Contacts of the helix formed by residues 30 - 42 (chain B) in PDB entry 3NSO
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 CYS 30 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 1.3 77.0 - - - +
31B GLN* 1.4 64.0 + - - +
32B ALA* 4.1 10.5 - - + +
33B GLU* 2.9 26.8 + - + +
34B LEU* 3.0 18.9 + - - +
66B LYS* 5.9 0.4 - - - -
67B ASP 3.5 6.1 - - - +
68B CYS* 2.0 46.0 - - - -
70B VAL* 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B CYS* 1.4 68.9 - - - +
32B ALA* 1.3 55.8 + - - +
34B LEU* 3.2 5.6 + - + +
35B LYS* 2.8 30.5 + - - +
61B VAL* 3.9 5.3 - - - +
62B LEU* 3.3 36.7 - - + +
65B ASN* 2.2 71.0 + - - +
67B ASP* 3.1 13.1 + - - +
70B VAL* 3.6 23.8 - - + +
74B GLU* 4.8 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B CYS* 3.1 8.5 - - + +
31B GLN* 1.3 77.9 - - - +
33B GLU* 1.3 57.5 + - + +
35B LYS* 3.3 7.8 + - - +
36B GLU* 2.9 27.8 + - - +
62B LEU 4.5 2.1 + - - -
65B ASN 4.6 2.8 + - - -
66B LYS* 4.0 30.2 - - + +
67B ASP 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 4.0 18.3 - - + +
20B ALA* 5.6 0.4 - - - -
22B ARG* 4.4 23.6 + - - +
23B CYS* 4.7 13.9 - - - +
28B LYS 4.7 1.2 - - - +
29B LEU* 3.4 24.9 - - + +
30B CYS* 2.9 43.3 + - + +
32B ALA* 1.3 77.2 - - + +
34B LEU* 1.3 62.1 + - - +
36B GLU* 3.2 9.9 + - - +
37B LEU* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.4 13.8 - - + +
30B CYS 3.0 11.4 + - - +
31B GLN* 3.6 13.5 - - + +
33B GLU* 1.3 76.1 - - - +
35B LYS* 1.3 62.9 + - - +
37B LEU* 3.3 6.1 + - + +
38B LEU* 2.9 41.8 + - + +
62B LEU* 3.9 24.2 - - + -
70B VAL* 4.1 17.9 - - + -
74B GLU* 5.0 5.8 - - + +
75B TYR* 3.8 27.8 - - + -
78B SER* 3.5 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN 2.8 20.7 + - - +
32B ALA* 3.7 7.6 - - - +
34B LEU* 1.3 75.0 - - - +
36B GLU* 1.3 61.9 + - - +
38B LEU* 3.9 2.2 - - - +
39B GLN* 2.8 68.3 + - + +
59B MET* 4.1 16.1 - - + +
62B LEU* 4.1 19.7 - - + +
63B ASP* 3.0 49.0 + - + +
66B LYS* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.9 3.9 - - + -
22B ARG* 2.8 43.9 + - - -
32B ALA 2.9 16.1 + - - +
33B GLU* 3.5 8.5 - - - +
35B LYS* 1.3 75.8 - - - +
37B LEU* 1.3 63.2 + - - +
39B GLN* 3.3 6.0 + - - -
40B LYS* 2.7 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.8 26.9 - - + -
15B THR* 3.9 12.6 - - + +
16B PHE* 4.9 1.3 - - - -
19B TYR* 3.7 49.3 - - + -
29B LEU* 4.3 11.4 - - + -
33B GLU 2.8 15.9 + - - +
34B LEU* 3.4 6.3 - - + +
36B GLU* 1.3 76.3 - - - +
38B LEU* 1.3 68.3 + - + +
41B GLU* 2.7 35.7 + - + +
75B TYR* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 2.9 27.4 + - + +
35B LYS* 3.9 2.7 - - - +
37B LEU* 1.3 83.2 - - + +
39B GLN* 1.3 63.8 + - - +
42B LEU* 3.1 34.2 + - + +
58B PHE* 4.1 17.0 - - + -
59B MET* 4.2 11.2 - - + +
62B LEU* 3.9 25.1 - - + -
78B SER* 3.9 20.2 - - - +
79B LEU* 3.7 30.3 - - + -
82B LEU* 3.9 22.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
35B LYS* 2.8 57.9 + - + +
36B GLU* 3.9 4.7 - - - +
38B LEU* 1.3 78.8 - - - +
40B LYS* 1.3 58.0 + - + +
42B LEU 5.5 0.2 - - - -
43B ALA* 3.3 25.9 - - - +
55B TYR* 5.7 1.8 + - - -
59B MET* 4.8 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.1 30.1 + - - +
19B TYR* 3.8 16.8 - - - +
22B ARG* 4.9 0.6 - - - +
36B GLU* 2.7 55.9 + - + +
39B GLN* 1.3 80.8 - - + +
41B GLU* 1.3 64.1 + - - +
42B LEU 3.4 0.6 + - - -
43B ALA* 3.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.6 13.9 + - - +
4A PRO* 5.3 10.0 - - - +
5A LEU* 3.7 34.0 + - + +
6A GLU* 3.4 17.3 + - - +
15B THR* 4.0 22.3 + - + +
18B GLU* 4.5 11.5 - - - +
19B TYR* 2.6 33.2 + - + +
37B LEU 2.7 23.8 + - - +
40B LYS* 1.3 81.0 - - - +
42B LEU* 1.4 59.2 + - - +
43B ALA 3.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.2 14.8 - - + +
6A GLU* 3.4 37.9 - - + +
9A VAL* 4.5 6.5 - - + -
38B LEU* 3.1 21.9 + - + +
41B GLU* 1.4 77.4 - - - +
43B ALA* 1.3 65.4 + - - +
44B THR 3.2 3.6 - - - -
45B TRP* 3.1 43.3 + - + +
79B LEU* 4.0 23.6 - - + -
82B LEU* 3.6 34.1 - - + -
----------------------------------------------------------
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