Contacts of the helix formed by residues 36 - 46 (chain B) in PDB entry 1XFB
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 36 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP 3.2 4.9 + - - -
35B GLU* 1.3 73.7 - - - +
37B VAL* 1.3 61.5 + - - +
38B GLY* 2.9 6.3 + - - -
39B SER* 2.6 32.3 + - - -
40B MET* 2.8 27.2 + - - +
80B PHE* 3.5 18.8 - - - -
108B LYS* 4.2 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU 3.6 1.2 + - - -
36B SER* 1.3 72.7 - - - +
38B GLY* 1.3 62.3 + - - +
40B MET* 3.7 7.7 - - - +
41B ALA 3.3 3.1 + - - -
51B ASN* 3.0 24.8 + - - +
56B ARG* 3.2 42.0 - - - +
80B PHE* 3.8 21.0 - - + -
82B GLU* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 2.9 6.8 + - - -
37B VAL* 1.3 81.7 - - - +
39B SER* 1.3 59.7 + - - -
40B MET 3.0 1.1 - - - -
41B ALA* 2.8 29.5 + - - +
42B LYS* 3.6 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.8 10.2 - - - +
36B SER* 2.6 38.4 + - - -
38B GLY* 1.3 73.0 - - - +
40B MET* 1.3 61.1 + - - +
42B LYS* 3.2 21.3 + - - +
43B ARG* 3.2 22.6 + - - +
108B LYS* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.4 23.6 - - + -
36B SER 2.8 18.7 + - - +
37B VAL* 3.7 6.3 - - - +
39B SER* 1.3 77.6 + - - +
41B ALA* 1.3 64.0 + - - +
43B ARG* 3.4 35.8 + - + -
44B LEU* 3.0 40.4 + - + +
51B ASN* 3.9 2.5 - - - +
56B ARG* 3.5 36.6 - - + -
59B TYR* 4.6 21.1 - - + -
60B ARG* 3.5 20.4 - - - +
311B LEU* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL 3.3 3.0 + - - +
38B GLY* 2.8 14.6 + - - +
40B MET* 1.3 79.8 - - - +
42B LYS* 1.3 58.0 + - + +
44B LEU* 3.9 1.2 - - - +
45B SER* 2.9 31.5 + - - -
51B ASN* 3.0 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.6 6.2 + - - +
39B SER* 3.2 13.3 + - - +
41B ALA* 1.3 79.5 - - + +
43B ARG* 1.3 62.8 + - + +
45B SER* 2.8 24.3 + - - -
46B GLN* 3.3 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 2.6 41.6 + - - +
39B SER* 3.2 16.2 + - - +
40B MET* 3.5 27.1 - - + -
41B ALA 3.3 0.2 - - - -
42B LYS* 1.3 78.4 - - + +
44B LEU* 1.3 63.7 + - - +
46B GLN* 3.4 23.5 + - - +
47B ILE* 3.9 7.8 + - - +
303B GLY* 4.2 2.2 - - - -
304B ARG* 2.8 68.9 - - - +
307B GLN* 4.2 7.9 - - - +
311B LEU* 4.0 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.0 26.0 + - + +
41B ALA* 3.9 3.6 - - - +
43B ARG* 1.3 74.6 - - - +
45B SER* 1.3 61.2 + - - +
47B ILE* 3.0 23.7 + - + +
48B GLY 2.4 22.1 - - - +
49B VAL* 3.6 36.8 - - + +
50B GLU 4.0 1.1 - - - +
51B ASN* 3.5 32.1 - - + +
55B ASN* 4.4 6.7 - - + -
56B ARG* 4.1 16.6 - - + -
59B TYR* 4.9 4.7 - - + -
311B LEU* 4.4 8.7 - - + -
314B TRP* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 2.9 17.1 + - - -
42B LYS* 2.8 18.0 + - - -
44B LEU* 1.3 77.2 - - - +
46B GLN* 1.3 64.2 + - - +
48B GLY* 3.0 21.2 + - - +
49B VAL 4.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 3.3 13.7 + - + +
43B ARG* 3.6 15.9 + - - +
44B LEU 3.2 0.6 - - - -
45B SER* 1.3 85.2 + - - +
47B ILE* 1.3 62.5 + - + +
48B GLY 3.5 0.2 - - - -
304B ARG* 2.6 34.2 - - - +
315B ARG* 4.5 6.8 + - - -
----------------------------------------------------------
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