Contacts of the helix formed by residues 24 - 45 (chain C) in PDB entry 4ADV
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 ASN 24 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.6 29.1 - - - -
23C ALA* 1.3 75.9 + - - +
25C THR* 1.3 55.6 + - - +
26C LYS* 2.5 24.1 + - + +
27C GLU* 2.6 27.5 + - - +
28C PHE* 2.9 12.3 + - - -
97J ASP* 4.6 7.8 + - - +
75N LYS* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255A G 4.2 17.3 + - - +
1256A A 5.1 12.6 - - - +
24C ASN* 1.3 71.5 - - - +
26C LYS* 1.3 65.4 + - - +
28C PHE* 4.1 3.8 - - - -
29C ALA* 3.7 8.5 + - - +
74N ARG* 3.2 42.0 + - + +
75N LYS* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASN* 2.5 12.6 + - + +
25C THR* 1.3 80.4 - - - +
27C GLU* 1.3 98.3 + - + +
29C ALA* 3.8 7.1 - - - +
30C ASP* 4.3 7.0 + - - +
74N ARG* 3.8 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE 4.4 1.7 - - - +
23C ALA* 3.1 21.8 - - - +
24C ASN* 2.6 40.4 + - - +
26C LYS* 1.3 103.1 - - + +
28C PHE* 1.3 56.3 + - - +
29C ALA 2.9 3.1 - - - -
30C ASP* 2.8 9.3 + - + +
31C ASN* 2.6 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 4.3 3.8 - + - -
23C ALA* 3.6 32.1 - - + -
24C ASN 2.9 20.9 + - - +
25C THR* 4.0 6.3 - - - +
27C GLU* 1.3 78.2 - - - +
29C ALA* 1.3 57.9 + - - +
31C ASN* 3.3 12.7 + - - -
32C LEU* 2.9 36.3 + - + +
13J PHE* 4.5 14.1 - + - -
67J ILE* 4.6 5.6 - - + -
75N LYS* 3.0 36.3 - - + +
76N PHE* 3.8 20.6 - + - -
92N ILE* 4.2 11.0 - - + -
93N PRO* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR 3.7 2.0 + - - -
26C LYS 3.8 5.4 - - - +
27C GLU 2.8 1.2 + - - -
28C PHE* 1.3 79.3 - - - +
30C ASP* 1.3 67.5 + - - +
32C LEU* 3.0 19.5 - - - +
64N ARG* 3.1 25.3 + - - +
74N ARG* 3.5 38.1 - - + +
75N LYS 3.7 11.5 + - - -
76N PHE 4.3 2.4 - - - +
77N GLY* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LYS* 4.3 9.1 - - - +
27C GLU* 2.8 9.0 + - - +
29C ALA* 1.3 81.1 - - - +
31C ASN* 1.3 62.8 + - - +
33C ASP* 2.9 26.7 - - + +
34C SER* 3.0 11.4 + - - -
64N ARG* 3.0 31.0 + - - +
74N ARG* 5.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.3 30.3 - - + -
22C PHE 4.6 1.6 + - - -
23C ALA* 4.0 5.1 - - - +
27C GLU* 2.6 44.6 + - - +
28C PHE* 3.3 11.2 + - - +
30C ASP* 1.3 68.3 - - - +
32C LEU* 1.3 64.0 + - - +
33C ASP 2.8 5.3 + - - -
34C SER* 3.1 12.5 + - - -
35C ASP* 2.8 21.7 - - - +
58C ARG* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 4.0 14.0 - - + -
28C PHE* 2.9 32.5 + - + +
29C ALA 3.0 20.9 - - - +
31C ASN* 1.3 78.5 - - - +
33C ASP* 1.3 67.3 + - - +
35C ASP* 3.5 12.8 - - - +
36C PHE* 3.3 18.0 + - - +
64N ARG* 5.2 0.7 - - - -
65N GLN* 5.6 1.2 + - - +
75N LYS 4.4 0.2 - - - +
76N PHE* 3.5 49.1 - - + +
78N LEU* 4.0 18.2 - - + -
86N ALA* 5.6 1.3 - - + -
91N GLU 5.0 8.1 - - - +
92N ILE* 4.4 14.1 - - + -
93N PRO* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA 3.9 0.2 - - - +
30C ASP* 2.9 20.3 - - - +
31C ASN 2.8 1.2 - - - -
32C LEU* 1.3 81.1 - - - +
34C SER* 1.3 68.5 + - - -
36C PHE* 2.9 14.6 + - - +
37C LYS* 3.1 46.7 + - - +
64N ARG* 3.0 51.8 + - - +
65N GLN* 5.1 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASP 3.0 7.9 + - - -
31C ASN* 3.1 3.9 + - - -
33C ASP* 1.3 81.1 + - - +
35C ASP* 1.3 75.0 + - - +
37C LYS* 2.8 24.1 + - - +
38C VAL* 2.8 18.2 + - - +
58C ARG* 3.0 26.0 + - - -
63C ILE* 6.0 0.3 - - - +
93C ILE 3.6 23.3 - - - -
94C ALA* 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C SER* 3.3 8.0 + - - +
21C TRP* 3.2 29.2 + - - -
31C ASN 2.8 21.7 - - - +
32C LEU* 3.5 14.8 - - - +
33C ASP 3.2 0.2 - - - -
34C SER* 1.3 80.8 + - - +
36C PHE* 1.3 57.3 + - - +
38C VAL* 3.0 11.5 - - - +
39C ARG* 2.9 39.0 + - - +
56C ILE* 3.7 16.2 - - + +
58C ARG* 2.9 29.3 + - - -
91N GLU 5.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU 3.3 8.5 + - - +
33C ASP 2.9 10.6 + - - +
35C ASP* 1.3 77.4 - - - +
37C LYS* 1.3 86.4 + - + +
39C ARG* 4.4 5.4 - - + +
40C GLN* 2.6 63.7 + - + +
65N GLN* 3.7 40.8 - - + +
91N GLU* 4.9 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASP* 3.1 49.3 + - - +
34C SER* 2.8 15.2 + - - +
36C PHE* 1.3 99.6 - - + +
38C VAL* 1.3 56.2 + - - +
40C GLN* 3.8 8.0 + - - +
41C TYR* 3.0 31.9 + - - +
93C ILE* 4.0 21.4 - - + +
64N ARG 4.0 9.3 + - - -
65N GLN* 4.0 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C SER* 2.8 25.0 + - - +
35C ASP* 3.0 23.1 - - - +
37C LYS* 1.3 71.0 - - - +
39C ARG* 1.3 70.5 + - - +
41C TYR* 3.4 2.1 + - - +
42C LEU* 2.9 44.6 + - + +
54C ILE* 5.9 0.9 - - + -
56C ILE* 4.2 11.2 - - + -
63C ILE* 5.0 15.5 - - + -
65C VAL* 5.7 4.9 - - + -
90C VAL* 4.9 9.4 - - + -
93C ILE* 3.3 45.8 - - + +
94C ALA* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN* 3.1 35.2 + - - +
19C SER* 3.4 11.5 + - - -
35C ASP* 2.9 20.6 + - - +
36C PHE* 3.8 5.1 - - + +
38C VAL* 1.3 80.9 - - + +
40C GLN* 1.3 66.5 + - - +
41C TYR 3.4 0.3 + - - -
42C LEU* 3.5 9.9 + - - +
43C THR* 3.5 14.9 + - - +
54C ILE* 3.4 45.8 + - + +
56C ILE* 3.1 27.0 - - + +
91N GLU* 3.1 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 2.6 47.8 + - + +
37C LYS* 3.8 8.9 + - - +
39C ARG* 1.3 75.4 - - - +
41C TYR* 1.3 75.9 + - - +
43C THR* 3.5 10.8 + - - -
44C LYS* 3.0 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LYS 3.0 19.8 + - - +
38C VAL* 3.7 4.9 - - - +
40C GLN* 1.3 76.8 - - - +
42C LEU* 1.3 61.1 + - + +
43C THR 2.8 12.0 + - - -
44C LYS* 2.9 48.9 + - + +
45C GLU* 3.0 47.7 + - + +
86C LEU* 6.1 2.5 - - + -
89C VAL* 4.3 26.7 - - + +
93C ILE* 4.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 2.9 39.7 + - + +
39C ARG 3.5 1.5 + - - +
41C TYR* 1.3 79.1 - - + +
43C THR* 1.3 57.5 + - - +
46C LEU* 3.0 32.3 - - + +
51C VAL* 5.2 2.5 - - - +
54C ILE* 3.8 23.1 - - + -
65C VAL* 5.0 9.2 - - + -
67C ILE* 3.3 35.5 - - + +
86C LEU* 3.6 36.1 - - + -
89C VAL* 6.0 4.5 - - + -
90C VAL* 4.9 13.9 - - + -
100C ILE* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.5 11.8 + - - +
40C GLN* 3.5 10.7 + - - -
41C TYR 2.9 0.6 - - - -
42C LEU* 1.3 79.1 - - - +
44C LYS* 1.3 60.5 + - - +
45C GLU 3.3 2.2 - - - -
46C LEU 4.4 3.4 - - - -
47C ALA* 2.7 44.9 + - + +
51C VAL* 4.9 14.8 - - + +
54C ILE* 5.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLN* 3.0 50.2 + - - +
41C TYR* 2.9 36.1 + - + +
43C THR* 1.3 79.4 - - - +
45C GLU* 1.3 64.9 + - + +
46C LEU 3.6 0.2 + - - -
47C ALA* 4.2 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 3.0 49.3 + - + +
43C THR 3.3 0.2 - - - -
44C LYS* 1.3 79.3 - - + +
46C LEU* 1.3 76.4 + - + +
47C ALA 3.8 0.9 - - - -
82C ASP* 5.4 1.2 - - - +
85C LYS* 3.9 31.5 + - - +
86C LEU* 4.7 8.4 - - + +
89C VAL* 4.6 8.3 - - - +
----------------------------------------------------------
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