Contacts of the helix formed by residues 32 - 42 (chain B) in PDB entry 1O0W
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 HIS 32 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 3.5 3.0 + - - +
31B CYS* 1.3 76.0 - - - +
33B SER* 1.3 78.9 + - - +
34B SER* 2.9 28.0 + - - +
35B TYR* 2.9 19.2 + - - +
36B ALA* 3.1 9.7 + - - +
49B SER* 4.2 0.4 - - - -
50B ASN* 4.5 12.5 - - - +
107B LEU* 6.0 1.1 - - + -
108B PHE 3.0 19.9 + - - +
109B LEU* 3.4 15.3 - - + -
113B GLU* 3.8 27.7 - - + +
124B ILE* 3.7 36.2 - - + +
127B ASP* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS 3.7 1.6 + - - -
32B HIS* 1.3 89.7 + - - +
34B SER* 1.3 58.6 + - - +
36B ALA* 3.8 1.3 - - - -
37B ASN* 2.8 47.1 + - - +
49B SER* 3.6 15.0 - - - -
50B ASN* 5.0 1.6 + - - -
51B GLU* 4.0 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 2.9 24.4 + - - -
33B SER* 1.3 81.3 + - - +
35B TYR* 1.3 60.9 + - - +
37B ASN* 4.1 6.5 - - - +
38B GLU* 3.1 24.6 + - - +
109B LEU* 3.7 1.9 - - - -
110B GLY* 2.8 29.2 + - - -
113B GLU* 3.4 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 4.4 3.8 + - - -
4B SER* 4.8 3.3 + - - -
5B GLU* 2.7 38.4 + - - +
27B PHE* 4.0 13.2 - + - -
31B CYS* 3.8 10.5 - - - -
32B HIS 2.9 6.4 + - - +
34B SER* 1.3 80.0 + - - +
36B ALA* 1.3 67.3 + - - +
38B GLU* 3.2 11.4 + - - +
39B GLN* 2.9 58.1 + - + +
44B ARG* 4.1 0.9 + - - -
47B VAL* 4.0 3.1 - - + -
108B PHE* 3.3 47.4 - + + +
109B LEU 3.5 22.9 - - - -
110B GLY* 3.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS* 5.1 1.1 - - + +
32B HIS 3.1 3.2 + - - +
33B SER* 3.8 6.1 - - - +
35B TYR* 1.3 80.0 - - - +
37B ASN* 1.3 59.0 + - - +
39B GLN* 3.3 0.9 + - - +
40B ASN* 2.8 39.5 + - - +
47B VAL* 3.7 24.5 - - + +
48B GLU 3.8 3.1 - - - -
49B SER* 3.5 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 2.8 36.6 + - - +
34B SER* 4.1 5.6 - - - +
36B ALA* 1.3 72.3 - - - +
38B GLU* 1.3 66.9 + - - +
40B ASN* 3.8 10.3 - - - +
41B GLN* 3.0 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER 3.1 18.5 + - - +
35B TYR* 3.5 12.4 - - - +
37B ASN* 1.3 78.5 - - - +
39B GLN* 1.3 82.9 + - - +
41B GLN* 3.4 12.2 + - - +
42B ALA* 3.2 20.4 + - + +
109B LEU 4.4 0.9 - - - +
110B GLY* 3.5 8.1 - - - -
111B LYS* 2.9 44.0 + - - +
112B GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 5.0 1.4 + - - -
35B TYR* 2.9 51.7 + - + +
36B ALA 3.8 2.7 - - - +
38B GLU* 1.3 102.0 + - - +
40B ASN* 1.3 66.3 + - - +
42B ALA* 3.0 17.8 + - - +
43B GLY 3.3 0.5 + - - -
44B ARG* 3.0 50.9 + - + +
47B VAL* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA* 2.8 34.7 + - - +
37B ASN* 3.8 13.4 - - - +
39B GLN* 1.3 71.2 - - - +
41B GLN* 1.3 59.2 + - + +
43B GLY* 2.8 18.0 + - - -
44B ARG 2.9 21.8 + - - -
45B LYS* 3.3 44.9 + - - +
47B VAL* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 3.0 36.8 + - - +
38B GLU* 3.6 9.4 - - - +
39B GLN 3.3 0.2 - - - -
40B ASN* 1.3 76.7 - - + +
42B ALA* 1.3 56.6 + - - +
43B GLY 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 3.2 11.8 + - + +
39B GLN* 3.0 19.9 + - - +
41B GLN* 1.3 77.5 - - - +
43B GLY* 1.3 59.6 + - - +
44B ARG* 3.5 7.5 + - + +
----------------------------------------------------------
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