Contacts of the helix formed by residues 31 - 49 (chain O) in PDB entry 1L0V
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 THR 31 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU 3.3 8.2 + - - -
28O ARG* 3.0 21.0 + - - -
29O GLU 2.6 5.7 + - - -
30O GLY* 1.3 75.5 - - - +
32O ALA* 1.3 61.0 + - - -
33O VAL 3.4 0.4 + - - -
34O PRO* 3.4 6.2 - - - +
35O ALA* 3.3 22.4 + - + +
78O ALA* 3.6 29.2 + - + +
79O ALA* 4.6 2.2 - - - +
81O LEU* 4.2 10.7 - - - +
82O HIS* 3.3 38.4 + - + +
81P ARG* 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O GLU 2.8 13.5 + - - +
30O GLY* 5.2 0.2 - - - -
31O THR* 1.3 79.1 - - - +
33O VAL* 1.3 65.2 - - + +
35O ALA* 3.1 19.4 - - - +
36O VAL* 3.1 12.1 + - - +
77P CYS* 6.3 0.2 - - - -
78P GLY* 3.3 29.3 - - - +
81P ARG* 3.7 23.1 - - + +
82P MET* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O GLY* 3.4 11.4 + - - +
32O ALA* 1.3 71.2 - - + +
34O PRO* 1.3 77.8 - - + +
35O ALA 2.7 5.4 + - - -
36O VAL* 2.8 24.9 + - + +
37O TRP* 3.0 16.1 + - + +
82P MET* 4.5 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 34 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O GLY 3.2 17.7 - - - +
31O THR 3.4 6.1 - - - +
33O VAL* 1.3 94.7 - - + +
35O ALA* 1.3 60.0 + - - +
37O TRP* 3.6 14.0 - - + -
38O PHE* 3.2 24.4 + - - +
74O ILE* 5.1 9.6 - - + -
75O THR* 3.8 24.9 - - + +
78O ALA* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O THR* 3.3 16.6 + - + +
32O ALA* 3.1 17.7 + - - +
33O VAL 2.7 1.6 + - - -
34O PRO* 1.3 81.9 - - - +
36O VAL* 1.3 58.0 + - + +
38O PHE* 3.8 6.9 + - - +
39O SER* 3.5 17.0 + - - -
75O THR* 5.7 0.4 - - - -
24P SER* 6.0 4.9 - - - -
74P PRO* 4.4 23.1 - - + +
77P CYS* 6.2 2.9 - - - -
78P GLY* 5.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O ALA 3.1 5.6 + - - +
33O VAL* 2.8 24.0 + - + +
35O ALA* 1.3 69.4 - - - +
37O TRP* 1.3 72.0 + - + +
38O PHE 3.0 1.6 - - - -
39O SER* 2.6 23.9 + - - -
40O ILE* 2.8 23.6 + - + +
75P LEU* 3.5 32.1 - - + +
78P GLY* 4.1 15.0 - - - -
79P LEU* 4.3 5.2 - - + +
82P MET* 3.5 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 37 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O VAL* 3.0 14.7 + - + +
34O PRO* 3.6 11.0 - - + -
36O VAL* 1.3 84.9 - - + +
38O PHE* 1.3 61.3 + - - +
40O ILE* 3.5 17.6 + - + +
41O GLU* 2.8 69.9 + - + +
62O PHE* 3.7 23.1 - + - -
68O ILE* 4.2 11.7 - - + -
71O ILE* 3.8 25.1 - - + +
72O ASN* 3.2 16.2 - - - +
75O THR* 3.3 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O PRO 3.2 16.9 + - - +
35O ALA* 3.8 7.0 - - - +
36O VAL 3.0 0.6 - - - -
37O TRP* 1.3 77.4 - - - +
39O SER* 1.3 61.7 + - - +
41O GLU* 3.2 20.5 + - + +
42O LEU* 2.8 61.9 + - + +
72O ASN* 4.9 2.0 - - - -
75O THR* 4.0 12.1 - - + -
28P ALA* 4.9 2.0 - - + -
31P MET* 3.8 13.0 - - + -
32P ILE* 3.7 50.0 - - + -
35P VAL* 4.5 16.8 - - + -
36P GLY* 5.0 2.9 - - - -
70P MET* 3.9 21.3 - - + -
74P PRO* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ALA 3.5 10.6 + - - -
36O VAL 2.6 17.8 + - - -
38O PHE* 1.3 73.1 - - - +
40O ILE* 1.3 61.8 + - - -
42O LEU* 3.1 12.9 + - - +
43O ILE* 3.0 25.1 + - - +
70P MET 4.2 0.8 + - - -
71P ILE* 2.3 46.2 + - - +
74P PRO* 4.1 6.7 - - - +
75P LEU* 3.6 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O VAL* 2.8 19.4 + - + +
37O TRP* 3.6 22.4 - - + +
39O SER* 1.3 73.2 - - - +
41O GLU* 1.3 69.9 + - - +
43O ILE* 2.8 28.6 + - + +
44O PHE* 3.0 37.7 + - + -
75P LEU* 5.3 3.4 - - + -
107P LEU* 5.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O TRP* 2.8 55.4 + - + +
38O PHE* 3.2 19.8 - - + +
40O ILE* 1.3 79.9 - - - +
42O LEU* 1.3 62.4 + - + +
44O PHE* 3.4 6.9 + - + +
45O GLY 3.2 17.3 + - - -
59O PHE* 3.5 17.7 - - + -
62O PHE* 3.8 13.3 - - + -
63O LEU* 3.8 7.8 - - + +
68O ILE* 3.7 10.7 - - - +
72O ASN* 2.8 37.4 + - - +
35P VAL* 5.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O PHE* 2.8 51.8 + - + +
39O SER* 3.1 9.8 + - - +
41O GLU* 1.3 76.9 - - - +
43O ILE* 1.3 56.2 + - - +
45O GLY* 3.5 1.8 + - - +
46O LEU* 2.9 27.9 + - - +
59O PHE* 5.2 2.9 - - + -
31P MET* 5.4 2.2 - - + -
35P VAL* 4.2 21.3 - - + -
67P LEU* 5.4 4.4 - - + +
70P MET* 3.9 31.9 - - + +
71P ILE* 3.8 17.4 - - + +
800P MQ7 4.0 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O SER 3.0 12.3 + - - +
40O ILE* 2.8 18.5 + - + +
42O LEU* 1.3 74.1 - - - +
44O PHE* 1.3 71.8 + - + +
46O LEU* 2.9 7.9 + - + +
47O PHE* 2.9 36.5 + - + +
71P ILE* 3.6 26.2 - - + -
75P LEU* 4.9 3.4 - - + -
107P LEU* 4.3 29.4 - - + +
110P VAL* 4.4 19.7 - - + -
111P THR* 3.6 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O ILE* 3.0 38.1 + - + -
41O GLU* 3.6 10.3 - - - +
43O ILE* 1.3 81.1 - - + +
45O GLY* 1.3 63.2 + - - +
47O PHE* 3.5 4.6 + - - +
48O ALA* 2.9 26.0 + - - +
59O PHE* 4.2 12.6 - + + -
62O PHE* 5.9 9.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O GLU 3.2 7.7 + - - -
42O LEU 3.9 2.0 - - - -
43O ILE 3.1 0.6 - - - -
44O PHE* 1.3 81.2 - - - +
46O LEU* 1.3 51.3 + - - +
48O ALA* 3.1 2.2 + - - +
49O LEU* 2.7 37.8 + - - +
56O TRP* 3.8 6.1 - - - -
59O PHE* 3.2 37.8 - - - -
800P MQ7 6.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O LEU 2.9 16.4 + - - +
43O ILE* 2.9 12.3 + - + +
45O GLY* 1.3 74.3 - - - +
47O PHE* 1.3 66.6 + - + +
49O LEU* 3.4 9.8 - - + +
50O LYS* 3.2 19.1 + - - +
58P ALA* 4.9 3.8 - - + -
67P LEU* 4.1 29.4 - - + -
71P ILE* 4.6 16.2 - - + -
111P THR* 4.5 10.1 - - + +
114P GLY* 3.9 32.1 - - - +
115P VAL* 3.9 12.6 - - + +
118P ILE* 4.7 17.5 - - + +
800P MQ7 6.1 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O ILE* 2.9 24.7 + - + +
44O PHE* 4.0 4.9 - - - +
46O LEU* 1.3 82.5 - - + +
48O ALA* 1.3 59.6 + - - +
49O LEU 3.1 1.6 - - - -
50O LYS* 2.8 32.1 + - + +
51O ASN* 2.8 25.8 + - - +
812O CE1 6.2 4.0 - - + -
110P VAL* 3.8 37.9 - - + -
111P THR* 5.6 0.4 - - - -
113P ILE* 4.9 6.7 - - + -
114P GLY* 3.2 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O PHE 2.9 18.6 + - - +
45O GLY 3.7 2.9 - - - +
47O PHE* 1.3 75.6 - - - +
49O LEU* 1.3 62.8 + - - +
50O LYS 3.2 0.3 + - - -
51O ASN* 3.3 14.4 + - - +
52O GLY 3.4 6.1 - - - +
55O ALA* 3.1 44.4 - - + +
56O TRP* 3.5 4.0 + - - +
59O PHE* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O GLY 2.7 18.1 + - - +
46O LEU* 3.4 15.5 - - + +
48O ALA* 1.3 76.5 - - - +
50O LYS* 1.3 61.0 + - - +
52O GLY 4.2 0.2 - - - -
56O TRP* 3.4 34.0 - - + -
51P TYR* 3.5 32.1 + - + -
54P VAL* 3.4 33.0 - - + -
55P LEU* 3.5 27.1 - - + +
58P ALA* 3.5 27.8 - - + -
67P LEU* 5.7 0.2 - - + -
118P ILE* 5.1 1.8 - - + -
800P MQ7 5.3 3.4 - - + -
----------------------------------------------------------
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