Contacts of the helix formed by residues 33 - 61 (chain B) in PDB entry 2WY2
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 ASP 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLN* 2.9 38.1 + - - +
29B ALA* 4.1 0.6 + - - -
31B GLN* 3.8 18.6 - - - +
32B GLY* 1.3 79.6 - - - +
34B PHE* 1.3 64.3 + - - +
35B ALA* 3.2 3.6 - - + +
36B ALA* 4.2 8.6 - - + +
37B ALA* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 4.9 12.6 - - + -
32B GLY* 3.4 13.4 + - - -
33B ASP* 1.3 70.3 - - - +
35B ALA* 1.3 61.1 + - - +
37B ALA* 3.6 4.9 - - - +
38B LYS* 2.9 34.7 + - + +
95B ILE* 4.7 7.9 - - + -
98B HIS* 4.1 7.4 - - + -
99B GLU* 3.4 55.0 - - + +
102B LYS 3.8 5.2 - - - -
103B ALA* 3.1 41.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP* 3.2 1.7 - - + +
34B PHE* 1.3 80.2 - - - +
36B ALA* 1.3 63.2 + - - +
38B LYS* 3.4 6.9 + - - +
39B ALA* 3.1 22.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
28B GLN* 3.3 28.7 - - + +
33B ASP* 3.5 11.8 + - + +
34B PHE 3.4 0.4 - - - -
35B ALA* 1.3 76.2 - - - +
37B ALA* 1.3 66.6 + - - +
39B ALA* 3.3 7.0 + - - +
40B MET* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.5 27.8 - - - +
28B GLN* 3.8 2.8 - - - +
29B ALA* 4.1 7.6 - - + +
33B ASP 3.1 17.5 + - - +
34B PHE* 3.6 8.7 - - - +
36B ALA* 1.3 77.3 - - - +
38B LYS* 1.3 63.6 + - - +
40B MET* 3.1 4.0 + - - +
41B MET* 2.9 28.2 + - - +
95B ILE* 4.2 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 2.9 19.7 + - + +
35B ALA* 3.6 6.7 - - - +
37B ALA* 1.3 76.7 - - - +
39B ALA* 1.3 61.0 + - - +
41B MET* 3.3 19.8 + - + +
42B ASP* 3.1 24.0 + - - +
95B ILE* 5.7 0.4 - - - +
99B GLU* 5.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA 3.1 14.2 + - - +
36B ALA* 3.6 10.3 - - - +
38B LYS* 1.3 77.3 - - - +
40B MET* 1.3 64.4 + - + +
42B ASP* 3.4 6.7 + - - +
43B GLN* 3.2 33.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
21B LEU* 3.9 31.6 - - + +
24B ALA* 3.6 31.2 - - + +
25B ALA* 3.5 25.1 - - + +
28B GLN* 4.7 8.7 - - + -
36B ALA* 2.9 23.7 + - + +
37B ALA 3.5 0.2 - - - +
39B ALA* 1.3 76.6 - - + +
41B MET* 1.3 59.3 + - - +
43B GLN* 3.4 15.8 + - - +
44B SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 6.0 0.9 - - - +
25B ALA* 4.0 6.7 - - + -
37B ALA 2.9 20.9 + - - +
38B LYS* 3.3 21.7 + - + +
40B MET* 1.3 75.0 - - - +
42B ASP* 1.3 58.3 + - - +
44B SER* 3.2 8.3 + - - -
45B ARG* 2.8 30.2 + - - +
88B ARG* 3.6 16.3 + - + +
91B ILE* 5.6 0.7 - - + -
92B THR* 3.3 43.3 - - + +
95B ILE* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS 3.1 10.7 + - - +
39B ALA* 3.5 11.4 - - - +
40B MET 3.2 0.2 - - - -
41B MET* 1.3 79.3 - - - +
43B GLN* 1.3 63.7 + - + +
45B ARG* 3.2 16.8 + - - +
46B MET* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 5.0 14.4 - - + +
39B ALA* 3.2 19.3 + - - +
40B MET* 3.8 18.1 - - - +
41B MET 3.3 0.2 - - - -
42B ASP* 1.3 75.3 - - + +
44B SER* 1.3 65.4 + - - +
46B MET* 3.2 15.4 + - - +
47B ALA* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 2.7 31.1 + - - +
21B LEU* 3.3 16.3 - - - +
22B ALA* 3.4 6.7 + - - +
40B MET 2.9 17.0 + - - -
41B MET* 3.2 8.3 + - - -
43B GLN* 1.3 76.7 - - - +
45B ARG* 1.3 63.1 + - - +
47B ALA* 3.1 8.4 + - - +
48B LEU* 2.9 29.2 + - - +
88B ARG* 4.0 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET 2.8 13.0 + - - +
42B ASP* 3.4 19.9 + - - +
44B SER* 1.3 75.9 - - - +
46B MET* 1.3 54.0 + - + +
48B LEU* 3.2 6.1 + - + +
49B ASN* 2.7 36.6 + - + +
88B ARG* 3.9 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 3.0 32.1 + - - +
43B GLN* 3.2 14.3 + - - +
45B ARG* 1.3 75.8 - - + +
47B ALA* 1.3 62.9 + - - +
49B ASN* 3.2 8.3 + - - +
50B GLU* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 3.7 24.1 + - - +
17B GLN* 6.3 0.7 - - + -
18B ALA* 4.6 12.3 - - + +
21B LEU* 5.1 6.7 - - + -
43B GLN 2.9 12.3 + - - +
44B SER* 3.4 12.1 - - - +
46B MET* 1.3 77.7 - - - +
48B LEU* 1.3 57.4 + - - +
50B GLU* 3.4 5.1 + - - +
51B ALA* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 5.0 4.3 - - - -
18B ALA* 3.3 26.5 - - + -
44B SER 2.9 15.6 + - - +
45B ARG* 3.5 7.4 - - + +
47B ALA* 1.3 73.3 - - - +
49B ASN* 1.3 56.2 + - - +
51B ALA* 3.1 5.1 + - + +
52B HIS* 2.6 38.9 + - + +
81B LEU* 5.0 9.7 - - + +
84B SER* 4.0 19.3 - - - +
85B MET* 4.1 27.8 - - + +
88B ARG* 3.3 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 2.7 23.9 + - + +
46B MET* 3.5 9.6 - - - +
48B LEU* 1.3 74.0 - - - +
50B GLU* 1.3 57.9 + - - +
52B HIS* 3.3 7.2 + - - +
53B LEU* 2.9 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 4.2 13.2 + - - +
46B MET 3.0 16.5 + - - +
47B ALA* 3.8 6.0 - - - +
49B ASN* 1.3 76.0 + - - +
51B ALA* 1.3 63.8 + - - +
53B LEU* 3.3 13.2 + - + +
54B VAL* 3.1 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 16.8 - - + +
14B ASN* 3.9 20.6 - - + +
15B SER 5.4 0.7 - - - +
47B ALA 3.0 18.0 + - - +
48B LEU* 3.5 7.4 - - + +
50B GLU* 1.3 77.4 - - - +
52B HIS* 1.3 62.3 + - - +
54B VAL* 3.2 6.5 + - - +
55B GLN* 3.0 22.0 + - - +
81B LEU* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU 2.6 21.6 + - - +
49B ASN* 3.6 7.4 - - - +
51B ALA* 1.3 72.0 - - - +
53B LEU* 1.3 56.1 + - - +
55B GLN* 3.1 15.3 + - + +
56B THR* 2.7 60.4 + - + -
81B LEU* 4.7 7.5 - - + +
82B MET* 6.4 1.6 - - - -
85B MET* 4.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASN* 2.9 41.4 + - - +
50B GLU* 3.5 10.8 - - + +
51B ALA 3.2 0.2 - - - -
52B HIS* 1.3 80.1 - - - +
54B VAL* 1.3 63.7 + - + +
56B THR* 3.2 19.7 + - - +
57B LYS* 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.1 12.8 - - + -
11B LEU* 4.0 15.7 - - + -
50B GLU* 3.1 22.9 + - + +
51B ALA* 3.5 8.3 - - - +
53B LEU* 1.3 76.5 - - + +
55B GLN* 1.3 64.5 + - - +
57B LYS* 3.2 9.0 + - - +
58B LEU* 3.0 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.9 3.1 - - + +
51B ALA 3.0 6.8 + - - +
52B HIS* 3.5 16.7 - - + +
54B VAL* 1.3 78.2 - - - +
56B THR* 1.3 64.7 + - - +
58B LEU* 2.8 24.8 + - + +
59B ILE* 2.8 19.0 + - + +
74B LEU* 3.4 24.1 + - + +
77B ALA* 3.9 3.8 - - - +
78B GLN* 3.3 46.7 - - - +
81B LEU* 2.8 41.8 - - + +
82B MET* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 2.7 51.1 + - + -
53B LEU* 3.2 15.4 + - + +
55B GLN* 1.3 73.0 - - - +
57B LYS* 1.3 57.6 + - - +
59B ILE* 3.0 16.5 + - + +
60B GLU* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU 3.2 6.9 + - - +
54B VAL* 3.2 11.8 + - - +
55B GLN 3.2 0.2 - - - -
56B THR* 1.3 79.7 - - - +
58B LEU* 1.3 66.7 + - + +
60B GLU* 3.9 13.1 - - - +
61B GLY* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.6 31.4 - - + +
7B VAL* 3.8 18.8 - - + -
8B VAL* 5.6 4.7 - - + -
11B LEU* 3.7 30.1 - - + -
54B VAL* 3.0 17.9 + - + +
55B GLN* 2.8 13.1 + - + +
57B LYS* 1.3 81.3 - - + +
59B ILE* 1.3 57.3 + - - +
61B GLY 4.2 1.2 - - - -
62B ASP* 3.5 22.9 + - - +
71B SER* 6.0 1.2 - - - -
74B LEU* 4.1 17.4 - - + +
77B ALA* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN* 2.8 16.5 + - + +
56B THR* 3.1 22.0 - - + +
58B LEU* 1.3 76.8 - - - +
60B GLU* 1.3 67.1 + - + +
61B GLY 3.3 1.6 - - - -
62B ASP* 3.0 32.0 - - - +
74B LEU* 3.9 28.0 - - + -
78B GLN* 5.2 6.3 - - - +
76C HIS* 4.7 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 2.9 19.5 + - + +
57B LYS* 3.9 12.8 - - + +
59B ILE* 1.3 82.0 - - + +
61B GLY* 1.3 56.9 + - - +
62B ASP* 3.4 4.9 + - - +
63B ALA* 5.1 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS 3.1 14.0 + - - -
58B LEU* 4.2 3.4 - - - -
60B GLU* 1.3 76.7 - - - +
62B ASP* 1.3 56.5 + - - +
63B ALA* 2.9 23.0 + - - +
----------------------------------------------------------
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