Contacts of the helix formed by residues 20 - 52 (chain L) in PDB entry 5LN3
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 LYS 20 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L HIS* 1.4 99.0 - - + +
21L GLU* 1.4 65.0 + - - +
23L ASP* 3.7 14.9 + - - +
24L GLY* 3.8 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L HIS 4.3 3.0 - - - +
20L LYS* 1.4 75.1 - - - +
22L ILE* 1.3 71.1 + - + +
23L ASP 3.3 0.5 + - - -
24L GLY* 3.4 4.1 + - - -
25L ARG* 3.3 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L HIS* 3.6 32.8 - - - +
20L LYS 3.3 0.8 - - - -
21L GLU* 1.3 83.6 - - + +
23L ASP* 1.3 55.4 + - - +
25L ARG* 3.5 6.8 + - - +
26L LEU* 3.1 27.1 + - - +
52M ILE* 4.8 15.0 - - + +
55M MET* 3.6 35.9 - - + +
56M LYS* 3.9 25.6 - - + +
59M VAL* 3.9 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L HIS 3.6 8.3 + - - +
20L LYS* 3.8 11.4 - - - +
22L ILE* 1.3 75.2 - - - +
24L GLY* 1.3 63.0 + - - +
26L LEU* 3.3 16.0 + - - +
27L LYS* 3.2 45.9 + - - +
55M MET* 3.8 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LYS 3.8 5.2 + - - -
21L GLU* 3.4 6.2 + - - -
22L ILE 3.4 0.4 - - - -
23L ASP* 1.3 78.5 + - - +
25L ARG* 1.4 61.6 + - - +
26L LEU 3.6 0.2 + - - -
27L LYS* 3.9 11.0 + - - +
28L GLU* 3.9 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L GLU* 3.3 31.9 + - + +
22L ILE* 3.6 9.2 - - - +
24L GLY* 1.4 74.2 + - - +
26L LEU* 1.3 64.4 + - - +
27L LYS 3.3 0.2 - - - -
28L GLU* 3.4 34.7 + - - +
29L LEU* 3.2 64.1 + - + +
59M VAL* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ILE 3.1 17.6 + - - +
23L ASP* 3.3 13.6 + - - +
25L ARG* 1.3 77.8 - - - +
27L LYS* 1.3 72.0 + - - +
29L LEU* 4.1 2.3 - - - +
30L ARG* 3.1 47.6 + - - +
55M MET* 4.6 7.9 - - + +
58M GLU* 3.2 52.3 - - + +
59M VAL* 3.8 24.5 - - + +
62M VAL* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ASP* 3.2 44.4 + - - +
24L GLY* 4.1 7.2 - - - +
26L LEU* 1.3 90.9 - - + +
28L GLU* 1.4 64.6 + - - +
30L ARG* 4.3 11.4 - - - +
31L GLU* 3.0 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLY 3.9 8.3 + - - +
25L ARG* 3.4 41.2 + - - +
26L LEU 3.4 0.6 - - - -
27L LYS* 1.4 79.8 - - - +
29L LEU* 1.4 70.4 + - - +
31L GLU* 4.1 3.1 - - - +
32L GLN* 3.2 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L ARG* 3.2 52.9 + - + +
26L LEU* 4.5 2.0 - - - +
28L GLU* 1.4 82.4 - - - +
30L ARG* 1.4 54.7 + - - +
32L GLN* 3.1 20.2 + - - +
33L LEU* 2.9 52.7 + - + +
59M VAL* 3.9 27.6 - - + -
62M VAL* 4.5 6.1 - - + -
63M THR* 5.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LEU* 3.1 45.8 + - - +
27L LYS* 3.8 14.2 - - - +
28L GLU 3.4 0.2 - - - -
29L LEU* 1.4 73.9 - - - +
31L GLU* 1.4 72.2 + - - +
33L LEU* 4.0 1.7 - - - +
34L LYS* 3.1 28.2 + - + +
58M GLU* 3.4 31.9 + - - +
61M ARG* 4.0 19.4 - - - +
62M VAL* 4.2 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L LYS* 3.0 33.1 + - - +
28L GLU* 4.2 3.1 - - - +
30L ARG* 1.4 88.7 - - - +
32L GLN* 1.4 65.6 + - - +
34L LYS* 3.2 34.7 + - - +
35L GLU* 3.6 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L GLU* 3.2 30.7 + - - +
29L LEU* 3.1 24.4 + - - +
31L GLU* 1.4 78.8 - - - +
33L LEU* 1.4 81.6 + - + +
35L GLU* 3.6 9.1 + - - +
36L LEU* 3.5 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L LEU* 2.9 27.1 + - + +
30L ARG* 4.3 3.4 - - - +
32L GLN* 1.4 93.6 - - + +
34L LYS* 1.4 57.5 + - - +
36L LEU* 3.3 7.6 + - + +
37L THR* 2.9 37.0 + - + +
62M VAL* 3.7 46.9 - - + +
63M THR* 4.2 11.0 - - + +
66M LEU* 3.5 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ARG* 3.1 22.1 + - + +
31L GLU* 3.2 40.1 + - - +
33L LEU* 1.4 70.0 - - - +
35L GLU* 1.3 74.7 + - - +
37L THR* 2.9 18.7 + - - -
38L LYS* 3.3 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLU* 3.6 18.1 + - + +
32L GLN* 3.9 8.8 - - - +
33L LEU 3.4 0.4 - - - -
34L LYS* 1.3 89.2 - - + +
36L LEU* 1.4 62.2 + - + +
38L LYS* 4.0 5.8 - - - +
39L GLN* 3.4 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L GLN* 3.5 19.6 + - + +
33L LEU* 3.3 19.7 + - + +
34L LYS 3.3 0.8 - - - -
35L GLU* 1.4 78.9 - - + +
37L THR* 1.4 57.7 + - - +
39L GLN* 3.7 2.5 + - - +
40L TYR* 3.0 62.9 + - + +
66M LEU* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L LEU* 2.9 27.4 + - + +
34L LYS* 2.9 19.1 + - - -
36L LEU* 1.4 71.9 - - + +
38L LYS* 1.4 56.4 + - - +
40L TYR* 3.5 3.3 - - + +
41L GLU* 3.0 32.1 + - - +
65M GLU* 4.1 14.6 - - + +
66M LEU* 3.8 30.5 - - + +
69M MET* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L LYS* 3.3 46.1 + - + +
35L GLU* 4.0 6.1 - - - +
37L THR* 1.4 78.4 + - - +
39L GLN* 1.4 62.0 + - + +
41L GLU* 3.5 15.2 - - - +
42L LYS* 3.3 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLU* 3.4 15.5 - - + +
36L LEU* 3.7 9.8 + - - +
37L THR 3.6 0.2 - - - -
38L LYS* 1.4 72.0 - - + +
40L TYR* 1.3 71.6 + - + +
42L LYS* 3.3 41.6 + - - +
43L SER* 3.4 10.5 + - - -
73M ILE* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L LEU* 3.0 54.7 - - + +
37L THR* 3.5 8.5 - - - +
39L GLN* 1.3 82.8 - - + +
41L GLU* 1.3 65.0 + - - +
43L SER* 3.2 20.1 + - - -
44L GLU* 3.4 10.6 + - - +
66M LEU* 4.5 7.2 - - + -
69M MET* 3.4 41.1 - - + +
70M LYS* 3.5 42.5 + - + +
72M LYS* 4.4 8.3 - - - +
73M ILE* 3.7 30.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L THR* 3.0 17.1 + - - +
38L LYS* 3.5 17.5 - - - +
40L TYR* 1.3 79.0 - - - +
42L LYS* 1.4 60.5 + - - +
44L GLU* 3.3 24.9 + - - +
45L ASN* 3.4 20.0 + - - +
69M MET* 4.0 29.4 - - - +
72M LYS* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L LYS* 3.3 22.6 + - - +
39L GLN* 3.3 33.4 + - - +
41L GLU* 1.4 75.8 - - - +
43L SER* 1.4 62.9 + - - +
45L ASN* 3.0 27.1 + - - +
46L ASP* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLN 3.4 12.0 + - - -
40L TYR 3.2 10.1 + - - -
42L LYS* 1.4 76.8 - - - +
44L GLU* 1.3 60.7 + - - +
46L ASP* 3.2 19.6 + - - +
47L LEU 3.3 0.5 + - - -
72M LYS 5.2 0.2 - - - -
73M ILE* 3.7 30.3 - - - +
76M ASN* 3.3 44.2 + - - -
139M LEU* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L TYR 3.4 3.9 + - - +
41L GLU* 3.3 17.2 + - - +
42L LYS 3.1 0.6 - - - -
43L SER* 1.3 77.0 - - - +
45L ASN* 1.4 64.5 + - - +
46L ASP 3.2 0.2 - - - -
47L LEU* 3.2 23.0 + - + +
48L LYS* 3.3 37.0 + - - +
72M LYS* 3.1 51.3 + - + +
75M GLU* 6.0 1.3 - - - +
76M ASN* 5.7 0.7 - - - -
85V GLU* 5.0 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L GLU* 3.4 21.4 + - - +
42L LYS* 3.0 20.4 + - - +
44L GLU* 1.4 62.6 + - - +
46L ASP* 1.4 63.0 + - - +
48L LYS* 3.2 33.8 + - - +
49L ALA* 3.4 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L LYS* 3.0 27.0 + - - +
43L SER* 3.3 16.3 - - - +
44L GLU 3.2 0.4 - - - -
45L ASN* 1.4 77.3 - - - +
47L LEU* 1.4 62.5 + - - +
49L ALA* 3.2 11.8 + - - +
50L LEU* 3.1 22.9 + - + +
76M ASN* 4.2 7.0 - - - +
137M ILE* 4.2 13.7 - - + +
138M GLY* 4.3 4.4 + - - -
139M LEU* 3.1 50.4 + - + +
159M LEU* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L SER 3.3 4.6 + - - +
44L GLU* 3.2 20.1 + - + +
46L ASP* 1.4 79.1 - - - +
48L LYS* 1.3 62.7 + - + +
50L LEU* 3.0 16.1 + - + +
51L GLN* 3.4 21.1 + - + +
72M LYS 5.9 0.7 - - - +
75M GLU* 3.4 36.8 - - + +
76M ASN* 3.8 19.9 - - + +
79M LYS* 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L GLU* 3.4 39.1 + - - +
45L ASN* 3.4 20.9 - - - +
46L ASP 3.2 0.2 - - - -
47L LEU* 1.3 78.3 - - + +
49L ALA* 1.3 62.1 + - - +
51L GLN* 3.4 31.4 + - - +
52L SER* 3.5 8.6 + - - -
80V THR* 4.2 25.1 - - + +
83V SER* 5.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L ASN 3.4 7.7 + - - +
46L ASP* 3.3 14.8 - - - +
48L LYS* 1.3 76.0 - - - +
50L LEU* 1.4 62.9 + - - +
52L SER* 2.9 27.4 + - - -
137M ILE* 4.8 8.3 - - + -
157M SER* 3.2 9.5 + - - -
159M LEU* 3.7 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ASP* 3.1 16.6 + - + +
47L LEU* 3.0 15.7 + - + +
49L ALA* 1.4 72.8 - - - +
51L GLN* 1.3 62.3 + - + +
52L SER 3.6 1.0 - - - +
76M ASN* 4.9 3.1 - - - +
79M LYS* 3.7 44.2 - - + -
80M ILE* 4.2 18.2 - - + -
139M LEU* 6.0 5.2 - - + -
154M ASN* 3.8 31.6 - - + +
156M ASP* 4.6 12.5 - - + +
157M SER* 3.5 31.9 + - - +
159M LEU* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L LEU* 3.6 16.6 + - + +
48L LYS* 3.4 22.3 + - - +
49L ALA 3.2 0.4 - - - -
50L LEU* 1.3 79.3 - - + +
52L SER* 1.3 60.6 + - - +
53L VAL* 3.7 1.2 + - - -
79M LYS* 6.4 1.6 - - - -
80V THR* 4.6 22.1 + - - +
83V SER* 5.1 8.3 + - - -
125V VAL* 5.0 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L LYS 3.5 10.1 + - - -
49L ALA* 2.9 22.0 + - - -
50L LEU 3.6 0.9 - - - +
51L GLN* 1.3 80.3 - - - +
53L VAL* 1.3 63.8 + - - +
157M SER* 2.6 30.3 + - - -
80V THR* 5.2 12.4 + - - +
----------------------------------------------------------
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