Contacts of the helix formed by residues 45 - 49 (chain D) in PDB entry 3F5O
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 GLU 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 3.2 36.3 + - - +
43D LYS* 3.6 27.1 - - + +
44D VAL* 1.3 78.6 - - - +
46D GLU* 1.3 69.1 - - - +
47D GLU* 3.2 7.9 - - + +
48D HIS* 2.9 33.7 + - + +
49D THR* 3.5 7.1 - - - +
96D LEU* 3.4 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 3.5 44.1 + - + +
20C ASN* 3.3 15.3 - - + +
45D GLU* 1.3 74.5 - - - +
47D GLU* 1.3 58.9 + - - +
48D HIS 2.9 4.7 + - - -
49D THR* 2.8 29.0 + - - +
96D LEU* 3.4 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG 3.6 16.1 + - - +
21C PHE* 3.4 16.1 + - - +
23C ARG* 2.8 41.2 + - - +
23D ARG 5.2 2.6 - - - +
24D VAL* 4.5 8.0 - - - +
26D GLY* 5.6 1.4 + - - -
27D LYS* 2.7 41.0 + - - +
45D GLU* 4.3 5.8 - - + +
46D GLU* 1.3 76.8 - - - +
48D HIS* 1.3 85.3 + - + +
49D THR 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.9 3.1 - + - -
24D VAL 4.1 15.2 + - - -
27D LYS* 3.7 32.2 - - + +
42D MET* 3.7 18.6 - - + +
43D LYS 3.5 19.0 + - - -
44D VAL* 3.8 3.6 - - + -
45D GLU* 2.9 34.1 + - + +
47D GLU* 1.3 96.9 - - + +
49D THR* 1.3 61.3 + - - +
55D LEU* 3.6 13.8 - - + +
56D HIS* 3.0 25.8 + - - +
59D LEU* 3.3 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASN* 3.2 12.5 - - - +
21C PHE* 2.8 32.1 + - - +
22C GLU 4.1 0.3 + - - -
44D VAL* 3.9 16.2 - - + -
45D GLU 3.5 15.7 - - - +
46D GLU* 2.8 21.3 + - - +
48D HIS* 1.3 80.9 - - - +
50D ASN* 1.3 67.9 + - - +
53D GLY* 3.8 21.7 - - - +
54D THR 3.1 13.0 - - - +
56D HIS* 4.0 2.5 - - - -
96D LEU* 4.2 14.1 - - + +
----------------------------------------------------------
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