Contacts of the helix formed by residues 33 - 61 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 2.9 37.7 + - - +
29A ALA* 4.1 0.6 + - - -
31A GLN* 3.8 18.6 - - - +
32A GLY* 1.3 80.3 - - - +
34A PHE* 1.3 66.2 + - - +
35A ALA* 3.2 2.9 - - + -
36A ALA* 4.2 8.6 - - + +
37A ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.8 12.6 - - + -
32A GLY* 3.4 13.4 + - - -
33A ASP* 1.3 71.1 - - - +
35A ALA* 1.3 59.9 + - - +
37A ALA* 3.6 5.0 - - - +
38A LYS* 2.9 34.8 + - + +
95A ILE* 4.7 8.3 - - + -
98A HIS* 4.1 7.2 - - + -
99A GLU* 3.4 55.0 - - + +
102A LYS 3.9 4.7 - - - -
103A ALA* 3.1 42.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 3.2 1.3 - - - +
34A PHE* 1.3 80.5 - - - +
36A ALA* 1.3 62.5 + - - +
38A LYS* 3.4 7.5 + - - +
39A ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 3.3 28.7 - - + +
33A ASP* 3.5 12.7 + - + +
34A PHE 3.4 0.2 - - - -
35A ALA* 1.3 75.8 - - - +
37A ALA* 1.3 66.5 + - - +
39A ALA* 3.3 7.0 + - - +
40A MET* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.5 27.8 - - - +
28A GLN* 3.8 3.5 - - - +
29A ALA* 4.1 7.4 - - + +
33A ASP 3.1 17.9 + - - +
34A PHE* 3.6 8.7 - - - +
35A ALA 3.2 0.2 - - - -
36A ALA* 1.3 77.4 - - - +
38A LYS* 1.3 63.8 + - - +
40A MET* 3.1 3.8 + - - +
41A MET* 2.9 29.9 + - - +
95A ILE* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 2.9 19.7 + - + +
35A ALA* 3.6 7.4 - - - +
37A ALA* 1.3 75.7 - - - +
39A ALA* 1.3 62.3 + - - +
41A MET* 3.3 22.0 + - + +
42A ASP* 3.1 23.1 + - - +
95A ILE* 5.7 0.8 - - - +
99A GLU* 5.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA 3.1 13.8 + - - +
36A ALA* 3.6 11.0 - - - +
38A LYS* 1.3 76.2 - - - +
40A MET* 1.3 64.4 + - + +
42A ASP* 3.4 7.2 + - - +
43A GLN* 3.2 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.9 31.6 - - + +
24A ALA* 3.6 31.4 - - + -
25A ALA* 3.5 25.1 - - + +
28A GLN* 4.7 8.1 - - + -
36A ALA* 2.9 25.1 + - + +
37A ALA 3.5 0.2 - - - +
39A ALA* 1.3 76.9 - - + +
41A MET* 1.3 59.9 + - - +
43A GLN* 3.4 14.5 + - - +
44A SER* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 6.0 0.9 - - - +
25A ALA* 4.0 6.7 - - + -
37A ALA 2.9 21.5 + - - +
38A LYS* 3.3 21.3 + - + +
40A MET* 1.3 75.7 - - - +
42A ASP* 1.3 57.9 + - - +
44A SER* 3.2 7.3 + - - -
45A ARG* 2.8 32.1 + - - +
88A ARG* 3.6 17.9 + - + +
91A ILE* 5.6 0.9 - - + -
92A THR* 3.3 42.0 - - + +
95A ILE* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS 3.1 10.5 + - - +
39A ALA* 3.5 11.4 - - - +
40A MET 3.2 0.2 - - - -
41A MET* 1.3 79.9 - - - +
43A GLN* 1.3 63.1 + - + +
45A ARG* 3.2 16.9 + - - +
46A MET* 3.0 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 5.0 14.7 - - + +
39A ALA* 3.2 19.1 + - - +
40A MET* 3.8 19.0 - - - +
42A ASP* 1.3 77.2 - - + +
44A SER* 1.3 64.5 + - - +
46A MET* 3.2 15.1 + - - +
47A ALA* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 2.6 33.1 + - - +
21A LEU* 3.4 15.1 - - - +
22A ALA* 3.5 8.0 + - - +
40A MET 2.9 18.6 + - - -
41A MET* 3.4 7.6 - - - -
43A GLN* 1.3 76.7 - - - +
45A ARG* 1.3 62.9 + - - +
47A ALA* 3.2 8.6 + - - +
48A LEU* 3.0 29.1 + - - +
88A ARG* 4.1 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET 2.8 13.0 + - - +
42A ASP* 3.2 21.2 + - - +
44A SER* 1.3 77.0 - - - +
46A MET* 1.3 59.5 + - + +
48A LEU* 3.2 7.2 + - + +
49A ASN* 2.8 31.1 + - + +
88A ARG* 3.9 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 3.0 32.8 + - - +
43A GLN* 3.2 15.2 + - - +
45A ARG* 1.3 78.3 - - + +
47A ALA* 1.3 63.9 + - - +
49A ASN* 3.2 8.7 + - - +
50A GLU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.7 23.3 + - - +
17A GLN* 6.3 0.2 - - + -
18A ALA* 4.6 12.6 - - + +
21A LEU* 5.1 6.3 - - + -
43A GLN 2.9 12.9 + - - +
44A SER* 3.4 12.3 - - - +
46A MET* 1.3 77.8 - - - +
48A LEU* 1.3 56.4 + - - +
50A GLU* 3.4 6.3 + - - +
51A ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 5.9 0.4 - - - -
15A SER* 4.9 4.9 - - - -
18A ALA* 3.4 26.9 - - + -
44A SER 3.0 16.9 + - - +
45A ARG* 3.5 7.0 - - + +
47A ALA* 1.3 72.4 - - - +
49A ASN* 1.3 56.8 + - - +
51A ALA* 3.0 4.2 + - + +
52A HIS* 2.6 40.6 + - + +
81A LEU* 5.0 9.5 - - + +
84A SER* 4.0 20.4 - - - +
85A MET* 4.1 29.2 - - + +
88A ARG* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 2.8 19.7 + - + +
46A MET* 3.2 10.1 + - - +
48A LEU* 1.3 77.2 - - - +
50A GLU* 1.3 57.5 + - - +
52A HIS* 3.3 6.6 + - - +
53A LEU* 2.9 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 4.2 13.4 + - - +
46A MET 3.0 15.6 + - - +
47A ALA* 3.7 5.9 - - - +
49A ASN* 1.3 76.6 - - - +
51A ALA* 1.3 63.4 + - - +
53A LEU* 3.3 12.6 + - + +
54A VAL* 3.1 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.7 17.1 - - + +
14A ASN* 3.9 19.7 - - + +
15A SER 5.4 0.7 - - - +
47A ALA 3.0 16.1 + - - +
48A LEU* 3.4 10.8 - - + +
50A GLU* 1.3 77.2 - - - +
52A HIS* 1.3 62.9 + - - +
54A VAL* 3.2 6.8 + - - +
55A GLN* 3.0 22.0 + - - +
81A LEU* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 2.6 21.4 + - - +
49A ASN* 3.6 7.4 - - - +
51A ALA* 1.3 72.8 - - - +
53A LEU* 1.3 54.6 + - + +
55A GLN* 3.1 15.5 + - + +
56A THR* 2.7 60.2 + - + -
81A LEU* 4.7 8.0 - - + +
82A MET* 6.4 1.3 - - - -
85A MET* 4.8 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 2.9 44.4 + - - +
50A GLU* 3.5 11.9 - - + +
52A HIS* 1.3 80.0 - - - +
54A VAL* 1.3 63.3 + - + +
56A THR* 3.2 20.3 + - + +
57A LYS* 3.2 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.1 12.3 - - + -
11A LEU* 4.0 15.3 - - + -
50A GLU* 3.1 23.9 + - + +
51A ALA* 3.5 8.3 - - - +
53A LEU* 1.3 76.6 - - + +
55A GLN* 1.3 64.8 + - - +
57A LYS* 3.2 8.9 + - - +
58A LEU* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.9 3.6 - - + +
51A ALA 3.0 6.8 + - - +
52A HIS* 3.5 16.8 - - + +
54A VAL* 1.3 74.3 - - - +
56A THR* 1.3 68.8 + - - +
58A LEU* 2.8 23.3 + - - +
59A ILE* 2.8 19.2 + - + +
74A LEU* 3.4 23.5 + - + +
77A ALA* 3.9 4.2 - - - +
78A GLN* 3.3 47.0 - - - +
81A LEU* 2.8 43.5 - - + +
82A MET* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 2.7 51.0 + - + -
53A LEU* 3.3 15.2 + - + +
55A GLN* 1.3 73.5 - - - +
57A LYS* 1.3 57.2 + - - +
59A ILE* 3.0 17.2 + - + +
60A GLU* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 3.2 6.7 + - - +
54A VAL* 3.2 11.8 + - - +
55A GLN 3.2 0.4 - - - -
56A THR* 1.3 79.2 - - - +
58A LEU* 1.3 67.8 + - + +
60A GLU* 3.9 13.1 - - - +
61A GLY* 3.1 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 31.6 - - + +
7A VAL* 3.8 18.4 - - + -
8A VAL* 5.6 4.9 - - + -
11A LEU* 3.7 31.0 - - + -
54A VAL* 3.0 16.0 + - + +
55A GLN* 2.8 13.1 + - + +
57A LYS* 1.3 79.6 - - + +
59A ILE* 1.3 56.5 + - - +
61A GLY 4.2 1.0 - - - -
62A ASP* 3.5 22.8 + - - +
71A SER* 6.0 1.6 - - - -
74A LEU* 4.1 16.9 - - + +
77A ALA* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 2.8 16.1 + - + +
56A THR* 3.0 21.5 + - + +
58A LEU* 1.3 79.0 - - - +
60A GLU* 1.3 66.3 + - + +
61A GLY 3.3 0.4 - - - -
62A ASP* 3.0 32.7 - - - +
74A LEU* 3.9 26.5 - - + -
78A GLN* 5.2 7.4 - - - +
76B HIS* 4.3 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 2.9 19.5 + - + +
57A LYS* 3.9 13.7 - - - +
59A ILE* 1.3 83.0 - - + +
61A GLY* 1.3 56.9 + - - +
62A ASP* 3.4 5.4 + - - +
63A ALA* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 3.1 11.6 + - - -
58A LEU* 4.2 3.1 - - - -
60A GLU* 1.3 78.0 - - - +
62A ASP* 1.3 56.9 + - - +
63A ALA* 2.9 23.1 + - - +
----------------------------------------------------------
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