Contacts of the helix formed by residues 54 - 78 (chain E) in PDB entry 5K58
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 SER 54 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E TYR* 3.9 11.4 - - - -
52E PHE* 3.2 12.0 - - - +
53E PRO* 1.3 86.3 - - - +
55E LYS* 1.3 64.3 + - - +
56E THR* 3.1 11.9 - - - +
57E ARG* 3.2 38.5 + - - +
58E MET* 3.6 4.5 + - - +
9T C 3.5 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 6.4 0.2 - - + -
31E ARG* 4.6 4.6 - - - +
32E ILE* 2.4 31.3 + - + +
33E THR* 4.0 0.9 - - - +
34E THR* 4.3 16.4 - - + +
37E LEU* 4.7 8.3 - - + -
49E TYR* 4.4 4.7 - - + +
54E SER* 1.3 69.9 - - - +
56E THR* 1.3 64.7 + - - +
58E MET* 3.2 38.0 - - + +
59E PHE* 3.6 22.3 + - + -
116E PHE 5.5 0.6 + - - -
117E GLU* 3.7 27.8 + - - +
8T A 3.3 38.9 + - - -
9T C 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER* 3.1 11.3 - - - +
55E LYS* 1.3 78.5 - - - +
57E ARG* 1.3 67.8 + - - +
59E PHE* 3.0 25.3 + - - +
60E ASP* 3.2 12.2 + - - +
117E GLU* 5.4 5.0 + - - +
118E GLN* 4.0 17.7 + - - +
120E ARG* 3.9 36.1 - - - +
121E LEU* 4.2 14.4 - - + +
9T C 4.9 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E PHE* 4.6 8.1 - - + -
53E PRO* 3.6 29.8 - - + +
54E SER* 3.2 25.2 + - - +
55E LYS 3.2 0.4 - - - -
56E THR* 1.3 76.3 - - - +
58E MET* 1.3 59.1 + - - +
59E PHE 2.9 5.2 - - - -
60E ASP* 2.5 55.4 + - - +
61E SER* 3.1 19.7 + - - +
120E ARG* 3.0 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ILE* 3.6 30.1 - - + -
16E LEU* 3.7 21.9 - - + +
19E LEU* 3.6 26.7 - - + +
37E LEU* 3.7 28.7 - - + -
48E LEU* 3.9 20.4 - - + -
52E PHE* 3.8 37.7 - - + -
54E SER 3.6 3.8 + - - +
55E LYS* 3.2 31.4 + - + +
57E ARG* 1.3 77.0 - - - +
59E PHE* 1.3 59.3 + - + +
61E SER 4.4 0.2 - - - -
62E LEU* 3.7 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 3.8 32.3 - - + -
23E LEU* 4.5 14.8 - - + -
32E ILE* 5.0 7.6 - - + -
55E LYS* 3.6 29.8 + - + -
56E THR* 3.0 9.7 + - - +
57E ARG 2.9 0.8 - - - -
58E MET* 1.3 76.0 - - - +
60E ASP* 1.3 62.8 + - - +
61E SER 3.5 0.7 - - - -
62E LEU* 3.8 22.1 - - + +
63E ILE* 3.1 29.8 + - - +
108E ILE* 5.2 4.7 - - + +
113E ALA* 5.0 11.0 - - + -
114E LEU* 5.4 10.1 - - + -
117E GLU* 3.2 47.3 - - + -
121E LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E THR* 3.2 8.1 + - - +
57E ARG* 2.5 44.8 + - - +
59E PHE* 1.3 78.6 - - - +
61E SER* 1.3 58.8 + - - +
63E ILE* 3.3 5.9 + - - +
64E GLU* 2.9 32.8 + - + +
120E ARG* 3.6 9.2 + - - -
121E LEU* 3.3 23.9 - - - +
124E ARG* 3.7 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ARG* 4.5 16.0 + - - -
16E LEU* 3.9 31.5 - - - +
52E PHE* 4.8 6.6 - - - -
57E ARG* 3.1 15.3 + - - +
60E ASP* 1.3 75.1 - - - +
62E LEU* 1.3 66.2 + - - +
64E GLU* 3.2 9.3 + - - +
65E PHE* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 4.2 31.4 - - + +
19E LEU* 3.8 17.0 - - + -
20E ALA* 5.5 2.9 - - + +
23E LEU* 3.8 29.6 - - + -
58E MET 3.7 12.9 + - - +
59E PHE* 3.8 20.4 + - + +
61E SER* 1.3 78.4 - - - +
63E ILE* 1.3 62.3 + - + +
65E PHE* 3.2 23.6 - - - +
66E ILE* 3.2 18.0 + - + +
105E LEU* 4.7 15.4 - - + +
108E ILE* 4.5 12.8 - - + -
377N PHE* 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E PHE 3.1 16.8 + - - +
60E ASP* 3.3 8.2 + - - +
61E SER 3.3 0.4 - - - -
62E LEU* 1.3 71.8 - - - +
64E GLU* 1.3 61.7 + - - +
66E ILE* 3.4 10.3 + - + +
67E GLU* 2.9 32.9 + - + +
108E ILE* 3.4 30.7 - - + -
114E LEU* 5.1 0.7 - - + -
121E LEU* 3.6 37.2 - - + +
124E ARG* 3.5 42.0 - - + +
125E ILE* 4.0 9.9 - - + -
128E LEU* 5.5 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ASP 2.9 16.3 + - - +
61E SER* 3.2 11.4 + - - +
63E ILE* 1.3 73.9 - - - +
65E PHE* 1.3 53.9 + - - +
67E GLU* 2.9 25.4 + - - +
68E ASP* 2.6 59.3 + - - +
124E ARG* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E SER 3.1 11.4 + - - +
62E LEU* 3.2 12.8 - - - +
64E GLU* 1.3 75.0 - - - +
66E ILE* 1.3 55.7 + - - +
68E ASP* 3.3 6.8 + - - +
69E SER* 2.6 50.4 + - - -
98E PHE* 4.3 11.2 - + - -
102E ASN* 5.0 0.2 - - - -
105E LEU* 3.4 23.8 - - + -
375N PRO* 4.7 13.7 - - + -
376N ALA 5.0 0.9 - - - -
377N PHE* 3.6 52.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LEU* 3.2 26.0 + - + +
63E ILE* 3.8 9.9 - - + +
65E PHE* 1.3 75.4 - - - +
67E GLU* 1.3 60.2 + - - +
69E SER* 4.6 0.9 - - - -
70E LEU* 3.3 40.7 + - + +
98E PHE* 3.5 29.8 - - + -
105E LEU* 3.6 32.1 - - + +
108E ILE* 4.1 16.6 - - + -
109E LEU* 4.3 16.4 - - + -
125E ILE* 5.7 3.1 - - + -
128E LEU* 3.7 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ILE* 2.9 21.2 + - + +
64E GLU* 3.0 30.5 - - - +
66E ILE* 1.3 78.4 - - - +
68E ASP* 1.3 61.5 + - - +
71E ILE* 3.2 29.6 - - - +
124E ARG* 4.5 24.5 + - - +
127E GLN* 5.8 2.1 - - - +
128E LEU* 4.0 23.9 + - + +
131E ARG* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU* 2.6 48.2 + - - +
65E PHE* 3.9 6.6 + - - +
67E GLU* 1.3 78.4 - - - +
69E SER* 1.3 58.3 + - - +
71E ILE* 4.5 2.4 - - - +
72E THR* 2.5 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E PHE* 2.6 41.2 + - - -
66E ILE 4.1 2.0 - - - -
67E GLU 3.4 0.2 - - - -
68E ASP* 1.3 75.7 - - - +
70E LEU* 1.3 68.7 + - - +
71E ILE 3.1 2.2 + - - -
72E THR* 3.3 10.2 + - - -
73E ARG* 3.3 24.4 + - - +
98E PHE* 4.5 11.7 - - - -
375N PRO* 4.2 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ILE* 3.3 33.3 + - + +
69E SER* 1.3 80.1 - - - +
71E ILE* 1.3 64.4 + - + +
74E ILE* 3.2 31.2 + - + +
94E LEU* 3.4 25.8 - - + +
95E LEU* 4.5 17.9 - - + +
98E PHE* 3.5 43.5 - - + -
109E LEU* 4.6 14.1 - - + -
128E LEU* 4.6 3.4 - - + -
132E ILE* 4.4 21.1 - - + -
375N PRO* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLU 3.2 20.7 + - - +
68E ASP* 4.5 3.8 - - - +
69E SER 3.1 0.8 - - - -
70E LEU* 1.3 79.9 - - + +
72E THR* 1.3 64.1 + - - +
73E ARG 3.3 0.4 - - - -
74E ILE* 3.8 22.1 - - + +
75E ASN* 2.7 47.8 + - - +
128E LEU* 3.7 27.4 - - + -
131E ARG* 4.1 37.2 - - + +
132E ILE* 4.3 9.9 - - + +
135E GLN* 5.0 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASP* 2.5 23.4 + - - +
69E SER* 3.3 6.4 + - - -
71E ILE* 1.3 81.1 - - - +
73E ARG* 1.3 73.1 + - - +
75E ASN* 3.2 13.5 + - - +
76E LEU* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E SER* 3.4 14.6 - - - +
70E LEU 3.7 1.8 - - - +
71E ILE 3.3 0.2 - - - -
72E THR* 1.3 92.2 - - - +
74E ILE* 1.3 53.7 + - - +
76E LEU* 2.8 20.2 + - + +
77E ILE* 2.7 41.6 + - + +
94E LEU* 3.4 41.9 - - + +
373N ASP* 2.4 50.4 + - - +
374N ILE* 5.0 0.4 - - - +
375N PRO* 3.8 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E LEU* 3.2 19.7 + - + +
71E ILE* 3.8 19.7 - - + +
72E THR 3.3 0.4 - - - -
73E ARG* 1.3 72.2 - - - +
75E ASN* 1.3 61.6 + - - +
76E LEU 2.9 8.5 + - - -
77E ILE* 3.2 18.3 + - + +
78E LEU* 3.7 11.6 + - - +
91E ILE* 4.9 20.6 - - + -
94E LEU* 4.4 8.5 - - + -
95E LEU* 5.0 7.4 - - + -
132E ILE* 4.4 17.0 - - + -
135E GLN* 3.2 55.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ILE* 2.7 34.4 + - - +
72E THR* 3.2 10.1 + - - +
74E ILE* 1.3 75.2 - - - +
76E LEU* 1.3 59.9 + - - +
77E ILE 3.6 0.4 - - - -
78E LEU* 4.7 4.8 - - - +
79E LYS* 4.3 17.0 + - - +
135E GLN* 4.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E THR* 3.0 16.8 + - + +
73E ARG* 2.8 29.4 + - + +
75E ASN* 1.3 83.1 - - - +
77E ILE* 1.3 61.2 + - - +
78E LEU 3.5 0.9 - - - -
79E LYS* 4.2 8.0 + - + +
80E ASP* 3.1 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ARG* 2.7 20.4 + - + +
74E ILE* 3.2 12.7 + - + +
76E LEU* 1.3 77.8 - - - +
78E LEU* 1.3 58.1 + - - +
80E ASP* 5.1 0.4 - - - -
81E GLU* 3.0 30.7 + - + +
87E ARG* 4.1 24.5 - - + +
90E LEU* 3.7 49.8 - - + +
91E ILE* 3.7 29.4 - - + -
94E LEU* 4.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE 3.7 8.9 + - - +
75E ASN* 5.2 3.4 - - - +
76E LEU 3.5 0.2 - - - -
77E ILE* 1.3 74.7 - - - +
79E LYS* 1.3 82.9 + - + +
80E ASP 2.6 17.3 + - - -
81E GLU 3.0 20.9 + - - +
82E LYS* 4.3 1.6 + - - +
87E ARG* 3.8 31.1 + - - +
138E GLN* 6.4 2.2 - - + -
142E GLU* 4.5 12.6 - - - +
146E ARG* 5.2 6.5 - - - +
----------------------------------------------------------
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