Contacts of the helix formed by residues 78 - 107 (chain F) in PDB entry 4O46
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 LYS 78 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 5.3 13.2 - - + +
70F THR* 5.3 6.3 - - - -
77F LYS* 1.4 80.0 - - + +
79F ILE* 1.4 60.2 + - - +
81F MET* 3.2 8.8 + - - +
82F VAL* 3.0 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU* 4.2 14.5 - - + +
70F THR* 4.0 17.6 - - - +
71F SER* 3.9 33.2 - - - +
77F LYS 3.5 3.9 - - - +
78F LYS* 1.4 77.0 - - - +
80F GLU* 1.4 55.4 + - - +
82F VAL* 3.5 4.9 + - - +
83F ARG* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LYS* 3.0 31.3 - - - +
78F LYS 3.2 0.2 - - - -
79F ILE* 1.4 76.9 - - - +
81F MET* 1.3 66.7 + - - +
83F ARG* 3.7 6.8 - - - +
84F ALA* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.9 30.3 - - + +
9E GLN* 5.1 9.2 - - + -
10E LYS* 3.8 30.5 - - + +
13E LEU* 4.4 13.3 - - + +
77F LYS 3.4 9.3 + - - +
78F LYS* 3.2 12.3 + - - +
80F GLU* 1.3 84.6 + - - +
82F VAL* 1.4 62.4 + - - +
83F ARG 3.3 0.4 - - - -
84F ALA* 3.5 10.8 + - + +
85F TYR* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 5.9 2.9 - - + +
13E LEU* 3.7 30.5 - - + -
63F ILE* 3.6 21.1 - - + +
66F ILE* 4.2 12.6 - - + -
67F GLU* 3.8 33.0 - - + +
70F THR* 4.9 5.8 - - - -
78F LYS* 3.0 21.0 + - + +
79F ILE* 3.8 7.6 - - - +
81F MET* 1.4 74.2 - - + +
83F ARG* 1.4 53.2 + - - +
85F TYR* 3.3 3.5 + - - +
86F ARG* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU* 3.4 23.5 + - - +
79F ILE* 3.0 19.1 + - + +
80F GLU* 3.7 8.7 - - - +
82F VAL* 1.4 73.7 - - - +
84F ALA* 1.4 57.4 + - - +
86F ARG* 3.4 3.0 + - - +
87F GLU* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F GLU 3.2 15.2 + - - +
81F MET* 3.6 13.5 - - + +
82F VAL 3.4 0.2 - - - -
83F ARG* 1.4 76.9 - - - +
85F TYR* 1.3 57.9 + - - +
87F GLU* 3.9 5.2 + - - +
88F LYS* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LYS* 5.2 6.1 - - + -
13E LEU* 4.3 13.0 - - + -
14E ALA* 3.6 21.7 - - + +
17E ALA* 3.9 7.9 - - + -
19E ARG* 3.1 27.4 + - - +
22E ASP* 3.0 29.5 + - + -
63F ILE* 3.7 29.6 - - + -
81F MET 3.2 13.7 + - - +
82F VAL* 3.5 10.5 - - - +
83F ARG 3.2 0.4 - - - -
84F ALA* 1.3 75.2 - - - +
86F ARG* 1.4 62.5 + - - +
87F GLU 3.3 0.4 - - - -
88F LYS* 3.2 23.0 + - + +
89F ILE* 3.1 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F TRP* 3.9 16.7 - - + +
63F ILE* 3.7 22.4 - - + +
64F SER* 5.3 2.7 - - - +
67F GLU* 4.4 18.6 - - - +
82F VAL 2.9 17.7 + - - +
83F ARG 3.4 6.0 + - - +
85F TYR* 1.4 74.1 - - - +
87F GLU* 1.4 55.9 + - - +
89F ILE* 3.7 3.6 + - - +
90F GLU* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ARG 3.1 15.8 + - - +
84F ALA* 4.1 6.5 - - - +
86F ARG* 1.4 75.0 - - - +
88F LYS* 1.4 57.6 + - - +
90F GLU* 3.6 9.6 - - - +
91F LYS* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ARG* 4.3 14.8 - - - +
22E ASP* 4.6 3.8 - - - +
84F ALA 3.2 16.0 + - - +
85F TYR* 3.2 35.3 + - + +
87F GLU* 1.4 76.5 - - - +
89F ILE* 1.4 61.3 + - - +
91F LYS* 3.5 6.3 + - - +
92F GLU* 3.2 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ALA* 4.8 0.2 - - + -
19E ARG* 4.0 29.6 - - - +
56F ARG* 3.4 34.7 - - + +
59F SER* 4.1 8.5 - - - -
60F TRP* 3.8 16.8 - - + +
63F ILE* 3.8 30.1 - - + -
85F TYR* 3.1 36.4 + - + +
86F ARG* 4.0 4.3 - - - +
88F LYS* 1.4 72.3 - - + +
90F GLU* 1.4 59.2 + - - +
92F GLU* 3.1 10.6 + - - +
93F LEU* 2.9 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F TRP* 2.8 31.6 + - + +
86F ARG* 3.0 21.0 + - - +
87F GLU* 3.6 10.7 - - - +
89F ILE* 1.4 75.2 - - - +
91F LYS* 1.4 56.4 + - + +
93F LEU* 3.2 8.0 + - - +
94F GLU* 2.9 48.4 + - - +
137F VAL* 3.0 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F GLU* 3.1 23.0 + - + +
88F LYS* 3.7 6.5 - - - +
90F GLU* 1.4 74.6 - - + +
92F GLU* 1.4 57.9 + - + +
94F GLU* 3.5 14.7 + - - +
95F ALA* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ARG* 3.0 43.8 + - - -
56F ARG* 3.2 29.6 + - + +
88F LYS* 3.2 23.8 + - + +
89F ILE* 3.1 11.5 + - - +
91F LYS* 1.4 75.7 - - + +
93F LEU* 1.4 61.8 + - - +
95F ALA* 3.3 8.3 + - - +
96F VAL* 3.1 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F VAL* 4.0 11.9 - - + -
56F ARG* 3.8 16.3 - - + +
57F ARG* 3.7 40.4 - - + +
60F TRP* 4.6 14.1 - - + -
89F ILE 2.9 11.9 + - - +
90F GLU* 3.3 10.8 - - - +
92F GLU* 1.4 73.8 - - - +
94F GLU* 1.3 60.5 + - + +
96F VAL* 3.1 8.4 + - - +
97F CYS* 3.0 45.9 + - - -
133F TYR* 3.8 25.6 - - + +
134F LEU* 4.8 3.1 - - - +
137F VAL* 5.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 2.9 41.0 + - + +
91F LYS* 3.8 15.1 - - - +
93F LEU* 1.3 77.5 - - + +
95F ALA* 1.4 57.3 + - - +
97F CYS* 3.5 2.3 + - - +
98F GLN* 3.0 29.7 + - - +
134F LEU* 3.8 31.1 - - + +
137F VAL* 5.0 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LYS 3.1 14.8 + - - +
92F GLU* 3.5 11.9 - - - +
93F LEU 3.3 0.4 - - - -
94F GLU* 1.4 71.6 - - - +
96F VAL* 1.4 64.9 + - + +
98F GLN* 3.4 8.2 - - - +
99F ASP* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F TYR* 3.9 19.9 - - + +
52F VAL* 3.8 31.2 - - + -
53F VAL* 3.8 26.5 - - + +
56F ARG* 4.7 11.9 - - - +
92F GLU 3.1 17.1 + - - +
93F LEU 3.1 7.2 + - - +
95F ALA* 1.4 73.1 - - + +
97F CYS* 1.4 64.9 + - - +
99F ASP* 3.3 15.2 + - - +
100F VAL* 3.2 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F VAL* 3.6 23.1 - - - -
93F LEU* 3.0 32.9 + - - +
94F GLU 3.8 0.2 - - - +
96F VAL* 1.4 75.0 - - - +
98F GLN* 1.4 59.7 + - - +
100F VAL* 3.6 1.4 + - - +
101F LEU* 3.2 32.3 + - - +
130F TYR* 3.8 32.8 - - + +
133F TYR* 3.9 8.1 - - - -
134F LEU* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU 3.0 18.0 + - - +
95F ALA* 3.4 11.0 - - - +
96F VAL 3.2 0.2 - - - -
97F CYS* 1.4 75.3 - - - +
99F ASP* 1.4 60.8 + - - +
101F LEU* 3.6 5.2 + - - +
102F SER* 2.9 31.4 + - - -
134F LEU* 5.5 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LYS* 3.5 31.9 + - - +
49F TYR* 4.3 19.5 + - + +
95F ALA* 3.2 13.7 + - - +
96F VAL* 3.3 9.6 + - - +
98F GLN* 1.4 73.9 - - - +
100F VAL* 1.4 59.8 + - - +
102F SER* 3.5 6.8 + - - -
103F LEU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 6.1 1.6 - - + -
49F TYR* 3.4 35.9 - - + -
96F VAL* 3.2 17.2 + - + +
97F CYS 3.9 4.9 - - - +
98F GLN 3.4 0.2 - - - -
99F ASP* 1.4 73.4 - - - +
101F LEU* 1.4 53.7 + - + +
103F LEU* 3.2 7.4 + - - +
104F LEU* 2.8 44.3 + - + +
126F MET* 3.7 30.7 - - + -
130F TYR* 3.7 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F CYS 3.2 18.2 + - - +
98F GLN* 4.2 4.5 - - - +
100F VAL* 1.4 72.0 - - - +
102F SER* 1.4 54.4 + - - +
104F LEU* 3.7 7.0 - - + +
105F ASP* 2.9 36.6 + - - +
127F LYS* 3.6 42.2 - - + +
130F TYR* 4.0 15.5 - - + -
131F TYR* 3.7 46.4 - - + +
134F LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F GLN 2.9 20.6 + - - -
99F ASP* 3.6 9.0 - - - -
101F LEU* 1.4 75.3 - - - +
103F LEU* 1.4 55.9 + - - +
105F ASP* 5.0 0.2 - - - -
106F ASN* 2.9 53.7 + - - +
107F TYR* 5.2 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LYS* 5.6 10.5 - - + -
31F THR* 4.1 19.5 - - + -
32F GLU* 6.4 1.3 - - + -
45F LEU* 5.8 5.6 - - + -
49F TYR* 6.2 2.7 - - + -
99F ASP 3.0 19.0 + - - +
100F VAL* 3.2 5.6 + - - +
102F SER* 1.4 75.9 + - - +
104F LEU* 1.4 58.3 + - - +
107F TYR* 3.2 23.0 + - + +
108F LEU* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F VAL* 2.8 34.8 + - + +
101F LEU* 3.7 12.3 - - + +
102F SER 3.3 0.2 - - - -
103F LEU* 1.4 74.3 - - - +
105F ASP* 1.3 58.9 + - - +
108F LEU* 3.6 22.1 + - + -
109F ILE* 2.7 36.3 + - + +
123F TYR* 4.4 22.0 - - + +
126F MET* 4.6 13.5 - - + -
127F LYS* 4.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU 2.9 20.0 + - - +
102F SER* 5.0 0.4 - - - -
104F LEU* 1.3 74.3 - - - +
106F ASN* 1.4 66.6 + - - +
107F TYR 3.5 0.4 + - - -
109F ILE* 4.9 4.2 - - - +
110F LYS* 3.8 17.7 + - - +
127F LYS* 5.0 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F SER* 2.9 32.6 + - - +
105F ASP* 1.4 83.4 - - - +
107F TYR* 1.4 81.7 + - + +
110F LYS* 3.4 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F THR* 3.4 31.9 - - + +
32F GLU* 3.6 44.9 + - + +
34F ASN* 3.5 31.4 + - - -
102F SER* 5.7 0.7 - - - -
103F LEU* 3.2 23.2 + - + +
105F ASP 3.5 0.8 - - - -
106F ASN* 1.4 97.4 - - + +
108F LEU* 1.3 62.8 + - + +
109F ILE 3.8 1.1 - - - -
110F LYS* 3.8 3.7 - - - +
111F ASN* 2.9 43.2 + - - +
----------------------------------------------------------
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