Contacts of the helix formed by residues 52 - 65 (chain G) in PDB entry 4FAO
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 52 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G THR 3.2 1.1 + - - +
51G PRO* 1.3 75.6 - - - +
53G LYS* 1.3 70.0 + - - +
54G HIS* 3.5 6.2 + - - +
55G ALA* 2.9 28.7 + - - +
56G ILE* 3.0 19.7 + - - +
109G CYS 4.0 0.6 + - - -
110G ARG* 3.4 38.8 + - + +
79H LEU* 4.0 25.1 - - + +
101H GLY* 5.9 0.2 - - - -
73I HIS* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G PRO 4.2 0.2 + - - -
52G THR* 1.3 71.8 - - - +
54G HIS* 1.3 65.6 + - - +
56G ILE* 2.8 20.6 + - + +
57G VAL* 2.9 16.8 + - + +
22H TRP* 5.9 3.4 - - + -
99H TYR* 3.8 15.0 - - + +
100H GLU 3.8 16.6 - - - +
101H GLY* 3.0 17.3 + - - +
102H MET* 3.8 18.8 - - - -
72I LEU 4.5 4.0 + - - -
73I HIS* 2.7 36.2 + - + +
75I GLU* 2.8 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G THR* 3.1 7.1 + - - +
53G LYS* 1.3 74.9 - - - +
55G ALA* 1.3 66.3 + - - +
57G VAL* 3.2 7.4 + - + +
58G GLN* 2.8 55.5 + - + +
110G ARG 4.2 7.5 + - - +
13H LEU* 5.0 0.4 - - + +
32H TYR* 5.3 0.2 - - - -
34H ALA* 4.1 9.6 - - + +
35H TYR 2.7 27.2 + - - -
36H GLU* 4.9 0.9 - - - -
76H PRO* 4.4 8.1 - - + +
79H LEU* 4.3 13.0 - - + -
101H GLY 2.9 19.2 + - - +
102H MET* 3.7 24.5 - - - +
103H SER 4.4 0.4 - - - -
104H VAL* 3.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LEU* 4.4 10.5 - - + -
51G PRO* 4.7 0.2 - - + -
52G THR* 2.9 27.2 + - - +
54G HIS* 1.3 77.2 + - - +
56G ILE* 1.3 57.5 + - - +
58G GLN* 4.0 3.1 - - - +
59G THR* 2.9 33.8 + - - -
72G ALA* 4.3 10.8 - - + +
109G CYS 3.8 22.2 - - - +
110G ARG* 4.0 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 4.5 12.1 - - + -
45G LEU* 4.1 19.3 - - + +
51G PRO* 4.1 21.3 - - + -
52G THR 3.0 17.3 + - - +
53G LYS* 2.8 17.1 + - + +
55G ALA* 1.3 71.4 - - - +
57G VAL* 1.3 67.2 + - + +
59G THR* 3.1 6.5 + - - +
60G LEU* 3.0 24.7 + - + +
22H TRP* 4.7 9.9 - - + -
73I HIS* 4.2 23.1 - - + +
76I LEU* 4.3 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS 2.9 12.0 + - - +
54G HIS* 3.6 8.5 - - + +
56G ILE* 1.3 79.0 - - - +
58G GLN* 1.3 64.4 + - - +
60G LEU* 2.9 10.5 + - - +
61G VAL* 2.9 22.0 + - + +
15H VAL* 3.7 40.8 - - + -
17H PHE* 5.8 0.2 - - + -
20H ILE* 4.4 7.0 - - + -
22H TRP* 4.1 28.5 - - + -
32H TYR* 3.9 18.6 - - + +
34H ALA* 5.1 2.2 - - + -
102H MET* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G HIS* 2.8 48.6 + - + +
55G ALA* 4.0 4.5 - - - +
57G VAL* 1.3 75.4 - - - +
59G THR* 1.3 64.2 + - - +
61G VAL* 3.2 8.1 + - - +
62G HIS* 2.8 21.7 + - - +
69G VAL* 3.9 8.9 - - + +
70G GLY* 3.1 26.6 + - - +
71G LYS 3.6 14.3 + - - +
72G ALA* 4.7 5.2 - - + +
110G ARG* 5.0 4.9 + - - +
13H LEU* 4.7 8.7 - - + -
35H TYR 4.4 0.2 - - - +
36H GLU* 4.1 28.9 + - - +
37H CYS 4.7 5.6 + - - +
76H PRO* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G CYS 4.2 10.4 + - - +
43G PHE* 3.4 43.5 - - + +
45G LEU* 4.1 12.4 - - + +
55G ALA 2.9 20.9 + - - -
56G ILE* 3.1 5.6 + - - +
58G GLN* 1.3 77.2 - - - +
60G LEU* 1.3 64.5 + - - +
62G HIS* 3.3 10.8 + - - +
63G LEU* 3.0 23.9 + - + +
71G LYS* 4.9 1.7 - - - +
72G ALA* 4.1 18.9 + - - +
58I GLU* 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 3.6 37.0 - - + -
56G ILE* 3.0 16.7 + - + +
57G VAL* 2.9 8.3 + - - +
59G THR* 1.3 72.2 - - - +
61G VAL* 1.3 68.8 + - - +
63G LEU* 2.8 33.3 + - + +
64G LYS 3.1 4.5 + - - -
20H ILE* 3.4 44.6 - - + +
22H TRP* 4.1 22.9 - - + +
76I LEU* 4.7 6.5 - - + -
84I PHE* 4.2 7.8 - - + -
85I VAL* 4.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G VAL 2.9 20.9 + - - +
58G GLN* 3.5 8.5 - - - +
60G LEU* 1.3 71.8 - - - +
62G HIS* 1.3 56.6 + - - +
64G LYS* 2.9 5.7 + - - -
65G PHE* 2.8 42.0 + - + +
69G VAL* 3.7 27.8 - - + -
13H LEU* 4.3 10.5 - - + -
14H ARG 6.0 0.7 - - - +
15H VAL* 3.8 39.7 - - + -
19H ASP* 6.2 2.0 - - + -
20H ILE* 3.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASP* 3.0 36.2 + - - -
70E GLN* 5.2 0.6 + - - -
58G GLN 2.8 15.2 + - - +
59G THR* 3.5 12.4 + - - +
61G VAL* 1.3 69.0 - - - +
63G LEU* 1.3 76.9 + - + +
65G PHE 4.2 0.7 - - - +
66G PRO* 3.0 34.9 - - + +
69G VAL* 2.7 41.6 - - + +
70G GLY* 3.8 10.8 - - - +
71G LYS* 3.5 40.0 - - + +
58I GLU* 4.8 7.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 4.3 14.4 - - + -
59G THR* 3.0 20.0 + - + +
60G LEU* 2.8 36.4 + - + +
62G HIS* 1.3 78.6 + - + +
64G LYS* 1.3 56.4 + - - +
66G PRO* 3.6 11.9 - - - +
56I VAL* 4.3 20.9 - - + -
57I ARG 5.0 2.7 - - - +
58I GLU* 3.4 49.6 - - + +
59I GLU 5.4 1.8 + - - +
84I PHE* 3.9 30.2 - - + +
85I VAL* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G LEU 3.1 4.0 + - - +
61G VAL* 2.9 6.8 + - - +
63G LEU* 1.3 76.1 - - - +
65G PHE* 1.3 94.8 + - + +
66G PRO* 3.3 11.0 - - - +
18H GLU 5.2 0.4 + - - -
19H ASP* 3.3 37.5 + - + +
20H ILE* 6.0 0.2 - - + -
83I GLU* 3.6 34.8 + - + -
84I PHE* 3.3 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G VAL* 2.8 33.9 + - + +
62G HIS 3.1 3.6 + - - -
64G LYS* 1.3 110.7 - - + +
66G PRO* 1.3 52.2 - - - +
67G THR* 2.7 20.7 + - - +
68G LYS* 2.8 26.9 + - + -
69G VAL* 2.9 18.7 + - + +
19H ASP* 4.0 20.2 - - + -
----------------------------------------------------------
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