Contacts of the helix formed by residues 109 - 132 (chain N) in PDB entry 5FLX
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 109 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9961 A 5.4 2.2 + - - -
10311 A 5.2 2.1 + - - +
10321 C 3.5 54.1 + - - +
10331 G 2.9 30.6 + - - +
107N LYS 3.8 11.4 - - - +
108N ASP* 1.3 74.8 + - - +
110N ASP* 1.3 59.9 + - - +
111N ALA 3.4 0.7 - - - -
112N LYS* 3.3 13.5 + - + +
113N PHE* 2.9 26.7 + - - +
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Residues in contact with ASP 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9341 G 3.8 24.6 + - - +
9351 G 4.0 15.6 - - - +
9951 G 4.7 8.6 + - - -
9961 A 5.4 5.8 + - - +
108N ASP* 2.6 26.5 + - - +
109N LYS* 1.3 70.9 - - - +
111N ALA* 1.3 57.3 + - - +
113N PHE* 3.1 10.0 + - - +
114N ARG* 2.9 54.6 + - - +
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Residues in contact with ALA 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10081 A 6.1 0.4 - - - +
98N VAL* 3.4 15.0 - - + +
101N HIS* 3.8 23.8 - - + +
102N LEU* 3.8 21.1 - - + -
108N ASP* 3.5 14.5 + - - +
109N LYS 3.4 0.2 - - - -
110N ASP* 1.3 78.7 - - - +
112N LYS* 1.3 58.1 + - - +
114N ARG* 4.6 5.8 - - - -
115N LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10311 A 2.8 51.1 + - - +
10321 C 3.3 13.0 + - - +
102N LEU* 4.3 15.8 - - + +
106N ARG* 5.9 2.8 - - - +
108N ASP 4.2 5.6 + - - +
109N LYS* 3.3 20.7 + - + +
110N ASP 3.1 0.4 - - - -
111N ALA* 1.3 77.6 - - - +
113N PHE* 1.3 59.5 + - - +
115N LEU* 3.3 10.6 + - + +
116N ILE* 2.9 38.2 + - + +
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Residues in contact with PHE 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6751 U 3.1 33.2 - - + -
6761 C 5.1 1.8 - - - -
9961 A 3.2 69.5 - + - +
10311 A 4.4 19.7 + + - +
10321 C 6.1 0.2 - - - -
109N LYS 2.9 14.6 + - - +
110N ASP* 3.1 10.5 + - - +
112N LYS* 1.3 76.3 - - - +
114N ARG* 1.3 67.6 + - + +
116N ILE* 2.9 32.8 + - + +
117N LEU* 3.0 43.8 + - + +
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Residues in contact with ARG 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9341 G 4.9 5.4 + - - +
9951 G 3.0 47.6 + - - -
9961 A 3.9 11.6 + - - -
10091 A 2.7 49.8 + - - +
10101 G 2.8 33.6 + - - -
98N VAL* 5.7 2.5 - - + -
110N ASP* 2.9 40.4 + - - +
111N ALA* 4.2 5.8 - - - +
113N PHE* 1.3 80.0 - - - +
115N LEU* 1.3 56.5 + - - +
117N LEU* 3.3 20.5 + - - +
118N ILE* 2.9 42.6 + - + +
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Residues in contact with LEU 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95N ALA* 4.8 3.6 - - + +
98N VAL* 3.7 20.8 - - + +
99N ARG* 3.7 32.8 - - + +
102N LEU* 3.6 26.2 - - + -
111N ALA 2.9 19.4 + - - +
112N LYS* 3.3 10.5 - - + +
113N PHE 3.1 0.2 - - - -
114N ARG* 1.3 77.7 - - - +
116N ILE* 1.3 61.1 + - + +
118N ILE* 3.4 6.6 + - - +
119N GLU* 2.9 67.4 + - + +
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Residues in contact with ILE 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6761 C 3.8 27.6 - - - +
10301 A 5.8 0.7 - - - +
10311 A 3.6 43.3 - - - +
112N LYS* 2.9 24.9 + - + +
113N PHE* 2.9 17.7 + - + +
115N LEU* 1.3 81.0 - - + +
117N LEU* 1.3 59.0 + - + +
119N GLU* 3.4 11.9 + - - +
120N SER* 2.9 26.3 + - - -
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Residues in contact with LEU 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6761 C 3.7 21.3 - - - -
9961 A 4.4 5.8 - - - +
5N HIS* 3.5 49.3 - - + +
113N PHE* 3.0 48.1 + - + +
114N ARG* 3.3 21.5 + - - +
116N ILE* 1.3 76.9 - - + +
118N ILE* 1.3 64.9 + - + +
120N SER* 3.0 7.7 + - - -
121N ARG* 3.0 32.6 + - - +
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Residues in contact with ILE 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10091 A 4.7 13.5 - - - +
10101 G 4.7 4.9 - - - +
91N LEU* 3.7 32.1 - - + +
94N LYS* 4.1 26.5 - - + +
95N ALA* 4.0 8.7 - - + -
98N VAL* 4.3 22.2 - - + -
114N ARG* 2.9 27.4 + - + +
115N LEU* 3.9 5.2 - - - +
117N LEU* 1.3 76.2 - - + +
119N GLU* 1.3 64.0 + - + +
121N ARG* 3.2 16.9 + - - +
122N ILE* 2.9 34.3 + - + +
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Residues in contact with GLU 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N ALA* 5.8 3.1 - - + -
99N ARG* 2.3 41.3 + - - +
115N LEU* 2.9 40.3 + - + +
116N ILE* 3.7 11.2 - - - +
118N ILE* 1.3 76.5 - - + +
120N SER* 1.3 59.7 + - - +
122N ILE* 3.0 12.4 + - + +
123N HIS* 2.9 48.3 + - + +
141N TYR* 5.0 8.5 - - + -
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Residues in contact with SER 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6761 C 3.2 17.8 + - - -
6771 G 2.4 41.0 + - - -
5N HIS* 4.9 2.4 - - - -
116N ILE 2.9 14.4 + - - -
117N LEU* 3.0 11.4 + - - -
119N GLU* 1.3 75.0 - - - +
121N ARG* 1.3 63.6 + - - +
123N HIS* 3.1 12.2 + - - +
124N ARG* 2.9 25.6 + - - +
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Residues in contact with ARG 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9241 G 4.1 14.2 + - - +
9251 G 2.3 37.9 + - - -
10101 G 5.1 8.1 + - - -
10111 A 5.0 10.9 + - - -
3N ARG* 6.0 0.8 - - - +
4N MET* 4.0 29.8 - - + +
5N HIS* 3.8 48.3 + - + +
91N LEU* 4.0 19.9 - - + +
117N LEU* 3.0 22.7 + - - +
118N ILE* 3.6 16.0 - - - +
120N SER* 1.3 74.6 - - - +
122N ILE* 1.3 58.3 + - - +
124N ARG* 3.3 8.2 + - - +
125N LEU* 2.9 37.2 + - + +
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Residues in contact with ILE 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N LEU* 3.7 23.2 - - + +
91N LEU* 3.9 39.7 - - + +
92N ILE* 4.4 2.0 - - + +
95N ALA* 4.0 6.7 - - + -
118N ILE* 2.9 26.0 + - + +
119N GLU* 3.0 12.8 + - + +
121N ARG* 1.3 77.2 - - - +
123N HIS* 1.3 60.2 + - - +
125N LEU* 3.9 1.9 - - - +
126N ALA* 2.9 31.2 + - + +
139N TRP* 4.9 2.0 - - + -
141N TYR* 3.8 50.5 - - + -
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Residues in contact with HIS 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N GLU* 2.9 43.8 + - + +
120N SER* 3.6 9.2 - - - +
122N ILE* 1.3 76.9 - - + +
124N ARG* 1.3 59.4 + - - +
126N ALA* 3.3 7.4 + - - +
127N ARG* 2.9 49.5 + - - +
141N TYR* 4.4 26.0 - + + +
142N GLU* 5.1 5.2 - - - -
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Residues in contact with ARG 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6771 G 2.8 48.3 + - - -
6781 U 4.2 6.1 + - - -
10221 U 4.4 5.9 + - - +
10231 A 3.2 34.2 + - - +
10241 A 4.4 10.9 + - - -
10261 C 4.2 11.7 - - - +
4N MET* 3.5 25.9 - - - +
120N SER* 2.9 17.7 + - - +
121N ARG* 3.3 8.0 + - - +
123N HIS* 1.3 75.9 - - - +
125N LEU* 1.3 64.2 + - + +
127N ARG* 3.1 35.5 + - - +
128N TYR* 3.0 21.3 + - - +
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Residues in contact with LEU 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9241 G 3.5 18.6 - - - +
10221 U 3.7 20.0 - - + +
10231 A 5.3 2.7 - - - +
87N ASP* 3.4 49.4 - - + +
88N LEU* 4.4 8.1 - - + +
91N LEU* 3.6 20.2 - - + -
121N ARG* 2.9 17.4 + - + +
122N ILE 4.1 2.2 - - - +
124N ARG* 1.3 78.1 - - + +
126N ALA* 1.3 57.0 + - - +
128N TYR* 3.3 7.5 + - + +
129N TYR* 2.9 53.0 + - + +
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Residues in contact with ALA 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N LEU* 5.1 2.4 - - + +
122N ILE* 2.9 21.4 + - + +
123N HIS* 3.5 10.1 - - - +
125N LEU* 1.3 76.3 - - - +
127N ARG* 1.3 56.5 + - + +
129N TYR* 3.3 4.0 + - - -
130N LYS* 2.9 42.8 + - - +
135N LEU* 3.9 7.3 - - + +
139N TRP* 3.7 28.3 - - + -
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Residues in contact with ARG 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6771 G 5.1 1.6 + - - -
6781 U 2.9 38.0 + - - -
123N HIS* 2.9 42.0 + - + +
124N ARG* 3.1 38.9 + - - +
126N ALA* 1.3 77.6 - - + +
128N TYR* 1.3 53.0 + - - +
130N LYS* 3.4 13.7 + - + +
131N THR* 2.7 37.4 + - - +
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Residues in contact with TYR 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10191 C 4.7 7.4 - - - -
10201 A 3.2 30.9 - - - -
10211 U 3.5 25.9 + - - -
10221 U 3.1 65.7 - + - +
124N ARG 3.0 8.3 + - - +
125N LEU* 3.6 9.9 - - + +
126N ALA 3.2 0.2 - - - -
127N ARG* 1.3 76.0 - - - +
129N TYR* 1.3 88.0 + + - +
131N THR* 2.9 24.9 + - + -
132N LYS* 2.9 40.3 + - + +
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Residues in contact with TYR 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10191 C 5.1 9.2 + - - -
85N PRO* 3.5 38.5 - - + +
87N ASP* 3.4 30.3 + - - +
88N LEU* 3.8 25.1 - - + -
125N LEU* 2.9 34.5 + - + +
126N ALA* 4.6 0.7 - - - -
128N TYR* 1.3 101.3 - + - +
130N LYS* 1.3 61.5 + - - +
132N LYS* 5.0 0.7 - - + -
133N ARG 3.3 11.1 + - - -
134N VAL* 3.4 21.2 + - + +
135N LEU* 3.3 41.1 + - + -
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Residues in contact with LYS 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N ALA* 2.9 29.2 + - - +
127N ARG* 3.7 11.7 - - + +
129N TYR* 1.3 76.8 - - - +
131N THR* 1.3 63.0 + - - +
133N ARG* 3.4 22.7 + - - +
135N LEU* 3.8 21.9 - - + +
136N PRO 4.5 7.9 - - - +
137N PRO* 4.0 21.3 + - + +
139N TRP* 3.2 30.1 + - - -
140N LYS* 4.7 11.5 - - - +
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Residues in contact with THR 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10221 U 5.4 7.0 - - - +
127N ARG* 2.7 20.2 + - - +
128N TYR* 2.9 15.8 + - + -
130N LYS* 1.3 79.2 - - - +
132N LYS* 1.3 72.7 + - + +
133N ARG* 3.2 8.9 + - - +
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Residues in contact with LYS 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10201 A 6.2 0.2 - - - -
10211 U 3.3 34.0 + - - +
10221 U 5.1 3.7 + - - -
128N TYR* 2.9 51.6 + - + +
129N TYR* 3.8 3.1 + - - +
131N THR* 1.3 84.7 - - + +
133N ARG* 1.3 68.1 + - - +
134N VAL* 3.1 13.8 + - + +
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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) + - + + + + + -
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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