Contacts of the helix formed by residues 41 - 66 (chain N) in PDB entry 2WWA
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 LEU 41 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LYS* 3.7 29.4 - - - +
418A GLU* 3.7 20.2 - - + +
79D A 3.3 20.4 - - - +
80D A 3.9 18.8 - - - +
39N PRO* 3.8 19.5 - - + +
40N SER* 1.4 74.8 + - - +
42N PRO* 1.3 68.9 - - + +
43N LYS* 3.1 16.4 - - + +
44N ILE* 3.6 28.8 - - + +
45N LYS* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D A 3.6 44.0 - - + +
80D A 3.4 31.4 - - - +
81D U 5.2 3.8 - - - +
40N SER* 4.1 4.0 - - - +
41N LEU* 1.3 89.1 - - + +
43N LYS* 1.4 56.0 + - - +
45N LYS* 4.0 9.8 - - + +
46N THR* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N GLU* 3.2 34.8 + - - +
28N LEU* 4.3 15.6 - - - +
31N LEU* 6.2 1.6 - - - +
41N LEU* 3.1 12.6 - - + +
42N PRO* 1.4 77.2 - - - +
44N ILE* 1.4 61.7 + - + +
46N THR* 3.4 3.2 + - - -
47N VAL* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LYS* 5.4 0.7 - - - +
49D G 6.2 1.6 - - - -
28N LEU* 3.7 18.0 - - + +
31N LEU* 3.6 31.9 - - + +
32N LYS* 3.7 26.2 - - - +
36N LEU* 3.7 25.6 - - + -
37N SER* 5.4 0.2 - - - +
39N PRO* 4.2 0.7 - - + -
40N SER 3.9 6.7 - - - +
41N LEU* 3.2 41.5 + - + +
43N LYS* 1.4 76.0 - - + +
45N LYS* 1.4 60.5 + - - +
48N ARG* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D G 3.4 72.4 + - - +
74D U 5.2 4.3 - - - +
40N SER* 3.2 26.0 + - - +
41N LEU 3.0 14.6 + - - +
42N PRO* 4.1 7.6 - - + +
44N ILE* 1.4 77.1 - - - +
46N THR* 1.4 61.0 + - - +
48N ARG* 3.7 4.2 - - - +
49N LYS* 3.3 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D U 5.3 2.5 + - - +
4N VAL* 5.8 7.2 - - + -
5N LYS* 5.2 16.2 - - + -
42N PRO* 2.9 22.5 + - - +
43N LYS* 3.8 4.3 - - - -
45N LYS* 1.4 78.8 - - - +
47N VAL* 1.4 55.6 + - + +
49N LYS* 3.3 5.1 + - - +
50N SER* 2.8 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N VAL* 5.6 9.9 - - + -
21N LEU* 5.7 0.8 - - + +
24N LEU* 3.5 45.1 - - + +
27N GLU* 4.9 2.7 - - - +
28N LEU* 3.8 18.4 - - + -
43N LYS* 2.9 39.2 + - + +
46N THR* 1.4 78.2 - - + +
48N ARG* 1.4 63.2 + - - +
49N LYS 3.2 0.4 - - - -
50N SER* 3.9 9.0 - - - -
51N ILE* 3.3 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D C 3.6 15.8 + - - -
48D A 3.2 41.0 + - - -
49D G 3.9 26.1 + - - -
60D U 4.4 0.3 - - - +
61D A 3.0 58.7 + - - +
28N LEU* 3.7 11.1 - - + +
32N LYS* 5.1 19.2 - - - +
44N ILE* 2.9 20.9 + - + +
45N LYS* 3.7 4.5 - - - +
47N VAL* 1.4 75.7 - - - +
49N LYS* 1.3 70.4 + - + +
50N SER 3.4 0.4 - - - -
51N ILE* 3.5 23.1 - - - +
52N ALA 3.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D A 5.7 0.2 - - - -
49D G 4.2 17.0 - - - -
61D A 3.4 23.8 + - - +
62D C 2.9 31.4 + - - -
63D G 3.4 31.6 + - - +
64D U 3.2 40.3 + - - +
45N LYS* 3.3 32.0 + - + +
46N THR* 3.3 6.7 + - - +
47N VAL 3.2 0.2 - - - -
48N ARG* 1.3 86.3 - - + +
50N SER* 1.4 57.2 + - - +
51N ILE 3.4 0.7 - - - -
52N ALA* 3.6 5.8 - - - +
53N CYS* 3.2 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N VAL* 5.1 11.4 - - - +
5N LYS* 5.3 9.7 - - - +
9N LEU* 5.4 4.7 - - - +
21N LEU* 3.7 6.3 - - - +
46N THR* 2.8 22.5 + - - -
47N VAL* 3.5 12.5 + - - -
48N ARG 3.4 0.2 - - - -
49N LYS* 1.4 76.4 - - - +
51N ILE* 1.4 60.7 + - - +
53N CYS* 3.8 9.4 - - - +
54N VAL* 3.1 37.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D U 4.4 12.3 - - - +
21N LEU* 3.9 25.8 - - + +
24N LEU 4.9 3.4 - - - +
25N LYS* 3.9 48.5 - - + +
28N LEU* 5.1 5.4 - - + -
47N VAL* 3.3 19.8 + - + +
48N ARG* 3.5 14.1 - - - +
49N LYS 3.4 0.2 - - - -
50N SER* 1.4 78.5 - - - +
52N ALA* 1.4 56.2 + - - +
55N LEU* 3.1 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D U 3.1 50.9 + - - +
61D A 3.6 4.7 - - - +
63D G 3.2 32.8 - - + +
48N ARG 3.7 1.6 + - - -
49N LYS* 3.6 6.3 - - - +
51N ILE* 1.4 79.4 - - - +
53N CYS* 1.4 57.5 + - - +
54N VAL 3.4 1.0 + - - -
56N THR* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 53 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D G 4.9 1.8 - - - +
64D U 3.3 49.4 + - - +
65D A 4.5 8.5 - - - -
5N LYS* 6.4 2.5 - - - -
49N LYS 3.2 17.5 + - - +
50N SER* 3.8 9.6 - - - +
51N ILE 3.4 0.4 - - - -
52N ALA* 1.4 77.9 - - - +
54N VAL* 1.4 64.0 + - + +
56N THR* 3.0 15.9 + - - -
57N VAL* 3.3 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N LYS* 6.5 0.2 - - + -
9N LEU* 3.5 34.8 - - + -
17N LEU* 3.9 12.7 - - + +
21N LEU* 3.6 31.9 - - + -
50N SER* 3.1 32.3 + - - +
52N ALA 3.3 0.2 - - - -
53N CYS* 1.4 86.3 - - + +
55N LEU* 1.4 60.6 + - - +
56N THR 3.3 0.7 - - - -
57N VAL* 3.6 13.1 - - + +
58N ILE* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D U 3.3 38.6 - - + +
21N LEU* 4.2 12.8 - - + -
25N LYS* 4.9 8.3 - - - +
51N ILE* 3.1 41.8 + - + +
54N VAL* 1.4 74.6 - - - +
56N THR* 1.4 58.6 - - - +
57N VAL 3.4 0.4 - - - -
58N ILE* 3.9 26.0 - - + +
59N ASN* 3.2 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D U 3.8 9.6 - - + +
63D G 5.6 3.4 - - + +
64D U 4.8 5.5 + - - -
97D A 3.1 42.1 + - + +
98D U 3.8 19.7 - - - +
52N ALA 3.2 15.2 + - - +
53N CYS* 3.0 23.0 + - - -
55N LEU* 1.4 77.4 - - - +
57N VAL* 1.4 56.1 + - - +
59N ASN* 3.9 1.5 - - - -
60N GLU* 3.0 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D A 6.3 1.6 - - - -
9N LEU* 5.2 5.8 - - + +
10N ARG* 3.7 59.1 + - - +
12N LYS 6.2 0.2 - - - +
17N LEU* 6.3 1.3 - - + -
53N CYS* 3.3 19.7 - - - +
54N VAL* 3.6 18.1 - - + +
55N LEU 3.4 0.4 - - - -
56N THR* 1.4 75.3 + - - +
58N ILE* 1.4 65.3 + - + +
60N GLU* 3.4 6.0 + - - +
61N GLN* 3.1 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N LYS* 5.3 7.4 - - + +
17N LEU* 4.0 23.6 - - + -
18N ALA* 4.9 15.0 - - + +
21N LEU* 4.6 6.7 - - + -
54N VAL 3.2 19.4 + - - +
55N LEU* 3.8 25.1 + - + +
56N THR 3.5 0.2 - - - -
57N VAL* 1.4 76.7 - - + +
59N ASN* 1.4 63.9 + - - +
61N GLN* 3.3 29.8 - - + +
62N GLN* 3.1 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D U 2.9 30.3 + - - +
98D U 3.3 28.4 + - - +
99D C 5.2 0.2 + - - -
55N LEU* 3.2 26.2 + - - +
56N THR 4.4 0.9 - - - +
58N ILE* 1.4 79.4 - - - +
60N GLU* 1.4 60.4 + - - +
62N GLN* 3.1 22.6 + - - +
63N ARG* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D A 5.1 2.8 + - - -
96D A 5.4 0.8 + - - -
97D A 3.6 39.1 + - - +
10N ARG* 3.2 34.2 + - - +
56N THR* 3.0 20.2 + - - +
57N VAL* 3.7 6.2 - - - +
58N ILE 3.3 0.2 - - - -
59N ASN* 1.4 75.1 - - - +
61N GLN* 1.4 60.2 + - - +
63N ARG* 3.2 6.4 + - - +
64N GLU* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N ARG* 5.2 3.0 + - - +
12N LYS 4.8 11.1 + - - -
14N LYS* 3.3 35.9 - - - +
57N VAL* 3.1 30.2 + - - +
58N ILE* 3.3 24.6 - - + +
60N GLU* 1.4 76.5 - - - +
62N GLN* 1.4 63.5 + - + +
64N GLU* 4.1 4.3 - - - +
65N ALA* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58N ILE* 3.1 27.8 + - + +
59N ASN* 3.1 32.0 + - - +
60N GLU 3.3 0.4 - - - -
61N GLN* 1.4 80.9 - - + +
63N ARG* 1.4 60.2 + - - +
65N ALA* 3.7 4.3 + - - +
66N VAL* 3.2 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D A 4.5 0.4 + - - -
97D A 2.6 46.0 + - - +
98D U 2.6 40.0 + - - +
99D C 4.9 12.5 - - - +
59N ASN 3.2 18.8 + - - +
60N GLU* 3.2 6.2 + - - +
62N GLN* 1.4 77.9 - - - +
64N GLU* 1.4 78.4 + - - +
66N VAL* 3.4 15.1 + - - +
67N ARG* 3.6 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D A 4.9 5.0 - - - +
60N GLU* 2.9 33.6 + - + +
61N GLN* 4.3 3.8 - - - +
63N ARG* 1.4 88.3 + - + +
65N ALA* 1.4 62.9 + - - +
67N ARG* 2.6 63.2 + - - +
68N GLN* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N GLN 3.1 19.6 + - - +
62N GLN* 3.9 6.5 - - - +
63N ARG 3.4 0.2 - - - -
64N GLU* 1.4 75.7 - - - +
66N VAL* 1.4 58.0 + - + +
68N GLN* 3.3 15.6 + - - +
69N LEU* 3.2 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N GLN* 3.2 18.3 + - + +
63N ARG* 3.7 7.9 - - - +
64N GLU 3.2 0.6 - - - -
65N ALA* 1.4 77.3 - - + +
67N ARG* 1.4 55.6 + - - +
68N GLN 3.4 0.2 - - - -
69N LEU* 3.3 28.1 - - + +
----------------------------------------------------------
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