Contacts of the helix formed by residues 56 - 74 (chain H) in PDB entry 3F5O
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 HIS 56 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 3.7 31.6 - + + +
22G GLU* 2.9 43.1 + - - -
62G THR* 4.0 9.2 - - + +
65G ASP* 3.8 7.2 + - - -
66G ASN* 3.1 23.6 + - - -
48H HIS 3.0 19.3 + - - +
49H THR 4.0 4.0 - - - -
50H ASN* 3.7 6.6 - - - +
54H THR 3.2 3.6 + - - -
55H LEU* 1.3 73.8 - - - +
57H GLY* 1.3 70.3 + - - +
58H GLY* 2.8 34.4 + - - -
59H LEU* 3.0 14.1 + - - +
60H THR* 3.0 12.2 + - - -
151H CL 3.8 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ASP* 3.6 12.1 - - - -
83G SER* 5.3 0.7 - - - -
86G MET* 5.2 0.4 - - - -
150G COA 4.3 7.5 - - - +
55H LEU 3.4 3.2 + - - -
56H HIS* 1.3 75.5 - - - +
58H GLY* 1.3 56.3 + - - +
59H LEU 3.3 0.2 - - - -
60H THR* 3.4 3.4 + - - -
61H ALA* 3.0 18.9 + - - +
90H TYR* 2.8 41.3 + - - -
151H CL 3.2 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 4.0 0.4 - - - -
58G GLY 3.8 0.9 - - - +
61G ALA 4.8 1.6 - - - -
62G THR* 3.2 36.4 + - - -
65G ASP* 3.4 4.8 + - - -
86G MET* 5.4 0.2 - - - -
56H HIS* 2.8 14.2 - - - -
57H GLY* 1.3 72.3 - - - +
59H LEU* 1.3 59.7 + - - +
61H ALA* 3.4 7.2 + - - +
62H THR* 2.9 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 3.6 40.0 - - + -
24H VAL* 4.4 4.7 - - + +
25H LEU* 3.6 29.6 - - + -
42H MET* 4.4 4.3 - - + -
48H HIS* 3.4 51.4 - - + +
55H LEU* 3.7 14.1 - - + -
56H HIS* 3.0 10.9 + - + +
58H GLY* 1.3 74.6 - - - +
60H THR* 1.3 59.8 + - - +
62H THR* 3.1 5.5 + - - -
63H LEU* 2.8 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G COA 5.8 0.3 - - - -
55H LEU* 3.2 25.0 + - - +
56H HIS 3.0 9.1 + - - -
57H GLY* 3.4 11.8 - - - -
58H GLY 3.4 0.2 - - - -
59H LEU* 1.3 76.3 - - - +
61H ALA* 1.3 61.4 + - - +
63H LEU* 3.2 12.9 + - - +
64H VAL* 3.0 22.3 + - - +
88H ILE* 4.2 6.1 - - + -
90H TYR* 3.8 23.1 - - + -
120H LEU* 4.0 16.2 - - + -
129H ILE* 5.3 2.8 - - + +
130H ALA* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLY* 4.8 0.9 - - - -
61G ALA* 3.5 26.0 - - + -
86G MET* 4.2 1.8 - - + -
57H GLY 3.0 12.2 + - - +
58H GLY 3.4 9.6 - - - +
59H LEU 3.2 0.2 - - - -
60H THR* 1.3 75.8 - - - +
62H THR* 1.3 58.3 + - - +
64H VAL* 3.3 3.6 + - - +
65H ASP* 2.9 30.6 + - - +
86H MET* 3.8 6.5 - - + +
88H ILE* 3.5 33.7 - - + -
90H TYR* 4.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 4.6 0.5 - - - -
56G HIS* 3.9 15.5 - - + +
58G GLY* 3.2 25.8 + - - -
21H PHE* 3.6 23.5 - - + -
24H VAL* 4.0 15.9 - - + -
25H LEU* 4.2 12.6 - - + -
58H GLY 2.9 16.3 + - - -
59H LEU* 3.1 14.4 + - - -
61H ALA* 1.3 76.8 - - - +
63H LEU* 1.3 55.2 + - - +
65H ASP* 3.3 2.2 + - - +
66H ASN* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 3.8 28.3 - - + -
28H ILE* 3.9 20.4 - - + -
42H MET* 4.2 13.5 - - + -
55H LEU* 4.6 2.9 - - + -
59H LEU* 2.8 25.8 + - + +
60H THR* 3.4 10.5 - - - +
62H THR* 1.3 70.2 - - - +
64H VAL* 1.3 64.9 + - - +
67H ILE* 2.9 38.2 + - + +
100H ILE* 4.1 15.9 - - + -
102H ILE* 4.2 20.9 - - + -
120H LEU* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H THR 3.0 20.2 + - - +
61H ALA* 3.5 8.3 - - - +
63H LEU* 1.3 74.8 - - - +
65H ASP* 1.3 56.3 + - - +
68H SER* 2.6 38.5 + - - -
86H MET* 4.3 19.5 - - + -
88H ILE* 4.5 16.2 - - + -
118H VAL* 3.6 27.2 - - + +
120H LEU* 3.9 21.5 - - + -
132H GLY* 4.3 24.0 - - - +
134H HIS* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G HIS* 3.9 9.7 + - - +
57G GLY* 3.5 12.8 + - - -
58G GLY 3.4 22.5 + - - +
90G TYR* 4.9 1.7 + - - -
151G CL 4.0 3.5 - - - +
61H ALA 2.9 18.4 + - - +
62H THR* 3.5 7.9 - - - +
64H VAL* 1.3 77.0 - - - +
66H ASN* 1.3 62.0 + - - +
68H SER* 3.0 13.2 + - - -
69H THR* 2.8 27.0 + - - -
83H SER* 3.8 8.5 + - - -
86H MET* 4.9 7.9 - - + -
134H HIS* 3.2 24.0 - - - -
136H LYS* 4.7 1.7 + - - -
149H UOC 4.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G HIS* 3.0 36.1 + - - -
15H MET* 4.1 12.2 - - - +
22H GLU* 2.8 20.5 + - - +
25H LEU* 3.5 29.4 - - + +
62H THR* 2.9 18.6 + - - +
63H LEU 4.3 0.4 - - - +
65H ASP* 1.3 74.9 + - - +
67H ILE* 1.3 66.0 + - + +
69H THR* 3.1 8.2 + - - -
70H MET* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ILE* 5.4 0.9 - - + -
25H LEU* 4.6 3.8 - - + -
28H ILE* 3.7 29.8 - - + -
38H VAL* 3.7 24.1 - - + +
40H CYS* 4.0 13.0 - - + -
63H LEU* 2.9 28.5 + - + +
66H ASN* 1.3 84.0 - - + +
68H SER* 1.3 65.9 + - - +
70H MET* 3.2 13.4 + - + +
71H ALA* 3.0 17.8 + - - +
102H ILE* 4.0 33.4 - - + +
104H ALA* 3.5 18.4 - - + +
118H VAL* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H VAL 2.6 25.0 + - - -
65H ASP 3.0 3.3 + - - -
67H ILE* 1.3 78.2 - - - +
69H THR* 1.3 59.3 + - - +
71H ALA* 3.1 6.0 + - - +
72H LEU* 3.1 21.2 + - - +
104H ALA* 3.8 11.9 - - - +
105H HIS 6.1 0.2 - - - -
116H THR* 3.0 37.5 + - - -
118H VAL* 3.7 11.2 - - - +
134H HIS* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ASP* 2.8 20.2 + - - -
66H ASN* 3.1 12.6 + - - -
68H SER* 1.3 79.4 + - - +
70H MET* 1.3 74.1 + - + +
72H LEU* 3.1 21.3 + - - +
73H LEU* 3.1 13.1 + - + +
80H PRO* 3.8 23.8 - - + +
136H LYS* 2.8 36.0 + - - +
149H UOC 4.5 10.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 3.9 32.1 - - + +
11H VAL* 4.9 1.8 - - - -
12H ILE* 4.0 21.8 - - + -
15H MET* 3.8 32.3 - - + +
38H VAL* 3.9 8.3 - - + -
66H ASN* 2.9 27.8 + - + +
67H ILE* 3.2 15.9 + - + +
69H THR* 1.3 90.9 - - + +
71H ALA* 1.3 60.9 + - - +
73H LEU* 3.1 37.1 + - + +
74H CYS* 3.3 16.5 + - - -
149H UOC 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLY* 3.8 7.8 - - - +
37H LYS 4.8 0.2 - - - +
38H VAL* 3.6 18.8 - - + +
67H ILE 3.0 12.3 + - - +
68H SER* 3.1 9.2 + - - +
70H MET* 1.3 76.4 - - - +
72H LEU* 1.3 61.1 + - - +
74H CYS* 3.2 18.2 + - - +
75H THR* 3.6 10.0 - - - +
104H ALA* 4.1 22.7 - - + +
105H HIS* 4.8 0.9 - - - -
106H VAL* 3.6 19.3 - - + +
116H THR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H SER 3.1 11.0 + - - +
69H THR* 3.3 11.4 - - - +
71H ALA* 1.3 75.4 - - - +
73H LEU* 1.3 56.5 + - - +
75H THR* 2.6 31.8 + - + +
78H GLY* 3.7 5.9 - - - -
79H ALA 3.8 20.1 - - - +
80H PRO* 3.9 7.9 - - + +
106H VAL* 3.6 28.5 - - + -
109H GLN* 5.3 3.6 - - + +
114H ALA* 3.6 32.8 - - + -
116H THR* 4.0 14.6 - - - +
136H LYS* 3.6 33.2 - - + -
138H LEU* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 4.6 6.7 - - + -
11H VAL* 4.4 10.5 - - + -
69H THR 3.1 15.4 + - - +
70H MET* 3.1 40.8 + - + +
72H LEU* 1.3 75.6 - - - +
74H CYS* 1.3 59.7 + - - +
75H THR 3.1 12.9 + - - +
78H GLY* 3.8 24.9 - - - +
80H PRO* 4.0 27.8 - - + -
149H UOC 4.3 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H MET* 3.7 29.4 - - - -
8H LEU* 3.9 28.0 - - - -
33H ALA* 4.0 8.1 - - - -
34H ALA 3.5 16.6 - - - +
35H PRO* 3.4 7.9 - - - +
36H GLY 2.8 22.6 + - - +
38H VAL* 4.0 4.5 - - - -
70H MET 3.5 12.6 - - - -
71H ALA* 3.2 11.4 + - - +
73H LEU* 1.3 75.0 - - - +
75H THR* 1.3 59.4 + - - +
----------------------------------------------------------
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