Contacts of the helix formed by residues 45 - 71 (chain X) in PDB entry 3AOI
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 45 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLU* 5.3 2.6 - - - +
554C ASP* 5.5 0.2 - - - +
556C ASN* 3.3 18.4 + - - +
557C ARG* 3.3 40.0 + - - -
560C MET* 5.3 2.1 - - - +
878C SER 5.0 1.9 - - - +
879C ARG* 4.2 10.2 - - - -
880C MET 5.2 0.5 + - - -
1084D THR* 5.3 3.8 - - - +
42X ASP* 3.8 25.7 - - - +
43X TYR 3.4 1.1 - - - +
44X ASP* 1.3 79.0 - - - +
46X SER* 1.3 84.1 + - - +
47X GLY* 3.3 5.6 + - - +
48X LEU* 4.1 8.2 + - - +
49X GLU* 4.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C ASP* 3.8 13.1 + - - -
556C ASN* 2.5 35.2 + - - +
878C SER 6.0 0.9 - - - -
880C MET* 4.6 15.5 - - - -
45X ASP* 1.3 86.6 + - - +
47X GLY* 1.3 64.0 - - - +
48X LEU 3.0 1.2 + - - -
49X GLU* 3.1 6.7 + - - +
50X ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878C SER 5.9 0.4 + - - -
1034D GLN* 4.3 17.9 + - - -
36X LEU* 3.0 25.3 - - - +
45X ASP* 3.3 5.6 + - - +
46X SER* 1.3 75.5 - - - +
48X LEU* 1.3 55.6 + - - +
50X ALA* 3.9 2.8 - - - +
51X ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087D ARG* 4.9 5.8 - - - +
1235D GLN* 3.7 21.5 - - + -
33X LEU* 3.9 14.4 - - + -
36X LEU* 3.3 35.4 - - + +
37X MET* 3.8 19.1 - - + +
43X TYR* 4.4 17.3 - - + +
45X ASP 4.1 6.6 + - - +
46X SER 3.0 2.4 + - - -
47X GLY* 1.3 69.1 - - - +
49X GLU* 1.3 67.1 + - - +
51X ALA* 3.1 2.1 + - - +
52X LYS* 2.7 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080D GLY* 3.9 22.5 - - - +
1083D ASP* 3.9 21.3 - - - +
1084D THR* 3.6 34.6 - - + +
1087D ARG* 4.1 8.5 + - - -
1237D THR* 4.4 8.6 - - - +
45X ASP 4.4 7.6 + - - +
46X SER* 3.1 8.1 + - - +
48X LEU* 1.3 84.2 - - - +
50X ALA* 1.3 57.7 + - - +
52X LYS* 4.0 17.9 + - - +
53X GLN* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033D GLN* 4.9 16.0 - - + +
1037D GLN* 5.4 8.3 - - - +
46X SER* 2.8 25.1 + - - +
47X GLY* 3.9 4.3 - - - +
49X GLU* 1.3 73.9 - - - +
51X ALA* 1.3 65.5 + - - +
53X GLN* 3.1 5.9 + - - +
54X GLU* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031D ASN* 5.7 0.9 - - - +
1033D GLN* 5.9 4.0 - - - +
29X ALA* 5.1 3.8 - - - +
32X ILE* 3.9 18.2 - - + -
33X LEU* 3.4 23.3 - - + +
36X LEU* 3.5 13.7 - - + -
47X GLY 3.0 17.5 + - - +
50X ALA* 1.3 78.7 - - - +
52X LYS* 1.3 56.9 + - - +
54X GLU* 3.8 5.1 - - - +
55X LYS* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087D ARG* 5.5 1.2 - - - +
1235D GLN* 2.5 40.0 + - - +
1237D THR* 5.1 8.3 - - + +
1359D GLN* 2.7 31.9 - - - +
33X LEU* 3.3 24.7 - - + -
37X MET* 4.1 7.2 - - - -
48X LEU* 2.7 45.1 + - - +
49X GLU* 4.0 20.3 + - - +
51X ALA* 1.3 70.6 - - - +
53X GLN* 1.3 59.8 + - - +
55X LYS* 3.3 4.4 + - - +
56X ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044D LEU 5.9 1.4 + - - -
1045D MET* 6.0 5.1 - - - +
1046D GLN* 2.8 45.7 + - - +
1076D GLY* 5.3 10.7 - - - +
1079D LYS* 5.8 2.3 - - - +
1080D GLY* 5.9 2.4 + - - -
49X GLU* 2.9 22.2 + - - +
50X ALA* 3.1 6.0 + - - +
52X LYS* 1.3 72.0 - - - +
54X GLU* 1.3 67.3 + - - +
56X ALA* 3.0 9.4 + - + +
57X ARG* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033D GLN* 2.8 42.9 + - - +
1036D ARG* 3.6 11.4 + - - -
29X ALA* 5.6 6.7 - - + -
50X ALA 2.9 15.9 + - - +
51X ALA* 3.8 5.6 - - - +
53X GLN* 1.3 76.4 - - - +
55X LYS* 1.3 64.8 + - - +
56X ALA 3.1 0.7 + - - -
57X ARG* 3.1 22.2 + - - +
58X ILE* 3.1 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357D ARG 5.6 0.2 - - - -
1358D ALA* 3.1 37.0 + - - +
26X LEU* 3.8 14.0 - - + +
29X ALA* 4.5 17.4 - - + +
30X THR* 4.2 22.8 + - - +
33X LEU* 3.4 19.3 - - + -
51X ALA 3.0 19.3 + - - +
52X LYS* 3.4 6.7 - - - +
53X GLN 3.2 0.2 - - - -
54X GLU* 1.3 75.7 - - - +
56X ALA* 1.3 57.7 + - - +
58X ILE* 3.4 8.2 - - - +
59X GLU* 2.5 69.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X LYS 2.9 13.2 + - - +
53X GLN* 3.0 13.4 + - + +
55X LYS* 1.3 72.9 - - - +
57X ARG* 1.3 68.9 + - - +
58X ILE 2.9 3.0 + - - -
59X GLU* 3.0 15.6 + - - +
60X ALA* 2.9 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997D THR* 5.7 9.4 - - + -
1044D LEU* 5.7 16.8 + - - +
1046D GLN* 2.6 30.3 + - - +
1050D GLY 4.6 1.4 + - - -
1052D THR* 2.7 35.7 - - - +
53X GLN* 3.0 27.6 + - - +
54X GLU* 3.1 21.7 + - - +
56X ALA* 1.3 75.3 - - - +
58X ILE* 1.3 66.0 + - + +
60X ALA* 3.5 8.0 + - - +
61X ARG* 3.3 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22X GLU* 2.8 40.2 - - - +
25X ARG* 4.5 20.2 - - + +
26X LEU* 3.2 39.7 - - + -
29X ALA* 5.3 3.8 - - + -
54X GLU* 3.1 21.0 + - + +
55X LYS* 3.4 9.9 - - - +
56X ALA 2.9 1.0 + - - -
57X ARG* 1.3 74.6 - - + +
59X GLU* 1.3 69.6 + - - +
60X ALA 3.0 1.3 - - - -
61X ARG* 2.9 24.4 + - - +
62X ILE* 3.0 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1358D ALA* 4.2 11.6 - - - +
26X LEU* 3.6 15.2 - - + +
55X LYS* 2.5 56.0 + - - +
56X ALA* 3.0 13.0 + - - +
58X ILE* 1.3 80.3 - - - +
60X ALA* 1.3 56.2 + - - +
62X ILE* 2.7 34.0 - - + +
63X ASP* 2.9 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X ALA 2.9 10.4 + - - +
57X ARG* 3.6 13.0 - - - +
59X GLU* 1.3 75.5 - - - +
61X ARG* 1.3 67.1 + - + +
63X ASP* 3.3 6.7 + - - +
64X SER* 3.1 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994D GLN* 2.8 36.0 + - - +
997D THR* 3.3 28.7 + - - +
18X GLN* 4.6 6.7 + - - +
22X GLU* 3.1 43.7 + - + +
25X ARG* 3.9 8.9 - - - +
57X ARG* 3.3 27.8 + - + +
58X ILE* 2.9 11.1 + - - +
60X ALA* 1.3 79.2 - - + +
62X ILE* 1.3 57.7 + - - +
64X SER* 3.6 5.5 + - - -
65X LEU* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127D GLU* 5.5 2.7 - - - +
19X LEU* 3.3 31.4 - - + +
22X GLU* 3.8 36.2 - - + +
23X ARG* 4.1 9.9 - - + +
26X LEU* 4.9 15.5 - - + -
58X ILE* 3.0 12.3 + - + +
59X GLU* 2.7 30.3 - - + +
61X ARG* 1.3 75.4 - - - +
63X ASP* 1.3 61.6 + - - +
65X LEU* 3.0 7.0 + - - +
66X GLU* 2.7 53.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127D GLU* 5.4 2.4 - - - +
1327D ARG* 4.8 12.8 + - - -
59X GLU* 2.9 18.0 + - - +
60X ALA* 3.3 7.7 + - - +
62X ILE* 1.3 86.9 - - - +
64X SER* 1.3 56.2 + - - +
66X GLU* 3.2 10.2 + - - +
67X ASP* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X ALA 3.1 16.5 + - - -
61X ARG* 4.0 6.3 - - - -
63X ASP* 1.3 75.7 - - - +
65X LEU* 1.3 62.3 + - - +
67X ASP* 3.8 7.2 + - - +
68X ILE* 3.2 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15X LEU* 4.3 18.2 - - + +
18X GLN* 3.8 38.1 - - + +
19X LEU* 3.5 45.5 - - + +
22X GLU* 4.5 9.0 - - + -
61X ARG* 3.0 26.0 + - + +
62X ILE 3.0 4.5 + - - +
64X SER* 1.3 80.9 - - - +
66X GLU* 1.3 57.1 + - - +
68X ILE* 4.3 3.8 - - + +
69X LEU* 3.1 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127D GLU* 2.4 54.5 - - - +
1128D VAL* 4.9 5.9 - - + +
1327D ARG* 5.5 5.8 + - - +
19X LEU* 3.4 28.2 - - + +
23X ARG* 3.4 24.0 + - - +
62X ILE* 2.7 35.4 + - - +
63X ASP* 3.9 9.6 - - - +
65X LEU* 1.3 70.3 - - - +
67X ASP* 1.3 53.8 + - - +
69X LEU* 4.1 2.8 - - - +
70X SER* 2.6 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310D ARG* 6.1 0.3 - - - -
1327D ARG* 4.8 18.0 + - - +
63X ASP 2.8 17.2 + - - +
64X SER* 3.8 9.0 + - - +
65X LEU 3.3 0.2 - - - -
66X GLU* 1.3 74.9 - - - +
68X ILE* 1.3 72.1 + - - +
70X SER* 3.0 17.4 + - - -
71X ARG* 2.9 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X VAL* 3.9 30.6 - - + +
7X LEU* 4.0 20.6 - - + -
15X LEU* 4.6 6.3 - - + -
64X SER* 3.2 22.9 + - - +
65X LEU* 4.3 5.6 - - + +
67X ASP* 1.3 91.5 - - - +
69X LEU* 1.3 63.5 + - + +
70X SER 3.5 0.2 + - - -
71X ARG* 3.7 8.0 + - - +
72X ALA* 3.3 22.5 + - - +
108X ALA* 3.9 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128D VAL* 5.8 3.6 - - + -
7X LEU* 5.0 4.9 - - + -
12X TYR* 4.2 31.8 - - + -
15X LEU* 3.7 37.9 - - + +
16X MET* 3.3 51.0 - - + +
19X LEU* 4.0 15.3 - - + -
65X LEU* 3.1 27.6 + - + +
66X GLU* 4.6 3.4 - - - +
68X ILE* 1.3 77.5 - - + +
70X SER* 1.3 63.7 + - - +
71X ARG 3.6 0.2 + - - -
72X ALA* 4.3 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127D GLU 5.6 1.3 - - - -
1128D VAL 3.9 21.8 - - - -
1129D THR* 5.6 2.0 - - - -
1312D LEU* 4.7 20.5 - - - +
1327D ARG* 4.7 1.9 + - - -
66X GLU 2.6 26.0 + - - -
67X ASP* 3.0 13.0 + - - -
68X ILE 3.3 0.2 - - - -
69X LEU* 1.3 78.5 - - - +
71X ARG* 1.3 62.0 + - - +
72X ALA 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310D ARG* 5.3 15.4 - - - +
1312D LEU* 5.0 14.8 - - + -
3X ARG* 4.1 22.9 - - - +
4X GLU* 3.9 14.4 - - - +
5X VAL* 3.4 38.7 + - - +
67X ASP* 2.9 53.0 + - - +
68X ILE* 3.7 5.3 + - - +
69X LEU 3.4 0.4 - - - -
70X SER* 1.3 82.4 - - - +
72X ALA* 1.3 60.2 + - - +
73X VAL* 4.2 1.0 + - - +
----------------------------------------------------------
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