 12.3 + - - +
59D ALA* 3.3 13.9 + - - +
61D LYS* 1.3 79.5 - - + +
63D ALA* 1.3 59.4 + - - +
64D THR 3.4 2.7 - - - -
67D ASP* 3.5 15.3 - - + +
68D ALA* 3.9 16.2 - - + +
71D TYR* 3.6 36.1 - - + -
----------------------------------------------------------
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