Contacts of the helix formed by residues 39 - 46 (chain B) in PDB entry 1F5Q
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 ASN 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 4.2 0.6 + - - -
38B VAL* 1.3 101.5 - - + +
40B VAL* 1.3 68.1 + - - +
41B ASP 3.5 2.0 - - - -
42B GLN* 2.6 36.5 + - + +
43B HIS* 3.2 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MET* 3.0 61.2 - - + +
37B GLY 4.0 13.7 - - - +
39B ASN* 1.3 76.8 - - - +
41B ASP* 1.3 71.6 + - - +
43B HIS* 3.1 6.6 + - - +
44B PHE* 3.0 23.1 - - + -
82B LEU* 3.7 12.6 - - + -
189B MET* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN 3.5 0.2 - - - -
40B VAL* 1.3 81.3 + - - +
42B GLN* 1.3 62.7 + - - +
44B PHE* 3.2 1.4 + - - -
45B THR* 3.0 35.5 + - + +
189B MET* 3.7 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN* 2.6 50.0 + - + +
40B VAL 3.2 0.6 - - - -
41B ASP* 1.3 78.4 - - - +
43B HIS* 1.3 62.4 + - - +
45B THR* 3.5 7.3 + - - +
46B SER* 3.2 24.8 + - - -
48B TYR* 5.2 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL 5.4 0.2 - - - +
39B ASN 3.2 8.3 + - - +
40B VAL 3.1 9.5 + - - +
42B GLN* 1.3 80.9 - - - +
44B PHE* 1.3 70.7 + + - +
46B SER* 2.7 21.7 + - - -
48B TYR* 2.4 45.2 + + - +
49B ARG* 3.5 24.1 - - + +
52B LEU* 6.0 0.2 - - + -
77B LEU* 5.3 2.3 - - + +
78B ASP* 3.1 28.0 + - - -
81B PHE* 3.3 38.7 - + + +
82B LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 5.5 2.9 - - - -
35B MET* 3.7 30.5 - - + -
40B VAL* 3.0 31.6 - - + -
41B ASP 3.2 6.5 + - - +
43B HIS* 1.3 81.8 - + - +
45B THR* 1.3 61.0 + - + +
46B SER 3.4 2.6 - - - +
49B ARG* 3.5 29.2 - - - +
50B LYS* 5.8 2.1 - - - +
78B ASP* 3.6 33.0 - - + -
82B LEU* 3.8 13.2 - - + -
185B GLY* 3.0 42.4 + - - +
186B ARG* 4.4 1.0 + - - -
188B ALA 4.1 4.5 - - - -
189B MET* 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.0 24.3 + - + +
42B GLN* 3.5 9.5 + - - +
44B PHE* 1.3 78.6 - - + +
46B SER* 1.3 70.7 + - - +
47B GLN* 3.7 1.4 + - - +
50B LYS* 3.9 12.9 + - - +
186B ARG* 4.3 38.3 + - + +
189B MET* 5.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN* 3.2 20.0 + - - -
43B HIS 2.7 16.6 + - - -
44B PHE 3.4 2.0 - - - +
45B THR* 1.3 82.9 - - - +
47B GLN* 1.3 62.6 + - - +
48B TYR* 3.2 33.2 - - - -
49B ARG* 3.3 16.1 + - - +
50B LYS* 3.5 15.4 + - - +
----------------------------------------------------------
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